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.

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.

Physarum machines: encapsulating reaction-diffusion to compute spanning tree

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2007-12-01

The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction-diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction-diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction-diffusion system is enclosed in a membrane with few ‘growth points’, sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction-diffusion computation by enriching it with ideas of slime mold computation.

Dynamical mechanism in aero-engine gas path system using minimum spanning tree and detrended cross-correlation analysis

NASA Astrophysics Data System (ADS)

Dong, Keqiang; Zhang, Hong; Gao, You

2017-01-01

Identifying the mutual interaction in aero-engine gas path system is a crucial problem that facilitates the understanding of emerging structures in complex system. By employing the multiscale multifractal detrended cross-correlation analysis method to aero-engine gas path system, the cross-correlation characteristics between gas path system parameters are established. Further, we apply multiscale multifractal detrended cross-correlation distance matrix and minimum spanning tree to investigate the mutual interactions of gas path variables. The results can infer that the low-spool rotor speed (N1) and engine pressure ratio (EPR) are main gas path parameters. The application of proposed method contributes to promote our understanding of the internal mechanisms and structures of aero-engine dynamics.

Potential exposure to human prescription pharmaceutical residues from wastewater

EPA Science Inventory

Pharmaceuticals in the environment (PiE) pose a complicated problem, involving multiple dissimilar compounds, multiple routes of potential exposure, and a range of potentially affected organisms that span the tree of life. Key uncertainties include not knowing which of the thous...

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

Efficiency/Equity Analysis of Water Resources Problems--A Game Theoretic Approach.

DTIC Science & Technology

1985-01-01

contained in the West Coast Regional Water Supply Authority’s master plan for Hillsborough, Pasco, and Pinellas counties in Florida (Ross et al...spanning tree, Networks, 3(4), 289-304, 1973. Converse, A.O., Optimum number and location of treatment plants , Journal of the Water Pollution Control

Finding minimum spanning trees more efficiently for tile-based phase unwrapping

NASA Astrophysics Data System (ADS)

Sawaf, Firas; Tatam, Ralph P.

2006-06-01

The tile-based phase unwrapping method employs an algorithm for finding the minimum spanning tree (MST) in each tile. We first examine the properties of a tile's representation from a graph theory viewpoint, observing that it is possible to make use of a more efficient class of MST algorithms. We then describe a novel linear time algorithm which reduces the size of the MST problem by half at the least, and solves it completely at best. We also show how this algorithm can be applied to a tile using a sliding window technique. Finally, we show how the reduction algorithm can be combined with any other standard MST algorithm to achieve a more efficient hybrid, using Prim's algorithm for empirical comparison and noting that the reduction algorithm takes only 0.1% of the time taken by the overall hybrid.

Performance Analysis of Evolutionary Algorithms for Steiner Tree Problems.

PubMed

Lai, Xinsheng; Zhou, Yuren; Xia, Xiaoyun; Zhang, Qingfu

2017-01-01

The Steiner tree problem (STP) aims to determine some Steiner nodes such that the minimum spanning tree over these Steiner nodes and a given set of special nodes has the minimum weight, which is NP-hard. STP includes several important cases. The Steiner tree problem in graphs (GSTP) is one of them. Many heuristics have been proposed for STP, and some of them have proved to be performance guarantee approximation algorithms for this problem. Since evolutionary algorithms (EAs) are general and popular randomized heuristics, it is significant to investigate the performance of EAs for STP. Several empirical investigations have shown that EAs are efficient for STP. However, up to now, there is no theoretical work on the performance of EAs for STP. In this article, we reveal that the (1+1) EA achieves 3/2-approximation ratio for STP in a special class of quasi-bipartite graphs in expected runtime [Formula: see text], where [Formula: see text], [Formula: see text], and [Formula: see text] are, respectively, the number of Steiner nodes, the number of special nodes, and the largest weight among all edges in the input graph. We also show that the (1+1) EA is better than two other heuristics on two GSTP instances, and the (1+1) EA may be inefficient on a constructed GSTP instance.

Traveling salesman problem, conformal invariance, and dense polymers.

PubMed

Jacobsen, J L; Read, N; Saleur, H

2004-07-16

We propose that the statistics of the optimal tour in the planar random Euclidean traveling salesman problem is conformally invariant on large scales. This is exhibited in the power-law behavior of the probabilities for the tour to zigzag repeatedly between two regions, and in subleading corrections to the length of the tour. The universality class should be the same as for dense polymers and minimal spanning trees. The conjectures for the length of the tour on a cylinder are tested numerically.

Identification of pests and diseases of Dalbergia hainanensis based on EVI time series and classification of decision tree

NASA Astrophysics Data System (ADS)

Luo, Qiu; Xin, Wu; Qiming, Xiong

2017-06-01

In the process of vegetation remote sensing information extraction, the problem of phenological features and low performance of remote sensing analysis algorithm is not considered. To solve this problem, the method of remote sensing vegetation information based on EVI time-series and the classification of decision-tree of multi-source branch similarity is promoted. Firstly, to improve the time-series stability of recognition accuracy, the seasonal feature of vegetation is extracted based on the fitting span range of time-series. Secondly, the decision-tree similarity is distinguished by adaptive selection path or probability parameter of component prediction. As an index, it is to evaluate the degree of task association, decide whether to perform migration of multi-source decision tree, and ensure the speed of migration. Finally, the accuracy of classification and recognition of pests and diseases can reach 87%--98% of commercial forest in Dalbergia hainanensis, which is significantly better than that of MODIS coverage accuracy of 80%--96% in this area. Therefore, the validity of the proposed method can be verified.

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

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…

Minimal spanning trees at the percolation threshold: A numerical calculation

NASA Astrophysics Data System (ADS)

Sweeney, Sean M.; Middleton, A. Alan

2013-09-01

The fractal dimension of minimal spanning trees on percolation clusters is estimated for dimensions d up to d=5. A robust analysis technique is developed for correlated data, as seen in such trees. This should be a robust method suitable for analyzing a wide array of randomly generated fractal structures. The trees analyzed using these techniques are built using a combination of Prim's and Kruskal's algorithms for finding minimal spanning trees. This combination reduces memory usage and allows for simulation of larger systems than would otherwise be possible. The path length fractal dimension ds of MSTs on critical percolation clusters is found to be compatible with the predictions of the perturbation expansion developed by T. S. Jackson and N. Read [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.021131 81, 021131 (2010)].

Spanning trees and the Eurozone crisis

NASA Astrophysics Data System (ADS)

Dias, João

2013-12-01

The sovereign debt crisis in the euro area has not yet been solved and recent developments in Spain and Italy have further deteriorated the situation. In this paper we develop a new approach to analyze the ongoing Eurozone crisis. Firstly, we use Maximum Spanning Trees to analyze the topological properties of government bond rates’ dynamics. Secondly, we combine the information given by both Maximum and Minimum Spanning Trees to obtain a measure of market dissimilarity or disintegration. Thirdly, we extend this measure to include a convenient distance not limited to the interval [0, 2]. Our empirical results show that Maximum Spanning Tree gives an adequate description of the separation of the euro area into two distinct groups: those countries strongly affected by the crisis and those that have remained resilient during this period. The measures of market dissimilarity also reveal a persistent separation of these two groups and, according to our second measure, this separation strongly increased during the period July 2009-March 2012.

Robust Sensor Placements at Informative and Communication-efficient Locations

DTIC Science & Technology

2010-08-01

tree T ∗ with cost `∗, spanning a setA∗. Then PSPIEL can find a tree T with costO (r dim(V,E))×`∗, spanning a setAwith expected sensing quality F (A...V, E), s, t ∈ V and an (r, γ)-local monotone submodular function F , PSPIEL will find an s− t path P with costO (r dim(V,E))× `∗, spanning a setA with

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.

Invasion Percolation and Global Optimization

NASA Astrophysics Data System (ADS)

Barabási, Albert-László

1996-05-01

Invasion bond percolation (IBP) is mapped exactly into Prim's algorithm for finding the shortest spanning tree of a weighted random graph. Exploring this mapping, which is valid for arbitrary dimensions and lattices, we introduce a new IBP model that belongs to the same universality class as IBP and generates the minimal energy tree spanning the IBP cluster.

If BZ medium did spanning trees these would be the same trees as Physarum built

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2009-03-01

A sub-excitable Belousov-Zhabotinsky (BZ) medium exhibits self-localized wave-fragments which may travel for relatively long time preserving their shape. Using Oregonator model of the BZ medium we imitate foraging behavior of a true slime mold, Physarum polycephalum, on a nutrient-poor substrate. We show that given erosion post-processing operations the BZ medium can approximate a spanning tree of a planar set and thus is computationally equivalent to Physarum in the domain of proximity graph construction.

Topology of correlation-based minimal spanning trees in real and model markets

NASA Astrophysics Data System (ADS)

Bonanno, Giovanni; Caldarelli, Guido; Lillo, Fabrizio; Mantegna, Rosario N.

2003-10-01

We compare the topological properties of the minimal spanning tree obtained from a large group of stocks traded at the New York Stock Exchange during a 12-year trading period with the one obtained from surrogated data simulated by using simple market models. We find that the empirical tree has features of a complex network that cannot be reproduced, even as a first approximation, by a random market model and by the widespread one-factor model.

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

The triangular kagomé lattices revisited

NASA Astrophysics Data System (ADS)

Liu, Xiaoyun; Yan, Weigen

2013-11-01

The dimer problem, Ising spins and bond percolation on the triangular kagomé lattice have been studied extensively by physicists. In this paper, based on the fact the triangular kagomé lattice with toroidal boundary condition can be regarded as the line graph of 3.12.12 lattice with toroidal boundary condition, we derive the formulae of the number of spanning trees, the energy, and the Kirchhoff index of the triangular kagomé lattice with toroidal boundary condition.

Cluster Stability Estimation Based on a Minimal Spanning Trees Approach

NASA Astrophysics Data System (ADS)

Volkovich, Zeev (Vladimir); Barzily, Zeev; Weber, Gerhard-Wilhelm; Toledano-Kitai, Dvora

2009-08-01

Among the areas of data and text mining which are employed today in science, economy and technology, clustering theory serves as a preprocessing step in the data analyzing. However, there are many open questions still waiting for a theoretical and practical treatment, e.g., the problem of determining the true number of clusters has not been satisfactorily solved. In the current paper, this problem is addressed by the cluster stability approach. For several possible numbers of clusters we estimate the stability of partitions obtained from clustering of samples. Partitions are considered consistent if their clusters are stable. Clusters validity is measured as the total number of edges, in the clusters' minimal spanning trees, connecting points from different samples. Actually, we use the Friedman and Rafsky two sample test statistic. The homogeneity hypothesis, of well mingled samples within the clusters, leads to asymptotic normal distribution of the considered statistic. Resting upon this fact, the standard score of the mentioned edges quantity is set, and the partition quality is represented by the worst cluster corresponding to the minimal standard score value. It is natural to expect that the true number of clusters can be characterized by the empirical distribution having the shortest left tail. The proposed methodology sequentially creates the described value distribution and estimates its left-asymmetry. Numerical experiments, presented in the paper, demonstrate the ability of the approach to detect the true number of clusters.

The Inference of Gene Trees with Species Trees

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

2015-01-01

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

Minimal Spanning Tree Graphs and Power Like Scaling in FOREX Networks

NASA Astrophysics Data System (ADS)

Górski, A. Z.; Kwapień, J.; Oświęcimka, P.; Drożdż, S.

2008-09-01

Correlation matrices of foreign exchange rate time series are investigated for 60 world currencies. Minimal spanning tree graphs for the gold, silver and platinum are presented. Inverse power like scaling is discussed for these graphs as well as for four distinct currency groups (major, liquid, less liquid and non-tradable). The worst scaling was found for USD and related currencies.

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.

A new method of optimal capacitor switching based on minimum spanning tree theory in distribution systems

NASA Astrophysics Data System (ADS)

Li, H. W.; Pan, Z. Y.; Ren, Y. B.; Wang, J.; Gan, Y. L.; Zheng, Z. Z.; Wang, W.

2018-03-01

According to the radial operation characteristics in distribution systems, this paper proposes a new method based on minimum spanning trees method for optimal capacitor switching. Firstly, taking the minimal active power loss as objective function and not considering the capacity constraints of capacitors and source, this paper uses Prim algorithm among minimum spanning trees algorithms to get the power supply ranges of capacitors and source. Then with the capacity constraints of capacitors considered, capacitors are ranked by the method of breadth-first search. In term of the order from high to low of capacitor ranking, capacitor compensation capacity based on their power supply range is calculated. Finally, IEEE 69 bus system is adopted to test the accuracy and practicality of the proposed algorithm.

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.

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.

Complexity of major UK companies between 2006 and 2010: Hierarchical structure method approach

NASA Astrophysics Data System (ADS)

Ulusoy, Tolga; Keskin, Mustafa; Shirvani, Ayoub; Deviren, Bayram; Kantar, Ersin; Çaǧrı Dönmez, Cem

2012-11-01

This study reports on topology of the top 40 UK companies that have been analysed for predictive verification of markets for the period 2006-2010, applying the concept of minimal spanning tree and hierarchical tree (HT) analysis. Construction of the minimal spanning tree (MST) and the hierarchical tree (HT) is confined to a brief description of the methodology and a definition of the correlation function between a pair of companies based on the London Stock Exchange (LSE) index in order to quantify synchronization between the companies. A derivation of hierarchical organization and the construction of minimal-spanning and hierarchical trees for the 2006-2008 and 2008-2010 periods have been used and the results validate the predictive verification of applied semantics. The trees are known as useful tools to perceive and detect the global structure, taxonomy and hierarchy in financial data. From these trees, two different clusters of companies in 2006 were detected. They also show three clusters in 2008 and two between 2008 and 2010, according to their proximity. The clusters match each other as regards their common production activities or their strong interrelationship. The key companies are generally given by major economic activities as expected. This work gives a comparative approach between MST and HT methods from statistical physics and information theory with analysis of financial markets that may give new valuable and useful information of the financial market dynamics.

Cell longevity and sustained primary growth in palm stems.

PubMed

Tomlinson, P Barry; Huggett, Brett A

2012-12-01

Longevity, or organismal life span, is determined largely by the period over which constituent cells can function metabolically. Plants, with modular organization (the ability continually to develop new organs and tissues) differ from animals, with unitary organization (a fixed body plan), and this difference is reflected in their respective life spans, potentially much longer in plants than animals. We draw attention to the observation that palm trees, as a group of monocotyledons without secondary growth comparable to that of lignophytes (plants with secondary growth from a bifacial cambium), retain by means of sustained primary growth living cells in their trunks throughout their organismal life span. Does this make palms the longest-lived trees because they can grow as individuals for several centuries? No conventional lignophyte retains living metabolically active differentiated cell types in its trunk for this length of time, even though the tree as a whole can exist for millennia. Does this contrast also imply that the long-lived cells in a palm trunk have exceptional properties, which allows this seeming immortality? We document the long-life of many tall palm species and their inherent long-lived stem cell properties, comparing such plants to conventional trees. We provide a summary of aspects of cell age and life span in animals and plants. Cell replacement is a feature of animal function, whereas conventional trees rely on active growth centers (meristems) to sustain organismal development. However, the long persistence of living cells in palm trunks is seen not as evidence for unique metabolic processes that sustain longevity, but is a consequence of unique constructional features. This conclusion suggests that the life span of plant cells is not necessarily genetically determined.

Counting spanning trees on fractal graphs and their asymptotic complexity

NASA Astrophysics Data System (ADS)

Anema, Jason A.; Tsougkas, Konstantinos

2016-09-01

Using the method of spectral decimation and a modified version of Kirchhoff's matrix-tree theorem, a closed form solution to the number of spanning trees on approximating graphs to a fully symmetric self-similar structure on a finitely ramified fractal is given in theorem 3.4. We show how spectral decimation implies the existence of the asymptotic complexity constant and obtain some bounds for it. Examples calculated include the Sierpiński gasket, a non-post critically finite analog of the Sierpiński gasket, the Diamond fractal, and the hexagasket. For each example, the asymptotic complexity constant is found.

Effects of urban tree management and species selection on atmospheric carbon dioxide

Treesearch

David J. Nowak; Jack C. Stevens; Susan M. Sisinni; Christopher J. Luley

2002-01-01

Trees sequester and store carbon in their tissue at differing rates and amounts based on such factors as tree size at maturity, life span, and growth rate. Concurrently, tree care practices release carbon back to the atmosphere based on fossil-fuel emissions from maintenance equipment (e.g., chain saws, trucks, chippers). Management choices such as tree locations for...

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

PubMed

O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-02-25

We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the phylogenetic tree topology of the homologous group. The classical QR factorization with pivoting, developed as a fast numerical solution to eigenvalue and linear least-squares problems of the form Ax=b, was designed to re-order the columns of A by increasing linear dependence. Removing the most linear dependent columns from A leads to the formation of a minimal basis set which well spans the phase space of the problem at hand. By recasting the problem of redundancy in multiple structural alignments into this framework, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to produce a minimal basis set of protein structures which best spans the evolutionary (phase) space. The non-redundant and representative profiles obtained from this procedure, termed evolutionary profiles, are shown in initial results to outperform well-tested profiles in homology detection searches over a large sequence database. A measure of structural similarity between homologous proteins, Q(H), is presented. By properly accounting for the effect and presence of gaps, a phylogenetic tree computed using this metric is shown to be congruent with the maximum-likelihood sequence-based phylogeny. The results indicate that evolutionary information is indeed recoverable from the comparative analysis of protein structure alone. Applications of the QR ordering and this structural similarity metric to analyze the evolution of structure among key, universally distributed proteins involved in translation, and to the selection of representatives from an ensemble of NMR structures are also discussed.

The use of minimal spanning trees in particle physics

DOE PAGES

Rainbolt, J. Lovelace; Schmitt, M.

2017-02-14

Minimal spanning trees (MSTs) have been used in cosmology and astronomy to distinguish distributions of points in a multi-dimensional space. They are essentially unknown in particle physics, however. We briefly define MSTs and illustrate their properties through a series of examples. We show how they might be applied to study a typical event sample from a collider experiment and conclude that MSTs may prove useful in distinguishing different classes of events.

The use of minimal spanning trees in particle physics

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

Rainbolt, J. Lovelace; Schmitt, M.

Minimal spanning trees (MSTs) have been used in cosmology and astronomy to distinguish distributions of points in a multi-dimensional space. They are essentially unknown in particle physics, however. We briefly define MSTs and illustrate their properties through a series of examples. We show how they might be applied to study a typical event sample from a collider experiment and conclude that MSTs may prove useful in distinguishing different classes of events.

Constraint-Based Local Search for Constrained Optimum Paths Problems

NASA Astrophysics Data System (ADS)

Pham, Quang Dung; Deville, Yves; van Hentenryck, Pascal

Constrained Optimum Path (COP) problems arise in many real-life applications and are ubiquitous in communication networks. They have been traditionally approached by dedicated algorithms, which are often hard to extend with side constraints and to apply widely. This paper proposes a constraint-based local search (CBLS) framework for COP applications, bringing the compositionality, reuse, and extensibility at the core of CBLS and CP systems. The modeling contribution is the ability to express compositional models for various COP applications at a high level of abstraction, while cleanly separating the model and the search procedure. The main technical contribution is a connected neighborhood based on rooted spanning trees to find high-quality solutions to COP problems. The framework, implemented in COMET, is applied to Resource Constrained Shortest Path (RCSP) problems (with and without side constraints) and to the edge-disjoint paths problem (EDP). Computational results show the potential significance of the approach.

Comovements in government bond markets: A minimum spanning tree analysis

NASA Astrophysics Data System (ADS)

Gilmore, Claire G.; Lucey, Brian M.; Boscia, Marian W.

2010-11-01

The concept of a minimum spanning tree (MST) is used to study patterns of comovements for a set of twenty government bond market indices for developed North American, European, and Asian countries. We show how the MST and its related hierarchical tree evolve over time and describe the dynamic development of market linkages. Over the sample period, 1993-2008, linkages between markets have decreased somewhat. However, a subset of European Union (EU) bond markets does show increasing levels of comovements. The evolution of distinct groups within the Eurozone is also examined. The implications of our findings for portfolio diversification benefits are outlined.

Exact and Approximate Stability of Solutions to Traveling Salesman Problems.

PubMed

Niendorf, Moritz; Girard, Anouck R

2018-02-01

This paper presents the stability analysis of an optimal tour for the symmetric traveling salesman problem (TSP) by obtaining stability regions. The stability region of an optimal tour is the set of all cost changes for which that solution remains optimal and can be understood as the margin of optimality for a solution with respect to perturbations in the problem data. It is known that it is not possible to test in polynomial time whether an optimal tour remains optimal after the cost of an arbitrary set of edges changes. Therefore, this paper develops tractable methods to obtain under and over approximations of stability regions based on neighborhoods and relaxations. The application of the results to the two-neighborhood and the minimum 1 tree (M1T) relaxation are discussed in detail. For Euclidean TSPs, stability regions with respect to vertex location perturbations and the notion of safe radii and location criticalities are introduced. Benefits of this paper include insight into robustness properties of tours, minimum spanning trees, M1Ts, and fast methods to evaluate optimality after perturbations occur. Numerical examples are given to demonstrate the methods and achievable approximation quality.

7 CFR 1410.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... mean a vegetative barrier with a linear configuration composed of trees, shrubs, or other vegetation... approved combinations of certain grasses, legumes, forbs, shrubs and trees with a life span of 10 or more...

17. DETAIL OF SOUTH PORTAL, SHOWING "TREE OF LIFE" RAILING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. DETAIL OF SOUTH PORTAL, SHOWING "TREE OF LIFE" RAILING DETAIL AS WELL AS BUILDER'S PLATE. - Falls Bridge, Spanning Schuylkill River, connecting East & West River Drives, Philadelphia, Philadelphia County, PA

Cooperative global optimal preview tracking control of linear multi-agent systems: an internal model approach

NASA Astrophysics Data System (ADS)

Lu, Yanrong; Liao, Fucheng; Deng, Jiamei; Liu, Huiyang

2017-09-01

This paper investigates the cooperative global optimal preview tracking problem of linear multi-agent systems under the assumption that the output of a leader is a previewable periodic signal and the topology graph contains a directed spanning tree. First, a type of distributed internal model is introduced, and the cooperative preview tracking problem is converted to a global optimal regulation problem of an augmented system. Second, an optimal controller, which can guarantee the asymptotic stability of the augmented system, is obtained by means of the standard linear quadratic optimal preview control theory. Third, on the basis of proving the existence conditions of the controller, sufficient conditions are given for the original problem to be solvable, meanwhile a cooperative global optimal controller with error integral and preview compensation is derived. Finally, the validity of theoretical results is demonstrated by a numerical simulation.

Annealing Ant Colony Optimization with Mutation Operator for Solving TSP.

PubMed

Mohsen, Abdulqader M

2016-01-01

Ant Colony Optimization (ACO) has been successfully applied to solve a wide range of combinatorial optimization problems such as minimum spanning tree, traveling salesman problem, and quadratic assignment problem. Basic ACO has drawbacks of trapping into local minimum and low convergence rate. Simulated annealing (SA) and mutation operator have the jumping ability and global convergence; and local search has the ability to speed up the convergence. Therefore, this paper proposed a hybrid ACO algorithm integrating the advantages of ACO, SA, mutation operator, and local search procedure to solve the traveling salesman problem. The core of algorithm is based on the ACO. SA and mutation operator were used to increase the ants population diversity from time to time and the local search was used to exploit the current search area efficiently. The comparative experiments, using 24 TSP instances from TSPLIB, show that the proposed algorithm outperformed some well-known algorithms in the literature in terms of solution quality.

Earthquake signals in tree-ring data from the New Madrid seismic zone and implications for paleoseismicity

NASA Astrophysics Data System (ADS)

van Arsdale, Roy B.; Stahle, David W.; Cleaveland, Malcolm K.; Guccione, Margaret J.

1998-06-01

Severe ground shaking and the formation of Reelfoot Lake during the great New Madrid earthquakes of a.d. 1811 1812 had a profound effect on baldcypress trees that still survive in Reelfoot Lake of northwestern Tennessee. Inundation greatly increased baldcypress radial growth from 1812 to 1819 and permanently decreased wood density after 1811. Ground shaking fractured the baldcypress stems that were present during the 1811 1812 event, but fractures are absent in the post-1811 growth. In contrast, the growth of old baldcypress trees in the St. Francis sunkland of northeastern Arkansas was severely suppressed for almost 50 yr following the 1811 1812 New Madrid earthquakes. Thus, there are two opposite but profound growth responses to the same earthquake events preserved in baldcypress trees of the New Madrid seismic zone. The tree-ring chronology at Reelfoot Lake extends from a.d. 1682 to 1990, but the 1812 1819 growth surge was the only extreme growth anomaly in this 309 yr period. The St. Francis sunkland chronology extends from a.d. 1321 to 1990, and the 1812 1857 growth suppression is the most severe and prolonged growth anomaly of this entire 670 year period. Thus, the tree-ring record indicates that there was not a great earthquake during the 129 yr prior to 1811 in the Reelfoot Lake basin, nor during the 490 yr prior to 1811 in the St. Francis sunkland.

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.

Minimal model of a cell connecting amoebic motion and adaptive transport networks.

PubMed

Gunji, Yukio-Pegio; Shirakawa, Tomohiro; Niizato, Takayuki; Haruna, Taichi

2008-08-21

A cell is a minimal self-sustaining system that can move and compute. Previous work has shown that a unicellular slime mold, Physarum, can be utilized as a biological computer based on cytoplasmic flow encapsulated by a membrane. Although the interplay between the modification of the boundary of a cell and the cytoplasmic flow surrounded by the boundary plays a key role in Physarum computing, no model of a cell has been developed to describe this interplay. Here we propose a toy model of a cell that shows amoebic motion and can solve a maze, Steiner minimum tree problem and a spanning tree problem. Only by assuming that cytoplasm is hardened after passing external matter (or softened part) through a cell, the shape of the cell and the cytoplasmic flow can be changed. Without cytoplasm hardening, a cell is easily destroyed. This suggests that cytoplasmic hardening and/or sol-gel transformation caused by external perturbation can keep a cell in a critical state leading to a wide variety of shapes and motion.

The archaebacterial origin of eukaryotes.

PubMed

Cox, Cymon J; Foster, Peter G; Hirt, Robert P; Harris, Simon R; Embley, T Martin

2008-12-23

The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.

Effect of habitat preference on frond life span in three Cyathea tree ferns

NASA Astrophysics Data System (ADS)

Chiu, Tzu Yun; Wang, Hsiang Hua; Lun Kuo, Yao; Kume, Tomonori

2013-04-01

It has been reported that plants living in various geographical areas had different physiological forms, as factors of microenvironment have strong impacts on physiological characters. However, the physiological characters of fronds have been scarcely reported in ferns. In this study, we investigated physiological differences in response to the habitat preference in the three tree ferns in northeast Taiwan, Cyathea lepifera, C. spinulosa, and C. podophylla, prefer to open site, edge of forest, and interior forest, respectively. The canopy openness above the individuals of C. lepifera, C. spinulosa and C. podophylla were 29.2 ± 14.10 , 7.0 ± 3.07 and 5.0 ± 2.24 %, respectively. Among three species, C. podophylla had the longest frond life span (13.0 ± 4.12 months) than the two others (C. lepifera (6.8 ± 1.29 months) and C. spinulosa (7.3 ±1.35 months). Our result supported the general patterns that shade intolerant species have a shorter leaf life span than shade tolerant species. The maximum net CO2 assimilation of C. lepifera, C. spinulosa and C. podophylla were 11.46 ± 1.34, 8.27 ± 0.69, and 6.34 ± 0.54 μmol CO2 m-2 s-1, respectively. As well, C. lepifera had the highest photosynthetic light saturation point (LSP), while C. podophylla had the lowest LSP among these three tree ferns. These suggested that C. lepifera could be more efficient for capturing and utilizing light resources under the larger canopy openness condition than the other two species. We also found that frond C : N ratio were positively correlated with frond life span among species. C. podophylla, with the longest frond life span, had the highest frond C : N ratio (22.17 ± 1.95), which was followed by C. spinulosa (18.58 ± 1.37) and C. lepifera (18.68 ± 2.63) with shorter frond life span. The results were consistent to the theory that the fronds and leaves of shade intolerant species have high photosynthetic abilities with low C : N ratio. Key words: Canopy openness, frond life span, tree fern, Cyathea, frond C : N ratio

Lignin composition is related to xylem embolism resistance and leaf life span in trees in a tropical semiarid climate.

PubMed

Lima, Taysla R A; Carvalho, Ellen C D; Martins, Fernando R; Oliveira, Rafael S; Miranda, Rafael S; Müller, Caroline S; Pereira, Luciano; Bittencourt, Paulo R L; Sobczak, Jullyana C M S M; Gomes-Filho, Enéas; Costa, Rafael C; Araújo, Francisca S

2018-05-16

Wood properties influence the leaf life span (LL) of tree crowns. As lignin is an important component of wood and the water transport system, we investigated its relationship with embolism resistance and the LL of several tree species in a seasonally dry tropical ecosystem. We determined total lignin and the monomer contents of guaiacyl (G) and syringyl (S) and related them to wood traits and xylem vulnerability to embolism (Ψ 50 ) for the most common species of the Brazilian semiarid, locally known as Caatinga. Leaf life span was negatively related to Ψ 50 and positively related to S : G, which was negatively related to Ψ 50 . This means that greater S : G increases LL by reducing Ψ 50 . Lignin content was not correlated with any variable. We found two apparently unrelated axes of drought resistance. One axis, associated with lignin monomeric composition, increases LL in the dry season as a result of lower xylem embolism vulnerability. The other, associated with wood density and stem water content, helps leafless trees to withstand drought and allows them to resprout at the end of the dry season. The monomeric composition of lignin (S : G) is therefore an important functional wood attribute affecting several key functional aspects of tropical tree species in a semiarid climate. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Sovereign debt crisis in the European Union: A minimum spanning tree approach

NASA Astrophysics Data System (ADS)

Dias, João

2012-03-01

In the wake of the financial crisis, sovereign debt crisis has emerged and is severely affecting some countries in the European Union, threatening the viability of the euro and even the EU itself. This paper applies recent developments in econophysics, in particular the minimum spanning tree approach and the associate hierarchical tree, to analyze the asynchronization between the four most affected countries and other resilient countries in the euro area. For this purpose, daily government bond yield rates are used, covering the period from April 2007 to October 2010, thus including yield rates before, during and after the financial crises. The results show an increasing separation of the two groups of euro countries with the deepening of the government bond crisis.

Fire frequency and tree canopy structure influence plant species diversity in a forest-grassland ecotone

Treesearch

David W. Peterson; Peter B. Reich

2008-01-01

Disturbances and environmental heterogeneity are two factors thought to influence plant species diversity, but their effects are still poorly understood in many ecosystems. We surveyed understory vegetation and measured tree canopy cover on permanent plots spanning an experimental fire frequency gradient to test fire frequency and tree canopy effects on plant species...

Life span and structure of ephemeral root modules of different functional groups from a desert system.

PubMed

Liu, Bo; He, Junxia; Zeng, Fanjiang; Lei, Jiaqiang; Arndt, Stefan K

2016-07-01

The terminal branch orders of plant root systems have been proposed as short-lived 'ephemeral' modules specialized for resource absorption. The occurrence of ephemeral root modules has so far only been reported for a temperate tree species and it is unclear if the concept also applies to other woody (shrub, tree) and herb species. Fine roots of 12 perennial dicotyledonous herb, shrub and tree species were monitored for two growing seasons using a branch-order classification, sequential sampling and rhizotrons in the Taklamakan desert. Two root modules existed in all three plant functional groups. Among the first five branch orders, the first two (perennial herbs, shrubs) or three (trees) root orders were ephemeral and had a primary anatomical structure, high nitrogen (N) concentrations, high respiration rates and very short life spans of 1-4 months, whereas the last two branch orders in all functional groups were perennial, with thicker diameters, no or collapsed cortex, distinct secondary growth, low N concentrations, low respiration rates, but much longer life spans. Ephemeral, short-lived root modules and long-lived, persistent root modules seem to be a general feature across many plant functional groups and could represent a basic root system design. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A cost–benefit analysis of acclimation to low irradiance in tropical rainforest tree seedlings: leaf life span and payback time for leaf deployment

PubMed Central

Coste, Sabrina; Roggy, Jean-Christophe; Schimann, Heidy; Epron, Daniel; Dreyer, Erwin

2011-01-01

The maintenance in the long run of a positive carbon balance under very low irradiance is a prerequisite for survival of tree seedlings below the canopy or in small gaps in a tropical rainforest. To provide a quantitative basis for this assumption, experiments were carried out to determine whether construction cost (CC) and payback time for leaves and support structures, as well as leaf life span (i) differ among species and (ii) display an irradiance-elicited plasticity. Experiments were also conducted to determine whether leaf life span correlates to CC and payback time and is close to the optimal longevity derived from an optimization model. Saplings from 13 tropical tree species were grown under three levels of irradiance. Specific-CC was computed, as well as CC scaled to leaf area at the metamer level. Photosynthesis was recorded over the leaf life span. Payback time was derived from CC and a simple photosynthesis model. Specific-CC displayed only little interspecific variability and irradiance-elicited plasticity, in contrast to CC scaled to leaf area. Leaf life span ranged from 4 months to >26 months among species, and was longest in seedlings grown under lowest irradiance. It was always much longer than payback time, even under the lowest irradiance. Leaves were shed when their photosynthesis had reached very low values, in contrast to what was predicted by an optimality model. The species ranking for the different traits was stable across irradiance treatments. The two pioneer species always displayed the smallest CC, leaf life span, and payback time. All species displayed a similar large irradiance-elicited plasticity. PMID:21511904

Currency crises and the evolution of foreign exchange market: Evidence from minimum spanning tree

NASA Astrophysics Data System (ADS)

Jang, Wooseok; Lee, Junghoon; Chang, Woojin

2011-02-01

We examined the time series properties of the foreign exchange market for 1990-2008 in relation to the history of the currency crises using the minimum spanning tree (MST) approach and made several meaningful observations about the MST of currencies. First, around currency crises, the mean correlation coefficient between currencies decreased whereas the normalized tree length increased. The mean correlation coefficient dropped dramatically passing through the Asian crisis and remained at the lowered level after that. Second, the Euro and the US dollar showed a strong negative correlation after 1997, implying that the prices of the two currencies moved in opposite directions. Third, we observed that Asian countries and Latin American countries moved away from the cluster center (USA) passing through the Asian crisis and Argentine crisis, respectively.

Basal area growth for 15 tropical trees species in Puerto Rico. Forest

Treesearch

B. R. Parresol

1995-01-01

The tabonuco forest of Puerto Rico support a diverse population of tree species valued for timber, fuel, food, wildlife food and cover, and erosion control among other use. tree basal area growth data spanning 39 years are avaible on 15 species from eigth permanent plots in Luquillo Experimental Forest. The complexity of the rain forest challeges current forest...

Basal area growth for 15 tropical tree species in Puerto Rico

Treesearch

Bernard R. Parresol

1995-01-01

The tabonuco forests of Puerto Rico support a diverse population of tree species valued for timber, fuel, food, wildlife food and cover, and erosion control among other uses. Tree basal area growth data spanning 39 years are available on 15 species from eight permanent plots in the Luquillo Experimental Forest. The complexity of the rain forest challenges current...

Annealing Ant Colony Optimization with Mutation Operator for Solving TSP

PubMed Central

2016-01-01

Ant Colony Optimization (ACO) has been successfully applied to solve a wide range of combinatorial optimization problems such as minimum spanning tree, traveling salesman problem, and quadratic assignment problem. Basic ACO has drawbacks of trapping into local minimum and low convergence rate. Simulated annealing (SA) and mutation operator have the jumping ability and global convergence; and local search has the ability to speed up the convergence. Therefore, this paper proposed a hybrid ACO algorithm integrating the advantages of ACO, SA, mutation operator, and local search procedure to solve the traveling salesman problem. The core of algorithm is based on the ACO. SA and mutation operator were used to increase the ants population diversity from time to time and the local search was used to exploit the current search area efficiently. The comparative experiments, using 24 TSP instances from TSPLIB, show that the proposed algorithm outperformed some well-known algorithms in the literature in terms of solution quality. PMID:27999590

Distributed-observer-based cooperative control for synchronization of linear discrete-time multi-agent systems.

PubMed

Liang, Hongjing; Zhang, Huaguang; Wang, Zhanshan

2015-11-01

This paper considers output synchronization of discrete-time multi-agent systems with directed communication topologies. The directed communication graph contains a spanning tree and the exosystem as its root. Distributed observer-based consensus protocols are proposed, based on the relative outputs of neighboring agents. A multi-step algorithm is presented to construct the observer-based protocols. In light of the discrete-time algebraic Riccati equation and internal model principle, synchronization problem is completed. At last, numerical simulation is provided to verify the effectiveness of the theoretical results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Observer-based consensus of networked thrust-propelled vehicles with directed graphs.

PubMed

Cang, Weiye; Li, Zhongkui; Wang, Hanlei

2017-11-01

In this paper, we investigate the consensus problem for networked underactuated thrust-propelled vehicles (TPVs) interacting on directed graphs. We propose distributed observer-based consensus protocols, which avoid the reliance on the measurements of translational velocities and accelerations. Using the input-output analysis, we present necessary and sufficient conditions to ensure that the observer-based protocols can achieve consensus for both the cases without and with constant communication delays, provided that the communication graph contains a directed spanning tree. Simulation examples are finally provided to illustrate the effectiveness of the control schemes. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Comparing minimum spanning trees of the Italian stock market using returns and volumes

NASA Astrophysics Data System (ADS)

Coletti, Paolo

2016-12-01

We have built the network of the top 100 Italian quoted companies in the decade 2001-2011 using four different methods, comparing the resulting minimum spanning trees for methods and industry sectors. Our starting method is based on Person's correlation of log-returns used by several other authors in the last decade. The second one is based on the correlation of symbolized log-returns, the third of log-returns and traded money and the fourth one uses a combination of log-returns with traded money. We show that some sectors correspond to the network's clusters while others are scattered, in particular the trading and apparel sectors. We analyze the different graph's measures for the four methods showing that the introduction of volumes induces larger distances and more homogeneous trees without big clusters.

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.

Location of the adsorption transition for lattice polymers

NASA Astrophysics Data System (ADS)

Madras, Neal

2017-02-01

We consider various lattice models of polymers: lattice trees, lattice animals, and self-avoiding walks. The polymer interacts with a surface (hyperplane), receiving an energy reward of β for each site in the surface. It is known that there is an adsorption transition at a critical value of β. We present a new proof of the result of Hammersley et al (1982 J. Phys. A: Math. Gen. 15 539-71) that the transition occurs at a strictly positive value of β when the surface is impenetrable, i.e. when the polymer is restricted to a half-space. In contrast, for a penetrable surface, it is an open problem to prove that the transition occurs at β =0 . We reduce this problem to proving that the fraction of N-site polymers whose span is less than N/{{log}2}N is not too small.

An adaptive critic-based scheme for consensus control of nonlinear multi-agent systems

NASA Astrophysics Data System (ADS)

Heydari, Ali; Balakrishnan, S. N.

2014-12-01

The problem of decentralised consensus control of a network of heterogeneous nonlinear systems is formulated as an optimal tracking problem and a solution is proposed using an approximate dynamic programming based neurocontroller. The neurocontroller training comprises an initial offline training phase and an online re-optimisation phase to account for the fact that the reference signal subject to tracking is not fully known and available ahead of time, i.e., during the offline training phase. As long as the dynamics of the agents are controllable, and the communication graph has a directed spanning tree, this scheme guarantees the synchronisation/consensus even under switching communication topology and directed communication graph. Finally, an aerospace application is selected for the evaluation of the performance of the method. Simulation results demonstrate the potential of the scheme.

Mutual proximity graphs for improved reachability in music recommendation.

PubMed

Flexer, Arthur; Stevens, Jeff

2018-01-01

This paper is concerned with the impact of hubness, a general problem of machine learning in high-dimensional spaces, on a real-world music recommendation system based on visualisation of a k-nearest neighbour (knn) graph. Due to a problem of measuring distances in high dimensions, hub objects are recommended over and over again while anti-hubs are nonexistent in recommendation lists, resulting in poor reachability of the music catalogue. We present mutual proximity graphs, which are an alternative to knn and mutual knn graphs, and are able to avoid hub vertices having abnormally high connectivity. We show that mutual proximity graphs yield much better graph connectivity resulting in improved reachability compared to knn graphs, mutual knn graphs and mutual knn graphs enhanced with minimum spanning trees, while simultaneously reducing the negative effects of hubness.

Mutual proximity graphs for improved reachability in music recommendation

PubMed Central

Flexer, Arthur; Stevens, Jeff

2018-01-01

This paper is concerned with the impact of hubness, a general problem of machine learning in high-dimensional spaces, on a real-world music recommendation system based on visualisation of a k-nearest neighbour (knn) graph. Due to a problem of measuring distances in high dimensions, hub objects are recommended over and over again while anti-hubs are nonexistent in recommendation lists, resulting in poor reachability of the music catalogue. We present mutual proximity graphs, which are an alternative to knn and mutual knn graphs, and are able to avoid hub vertices having abnormally high connectivity. We show that mutual proximity graphs yield much better graph connectivity resulting in improved reachability compared to knn graphs, mutual knn graphs and mutual knn graphs enhanced with minimum spanning trees, while simultaneously reducing the negative effects of hubness. PMID:29348779

Maintenance of a Minimum Spanning Forest in a Dynamic Planar Graph

DTIC Science & Technology

1990-01-18

v): Delete the edge from v to its parent , thereby dividing the tree containing v into two trees. evert(v): Make v the root of its tree by reversing...the path from v to the original root. find parent (v): Return the parent of v, or null if v is the root of its tree. find Ica(u, v): Return the least...given node (including the parent edge). The ordered set of edges adjacent to node v is called the edge list for v. For example, in our application we

Contributions of public gardens to tree gene conservation

Treesearch

P.A. Allenstein

2017-01-01

American Public Gardens Association, founded in 1940, represents over 600 member gardens spanning North America and 24 countries. Its diverse membership includes botanic gardens, arboreta, and other public gardens which contribute to tree gene conservation. Some maintain ex situ collections nationally accredited through the Association’s Plant Collections Network, a 21...

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

Ultra-fast consensus of discrete-time multi-agent systems with multi-step predictive output feedback

NASA Astrophysics Data System (ADS)

Zhang, Wenle; Liu, Jianchang

2016-04-01

This article addresses the ultra-fast consensus problem of high-order discrete-time multi-agent systems based on a unified consensus framework. A novel multi-step predictive output mechanism is proposed under a directed communication topology containing a spanning tree. By predicting the outputs of a network several steps ahead and adding this information into the consensus protocol, it is shown that the asymptotic convergence factor is improved by a power of q + 1 compared to the routine consensus. The difficult problem of selecting the optimal control gain is solved well by introducing a variable called convergence step. In addition, the ultra-fast formation achievement is studied on the basis of this new consensus protocol. Finally, the ultra-fast consensus with respect to a reference model and robust consensus is discussed. Some simulations are performed to illustrate the effectiveness of the theoretical results.

Modification of Prim’s algorithm on complete broadcasting graph

NASA Astrophysics Data System (ADS)

Dairina; Arif, Salmawaty; Munzir, Said; Halfiani, Vera; Ramli, Marwan

2017-09-01

Broadcasting is an information dissemination from one object to another object through communication between two objects in a network. Broadcasting for n objects can be solved by n - 1 communications and minimum time unit defined by ⌈2log n⌉ In this paper, weighted graph broadcasting is considered. The minimum weight of a complete broadcasting graph will be determined. Broadcasting graph is said to be complete if every vertex is connected. Thus to determine the minimum weight of complete broadcasting graph is equivalent to determine the minimum spanning tree of a complete graph. The Kruskal’s and Prim’s algorithm will be used to determine the minimum weight of a complete broadcasting graph regardless the minimum time unit ⌈2log n⌉ and modified Prim’s algorithm for the problems of the minimum time unit ⌈2log n⌉ is done. As an example case, here, the training of trainer problem is solved using these algorithms.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

PubMed

Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Kelley, Scott T

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .

M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree.

PubMed

Wan, Zhijiang; He, Yishan; Hao, Ming; Yang, Jian; Zhong, Ning

2017-03-29

Understanding the working mechanism of the brain is one of the grandest challenges for modern science. Toward this end, the BigNeuron project was launched to gather a worldwide community to establish a big data resource and a set of the state-of-the-art of single neuron reconstruction algorithms. Many groups contributed their own algorithms for the project, including our mean shift and minimum spanning tree (M-MST). Although M-MST is intuitive and easy to implement, the MST just considers spatial information of single neuron and ignores the shape information, which might lead to less precise connections between some neuron segments. In this paper, we propose an improved algorithm, namely M-AMST, in which a rotating sphere model based on coordinate transformation is used to improve the weight calculation method in M-MST. Two experiments are designed to illustrate the effect of adapted minimum spanning tree algorithm and the adoptability of M-AMST in reconstructing variety of neuron image datasets respectively. In the experiment 1, taking the reconstruction of APP2 as reference, we produce the four difference scores (entire structure average (ESA), different structure average (DSA), percentage of different structure (PDS) and max distance of neurons' nodes (MDNN)) by comparing the neuron reconstruction of the APP2 and the other 5 competing algorithm. The result shows that M-AMST gets lower difference scores than M-MST in ESA, PDS and MDNN. Meanwhile, M-AMST is better than N-MST in ESA and MDNN. It indicates that utilizing the adapted minimum spanning tree algorithm which took the shape information of neuron into account can achieve better neuron reconstructions. In the experiment 2, 7 neuron image datasets are reconstructed and the four difference scores are calculated by comparing the gold standard reconstruction and the reconstructions produced by 6 competing algorithms. Comparing the four difference scores of M-AMST and the other 5 algorithm, we can conclude that M-AMST is able to achieve the best difference score in 3 datasets and get the second-best difference score in the other 2 datasets. We develop a pathway extraction method using a rotating sphere model based on coordinate transformation to improve the weight calculation approach in MST. The experimental results show that M-AMST utilizes the adapted minimum spanning tree algorithm which takes the shape information of neuron into account can achieve better neuron reconstructions. Moreover, M-AMST is able to get good neuron reconstruction in variety of image datasets.

Using certification trails to achieve software fault tolerance

NASA Technical Reports Server (NTRS)

Sullivan, Gregory F.; Masson, Gerald M.

1993-01-01

A conceptually novel and powerful technique to achieve fault tolerance in hardware and software systems is introduced. When used for software fault tolerance, this new technique uses time and software redundancy and can be outlined as follows. In the initial phase, a program is run to solve a problem and store the result. In addition, this program leaves behind a trail of data called a certification trail. In the second phase, another program is run which solves the original problem again. This program, however, has access to the certification trail left by the first program. Because of the availability of the certification trail, the second phase can be performed by a less complex program and can execute more quickly. In the final phase, the two results are accepted as correct; otherwise an error is indicated. An essential aspect of this approach is that the second program must always generate either an error indication or a correct output even when the certification trail it receives from the first program is incorrect. The certification trail approach to fault tolerance was formalized and it was illustrated by applying it to the fundamental problem of finding a minimum spanning tree. Cases in which the second phase can be run concorrectly with the first and act as a monitor are discussed. The certification trail approach was compared to other approaches to fault tolerance. Because of space limitations we have omitted examples of our technique applied to the Huffman tree, and convex hull problems. These can be found in the full version of this paper.

A restricted Steiner tree problem is solved by Geometric Method II

NASA Astrophysics Data System (ADS)

Lin, Dazhi; Zhang, Youlin; Lu, Xiaoxu

2013-03-01

The minimum Steiner tree problem has wide application background, such as transportation system, communication network, pipeline design and VISL, etc. It is unfortunately that the computational complexity of the problem is NP-hard. People are common to find some special problems to consider. In this paper, we first put forward a restricted Steiner tree problem, which the fixed vertices are in the same side of one line L and we find a vertex on L such the length of the tree is minimal. By the definition and the complexity of the Steiner tree problem, we know that the complexity of this problem is also Np-complete. In the part one, we have considered there are two fixed vertices to find the restricted Steiner tree problem. Naturally, we consider there are three fixed vertices to find the restricted Steiner tree problem. And we also use the geometric method to solve such the problem.

A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery Using a Probabilistic Learning Framework

NASA Technical Reports Server (NTRS)

Basu, Saikat; Ganguly, Sangram; Michaelis, Andrew; Votava, Petr; Roy, Anshuman; Mukhopadhyay, Supratik; Nemani, Ramakrishna

2015-01-01

Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets, which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

Rethinking plant functional types in Earth System Models: pan-tropical analysis of tree survival across environmental gradients

NASA Astrophysics Data System (ADS)

Johnson, D. J.; Needham, J.; Xu, C.; Davies, S. J.; Bunyavejchewin, S.; Giardina, C. P.; Condit, R.; Cordell, S.; Litton, C. M.; Hubbell, S.; Kassim, A. R. B.; Shawn, L. K. Y.; Nasardin, M. B.; Ong, P.; Ostertag, R.; Sack, L.; Tan, S. K. S.; Yap, S.; McDowell, N. G.; McMahon, S.

2016-12-01

Terrestrial carbon cycling is a function of the growth and survival of trees. Current model representations of tree growth and survival at a global scale rely on coarse plant functional traits that are parameterized very generally. In view of the large biodiversity in the tropical forests, it is important that we account for the functional diversity in order to better predict tropical forest responses to future climate changes. Several next generation Earth System Models are moving towards a size-structured, trait-based approach to modelling vegetation globally, but the challenge of which and how many traits are necessary to capture forest complexity remains. Additionally, the challenge of collecting sufficient trait data to describe the vast species richness of tropical forests is enormous. We propose a more fundamental approach to these problems by characterizing forests by their patterns of survival. We expect our approach to distill real-world tree survival into a reasonable number of functional types. Using 10 large-area tropical forest plots that span geographic, edaphic and climatic gradients, we model tree survival as a function of tree size for hundreds of species. We found surprisingly few categories of size-survival functions emerge. This indicates some fundamental strategies at play across diverse forests to constrain the range of possible size-survival functions. Initial cluster analysis indicates that four to eight functional forms are necessary to describe variation in size-survival relations. Temporal variation in size-survival functions can be related to local environmental variation, allowing us to parameterize how demographically similar groups of species respond to perturbations in the ecosystem. We believe this methodology will yield a synthetic approach to classifying forest systems that will greatly reduce uncertainty and complexity in global vegetation models.

A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery using a Probabilistic Learning Framework

NASA Astrophysics Data System (ADS)

Basu, S.; Ganguly, S.; Michaelis, A.; Votava, P.; Roy, A.; Mukhopadhyay, S.; Nemani, R. R.

2015-12-01

Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

Photosynthesis, photoinhibition, and nitrogen use efficiency in native and invasive tree ferns in Hawaii.

PubMed

Durand, Leilani Z; Goldstein, Guillermo

2001-02-01

Photosynthetic gas exchange, chlorophyll fluorescence, nitrogen use efficiency, and related leaf traits of native Hawaiian tree ferns in the genus Cibotium were compared with those of the invasive Australian tree fern Sphaeropteris cooperi in an attempt to explain the higher growth rates of S. cooperi in Hawaii. Comparisons were made between mature sporophytes growing in the sun (gap or forest edge) and in shady understories at four sites at three different elevations. The invasive tree fern had 12-13 cm greater height increase per year and approximately 5 times larger total leaf surface area per plant compared to the native tree ferns. The maximum rates of photosynthesis of S. cooperi in the sun and shade were significantly higher than those of the native Cibotium spp (for example, 11.2 and 7.1 µmol m -2  s -1 , and 5.8 and 3.6 µmol m -2  s -1 respectively for the invasive and natives at low elevation). The instantaneous photosynthetic nitrogen use efficiency of the invasive tree fern was significantly higher than that of the native tree ferns, but when integrated over the life span of the frond the differences were not significant. The fronds of the invasive tree fern species had a significantly shorter life span than the native tree ferns (approximately 6 months and 12 months, respectively), and significantly higher nitrogen content per unit leaf mass. The native tree ferns growing in both sun and shade exhibited greater photoinhibition than the invasive tree fern after being experimentally subjected to high light levels. The native tree ferns recovered only 78% of their dark-acclimated quantum yield (F v /F m ), while the invasive tree fern recovered 90% and 86% of its dark-acclimated F v /F m when growing in sun and shade, respectively. Overall, the invasive tree fern appears to be more efficient at capturing and utilizing light than the native Cibotium species, particularly in high-light environments such as those associated with high levels of disturbance.

Status of Mississippi gulf coast Live Oak trees after Hurricane Katrina

Treesearch

Julie Ann Dobbs; David W. Held; Nebeker T. Evan

2006-01-01

Live oak trees, Quercus virginiana, have long been considered to be the symbol of the Old South. Part of the attraction of the Atlantic and Gulf Coasts is the stately live oaks. These majestic live oaks have weathered many hurricanes in their >200 yr life span. Most recently, on 29 August 2005 Hurricane Katrina, with sustained winds exceeding 160...

A Simple Model for the Earthquake Cycle Combining Self-Organized Criticality with Critical Point Behavior

NASA Astrophysics Data System (ADS)

Newman, W. I.; Turcotte, D. L.

2002-12-01

We have studied a hybrid model combining the forest-fire model with the site-percolation model in order to better understand the earthquake cycle. We consider a square array of sites. At each time step, a "tree" is dropped on a randomly chosen site and is planted if the site is unoccupied. When a cluster of "trees" spans the site (a percolating cluster), all the trees in the cluster are removed ("burned") in a "fire." The removal of the cluster is analogous to a characteristic earthquake and planting "trees" is analogous to increasing the regional stress. The clusters are analogous to the metastable regions of a fault over which an earthquake rupture can propagate once triggered. We find that the frequency-area statistics of the metastable regions are power-law with a negative exponent of two (as in the forest-fire model). This is analogous to the Gutenberg-Richter distribution of seismicity. This "self-organized critical behavior" can be explained in terms of an inverse cascade of clusters. Individual trees move from small to larger clusters until they are destroyed. This inverse cascade of clusters is self-similar and the power-law distribution of cluster sizes has been shown to have an exponent of two. We have quantified the forecasting of the spanning fires using error diagrams. The assumption that "fires" (earthquakes) are quasi-periodic has moderate predictability. The density of trees gives an improved degree of predictability, while the size of the largest cluster of trees provides a substantial improvement in forecasting a "fire."

Exact solutions for species tree inference from discordant gene trees.

PubMed

Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

2013-10-01

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions.

Topology for efficient information dissemination in ad-hoc networking

NASA Technical Reports Server (NTRS)

Jennings, E.; Okino, C. M.

2002-01-01

In this paper, we explore the information dissemination problem in ad-hoc wirless networks. First, we analyze the probability of successful broadcast, assuming: the nodes are uniformly distributed, the available area has a lower bould relative to the total number of nodes, and there is zero knowledge of the overall topology of the network. By showing that the probability of such events is small, we are motivated to extract good graph topologies to minimize the overall transmissions. Three algorithms are used to generate topologies of the network with guaranteed connectivity. These are the minimum radius graph, the relative neighborhood graph and the minimum spanning tree. Our simulation shows that the relative neighborhood graph has certain good graph properties, which makes it suitable for efficient information dissemination.

Combining a generic process-based productivity model classification method to predict the presence and absence species in the Pacific Northwest, U.S.A

Treesearch

Nicholas C. Coops; Richard H. Waring; Todd A. Schroeder

2009-01-01

Although long-lived tree species experience considerable environmental variation over their life spans, their geographical distributions reflect sensitivity mainly to mean monthly climatic conditions.We introduce an approach that incorporates a physiologically based growth model to illustrate how a half-dozen tree species differ in their responses to monthly variation...

Comparison of charcoal and tree-ring records of recent fires in the eastern Klamath Mountains, California, USA

Treesearch

Cathy Whitlock; Carl N. Skinner; Patrick J. Bartlein; Thomas Minckley; Jerry A. Mohr

2004-01-01

Fire-history reconstructions are based on tree-ring records that span the last few centuries and charcoal data from lake-sediment cores that extend back several thousand years. The two approaches have unique strengths and weaknesses in their ability to depict past fire events and fire regimes, and most comparisons of these datasets in western conifer forests have...

Changes in gas exchange characteristics during the life span of giant sequoia: implications for response to current and future concentrations of atmospheric ozone.

PubMed

Grulke, N. E.; Miller, P. R.

1994-01-01

Native stands of giant sequoia (Sequoiadendron giganteum Bucholz) are being exposed to relatively high concentrations of atmospheric ozone produced in urban and agricultural areas upwind. The expected change in environmental conditions over the next 100 years is likely to be unprecedented in the life span (about 2,500 years) of giant sequoia. We determined changes in physiological responses of three age classes of giant sequoia (current-year, 12-, and 125-year-old) to differing concentrations of ozone, and assessed age-related differences in sensitivity to pollutants by examining physiological changes (gas exchange, water use efficiency) across the life span of giant sequoia (current-year, 2-, 5-, 20-, 125-, and > 2,000-year-old trees). The CO(2) exchange rate (CER) was greater in current-year (12.1 micro mol CO(2) m(-2) s(-1)) and 2-year-old seedlings (4.8 micro mol CO(2) m(-2) s(-1)) than in all older trees (3.0 micro mol CO(2) m(-2) s(-1), averaged across the four older age classes). Dark respiration was highest for current-year seedlings (-6.5 +/- 0.7 micro mol CO(2) m(-2) s(-1)) and was increased twofold in symptomatic individuals exposed to elevated ozone concentrations. Stomatal conductance (g(s)) was greater in current-year (355 mmol H(2)O m(-2) s(-1)) and 2-year-old seedlings (200 mmol H(2)O m(-2) s(-1)) than in all older trees (50 mmol H(2)O m(-2) s(-1)), indicating that the ozone concentration in substomatal cavities is higher in young seedlings than in trees. Significant changes in water use efficiency, as indicated by C(i)/C(a), occurred in trees between ages 5 and 20 years. We conclude that giant sequoias seedlings are sensitive to atmospheric ozone until they are about 5 years old. Low conductance, high water use efficiency, and compact mesophyll all contribute to a natural ozone tolerance, or defense, or both, in foliage of older trees.

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.

Constructing Phylogenies.

ERIC Educational Resources Information Center

Bilardello, Nicholas; Valdes, Linda

1998-01-01

Introduces a method for constructing phylogenies using molecular traits and elementary graph theory. Discusses analyzing molecular data and using weighted graphs, minimum-weight spanning trees, and rooted cube phylogenies to display the data. (DDR)

Image Segmentation Using Minimum Spanning Tree

NASA Astrophysics Data System (ADS)

Dewi, M. P.; Armiati, A.; Alvini, S.

2018-04-01

This research aim to segmented the digital image. The process of segmentation is to separate the object from the background. So the main object can be processed for the other purposes. Along with the development of technology in digital image processing application, the segmentation process becomes increasingly necessary. The segmented image which is the result of the segmentation process should accurate due to the next process need the interpretation of the information on the image. This article discussed the application of minimum spanning tree on graph in segmentation process of digital image. This method is able to separate an object from the background and the image will change to be the binary images. In this case, the object that being the focus is set in white, while the background is black or otherwise.

Evolutionary Topology of a Currency Network in Asia

NASA Astrophysics Data System (ADS)

Feng, Xiaobing; Wang, Xiaofan

Although recently there are extensive research on currency network using minimum spanning trees approach, the knowledge about the actual evolution of a currency web in Asia is still limited. In the paper, we study the structural evolution of an Asian network using daily exchange rate data. It was found that the correlation between Asian currencies and US Dollar, the previous regional key currency has become weaker and the intra-Asia interactions have increased. This becomes more salient after the exchange rate reform of China. Different from the previous studies, we further reveal that it is the trade volume, national wealth gap and countries growth cycle that has contributed to the evolutionary topology of the minimum spanning tree. These findings provide a valuable platform for theoretical modeling and further analysis.

Hyperspectral Super-Resolution of Locally Low Rank Images From Complementary Multisource Data.

PubMed

Veganzones, Miguel A; Simoes, Miguel; Licciardi, Giorgio; Yokoya, Naoto; Bioucas-Dias, Jose M; Chanussot, Jocelyn

2016-01-01

Remote sensing hyperspectral images (HSIs) are quite often low rank, in the sense that the data belong to a low dimensional subspace/manifold. This has been recently exploited for the fusion of low spatial resolution HSI with high spatial resolution multispectral images in order to obtain super-resolution HSI. Most approaches adopt an unmixing or a matrix factorization perspective. The derived methods have led to state-of-the-art results when the spectral information lies in a low-dimensional subspace/manifold. However, if the subspace/manifold dimensionality spanned by the complete data set is large, i.e., larger than the number of multispectral bands, the performance of these methods mainly decreases because the underlying sparse regression problem is severely ill-posed. In this paper, we propose a local approach to cope with this difficulty. Fundamentally, we exploit the fact that real world HSIs are locally low rank, that is, pixels acquired from a given spatial neighborhood span a very low-dimensional subspace/manifold, i.e., lower or equal than the number of multispectral bands. Thus, we propose to partition the image into patches and solve the data fusion problem independently for each patch. This way, in each patch the subspace/manifold dimensionality is low enough, such that the problem is not ill-posed anymore. We propose two alternative approaches to define the hyperspectral super-resolution through local dictionary learning using endmember induction algorithms. We also explore two alternatives to define the local regions, using sliding windows and binary partition trees. The effectiveness of the proposed approaches is illustrated with synthetic and semi real data.

Bedrock composition limits mountain ecosystem productivity and landscape evolution (Invited)

NASA Astrophysics Data System (ADS)

Riebe, C. S.; Hahm, W.; Lukens, C.

2013-12-01

We used measurements of bedrock geochemistry, forest productivity and cosmogenic nuclides to explore connections among lithology, ecosystem productivity and landscape evolution across a lithosequence of 21 sites in the Sierra Nevada Batholith, California. Our sites span a narrow range in elevations and thus share similar climatic conditions. Meanwhile, underlying bedrock varies from granite to diorite and spans nearly the entire range of geochemical compositions observed in Cordilleran granitoids. Land cover varies markedly, from groves of Giant Sequoia, the largest trees on Earth, to pluton-spanning swaths of little or no soil and vegetative cover. This is closely reflected in measures of forest productivity, such as remotely sensed tree-canopy cover, which varies by more than an order of magnitude across our sites and often changes abruptly at mapped contacts between rock types. We find that tree-canopy cover is closely correlated with the concentrations in bedrock of major and minor elements, including several plant-essential nutrients. For example, tree-canopy cover is virtually zero where there is less than 0.3 mg/g phosphorus in bedrock. Erosion rates from these nearly vegetation-free, nutrient deserts are more than 2.5 times slower on average than they are from surrounding, relatively nutrient-rich, soil-mantled bedrock. Thus by influencing soil and forest cover, bedrock nutrient concentrations may provoke weathering-limited erosion and thus may strongly regulate landscape evolution. Our analysis suggests that variations in bedrock nutrient concentrations can also provoke an intrinsic limitation on primary productivity. These limitations appear to apply across all our sites. To the extent that they are broadly representative of conditions in granitic landscapes elsewhere around the world, our results are consistent with widespread, but previously undocumented lithologic control of the distribution and diversity of vegetation in mountainous terrain.

A new method for separating the climatic and biological trend components from tree ring series, with implications for paleoclimate reconstructions

NASA Astrophysics Data System (ADS)

Bouldin, J.

2010-12-01

In the reconstruction of past climates from tree rings multi-decadal to multi-centennial periods, one longstanding problem is the confounding of the natural biological growth trend of the tree with any existing long term trends in the climate. No existing analytical method is capable of resolving these two change components, so it remains unclear how accurate existing ring series standardizations are, and by implication, climate reconstructions based upon them. For example, dendrochronological at the ITRDB are typically standardized by detrending, at each site, each individual tree core, using a relatively stiff deterministic function such as a negative exponential curve or smoothing spline. Another approach, referred to as RCS (Regional Curve Standardization) attempts to solve some problems of the individual series detrending, by constructing a single growth curve from the aggregated cambial ages of the rings of the cores at a site (or collection of sites). This curve is presumed to represent the “ideal” or expected growth of the trees from which it is derived. Although an improvement in some respects, this method will be degraded in direct proportion to the lack of a mixture of tree sizes or ages throughout the span of the chronology. I present a new method of removing the biological curve from tree ring series, such that temporal changes better represent the environmental variation captured by the tree rings. The method institutes several new approaches, such as the correction for the estimated number of missed rings near the pith, and the use of tree size and ring area relationships instead of the traditional tree ages and ring widths. The most important innovation is a careful extraction of the existing information on the relationship between tree size (basal area) and ring area that exists within each single year of the chronology. This information is, by definition, not contaminated by temporal climatic changes, and so when removed, leaves the climatically caused, and random error components of the chronology. A sophisticated algorithm, based on pair-wise ring comparisons in which tree size is standardized both within and between years, forms the basis of the method. Evaluations of the method are underway with both simulated and actual (ITRDB) data, to evaluate the potentials and drawbacks of the method relative to existing methods. The ITRDB test data consists of a set of about 50 primarily high elevation sites from across western North America. Most of these sites show a pronounced 20th Century warming relative to earlier centuries, in accordance with current understanding, albeit at a non-global scale. A relative minority show cooling, occasionally strongly. Current and future work emphasizes evaluation of the method with varying, simulated data, and more thorough empirical evaluations of the method in situations where the type, and intensity, of the primary environmentally limiting factor varies (e.g temperature versus soil moisture limited sites).

Capacity of old trees to respond to environmental change.

PubMed

Phillips, Nathan G; Buckley, Thomas N; Tissue, David T

2008-11-01

Atmospheric carbon dioxide [CO2] has increased dramatically within the current life spans of long-lived trees and old forests. Consider that a 500-year-old tree in the early twenty-first century has spent 70% of its life growing under pre-industrial levels of [CO2], which were 30% lower than current levels. Here we address the question of whether old trees have already responded to the rapid rise in [CO2] occurring over the past 150 years. In spite of limited data, aging trees have been shown to possess a substantial capacity for increased net growth after a period of post-maturity growth decline. Observations of renewed growth and physiological function in old trees have, in some instances, coincided with Industrial Age increases in key environmental resources, including [CO2], suggesting the potential for continued growth in old trees as a function of continued global climate change.

SLE as a Mating of Trees in Euclidean Geometry

NASA Astrophysics Data System (ADS)

Holden, Nina; Sun, Xin

2018-05-01

The mating of trees approach to Schramm-Loewner evolution (SLE) in the random geometry of Liouville quantum gravity (LQG) has been recently developed by Duplantier et al. (Liouville quantum gravity as a mating of trees, 2014. arXiv:1409.7055). In this paper we consider the mating of trees approach to SLE in Euclidean geometry. Let {η} be a whole-plane space-filling SLE with parameter {κ > 4} , parameterized by Lebesgue measure. The main observable in the mating of trees approach is the contour function, a two-dimensional continuous process describing the evolution of the Minkowski content of the left and right frontier of {η} . We prove regularity properties of the contour function and show that (as in the LQG case) it encodes all the information about the curve {η} . We also prove that the uniform spanning tree on {Z^2} converges to SLE8 in the natural topology associated with the mating of trees approach.

Connectivity Restoration in Wireless Sensor Networks via Space Network Coding.

PubMed

Uwitonze, Alfred; Huang, Jiaqing; Ye, Yuanqing; Cheng, Wenqing

2017-04-20

The problem of finding the number and optimal positions of relay nodes for restoring the network connectivity in partitioned Wireless Sensor Networks (WSNs) is Non-deterministic Polynomial-time hard (NP-hard) and thus heuristic methods are preferred to solve it. This paper proposes a novel polynomial time heuristic algorithm, namely, Relay Placement using Space Network Coding (RPSNC), to solve this problem, where Space Network Coding, also called Space Information Flow (SIF), is a new research paradigm that studies network coding in Euclidean space, in which extra relay nodes can be introduced to reduce the cost of communication. Unlike contemporary schemes that are often based on Minimum Spanning Tree (MST), Euclidean Steiner Minimal Tree (ESMT) or a combination of MST with ESMT, RPSNC is a new min-cost multicast space network coding approach that combines Delaunay triangulation and non-uniform partitioning techniques for generating a number of candidate relay nodes, and then linear programming is applied for choosing the optimal relay nodes and computing their connection links with terminals. Subsequently, an equilibrium method is used to refine the locations of the optimal relay nodes, by moving them to balanced positions. RPSNC can adapt to any density distribution of relay nodes and terminals, as well as any density distribution of terminals. The performance and complexity of RPSNC are analyzed and its performance is validated through simulation experiments.

On the Shapley Value of Unrooted Phylogenetic Trees.

PubMed

Wicke, Kristina; Fischer, Mareike

2018-01-17

The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows for the calculation of the Shapley value from the edge lengths of a tree. We show that non-isomorphic trees may have permutation-equivalent Shapley transformation matrices and permutation-equivalent null spaces. This implies that estimating the split counts associated with a tree or the Shapley values of its leaves does not suffice to reconstruct the correct tree topology. We then turn to the use of the Shapley value as a prioritization criterion in biodiversity conservation and compare it to a greedy solution concept. Here, we show that for certain phylogenetic trees, the Shapley value may fail as a prioritization criterion, meaning that the diversity spanned by the top k species (ranked by their Shapley values) cannot approximate the total diversity of all n species.

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.

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

PubMed

Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

2017-04-01

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

Long-term scenarios of the invasive black cherry in pine-oak forest: Impact of regeneration success

NASA Astrophysics Data System (ADS)

Vanhellemont, Margot; Baeten, Lander; Verbeeck, Hans; Hermy, Martin; Verheyen, Kris

2011-05-01

The spread of invasive tree species in forests can be slow because of their long life span and the lag phases that may occur during the invasion process. Models of forest succession are a useful tool to explore how these invasive species might affect long-term forest development. We used the spatially explicit individual tree model SORTIE-ND to gain insight into the long-term development of a gap-dependent invasive tree species, Prunus serotina, in a pine-oak forest on sandy soil, the forest type in which P. serotina occurs most often in its introduced range. Forest inventory data, tree ring data, and photographs of the tree crowns were collected in a forest reserve in the Netherlands, characterized by high game densities. The collected data were then combined with data from literature to parameterize the model. We ran the model for two different scenarios in order to evaluate the impact of differences in the regeneration success of the native Quercus robur and the invasive P. serotina. The outcome of the simulations shows two differing courses of forest development. The invasive P. serotina became the dominant species when the regeneration of Q. robur was hindered, e.g., because of high herbivore densities. When both Q. robur and P. serotina were able to regenerate, Q. robur became the most abundant species in the long-term. We hypothesize that the relatively short life span of P. serotina may preclude its dominance if other long-lived tree species are present and able to regenerate.

Faster Bit-Parallel Algorithms for Unordered Pseudo-tree Matching and Tree Homeomorphism

NASA Astrophysics Data System (ADS)

Kaneta, Yusaku; Arimura, Hiroki

In this paper, we consider the unordered pseudo-tree matching problem, which is a problem of, given two unordered labeled trees P and T, finding all occurrences of P in T via such many-one embeddings that preserve node labels and parent-child relationship. This problem is closely related to tree pattern matching problem for XPath queries with child axis only. If m > w , we present an efficient algorithm that solves the problem in O(nm log(w)/w) time using O(hm/w + mlog(w)/w) space and O(m log(w)) preprocessing on a unit-cost arithmetic RAM model with addition, where m is the number of nodes in P, n is the number of nodes in T, h is the height of T, and w is the word length. We also discuss a modification of our algorithm for the unordered tree homeomorphism problem, which corresponds to a tree pattern matching problem for XPath queries with descendant axis only.

Remeasured FIA plots reveal tree-level diameter growth and tree mortality impacts of nitrogen deposition on California’s forests

Treesearch

Mark E. Fenn; Jeremy S. Fried; Haiganoush K. Preisler; Andrzej Bytnerowicz; Susan Schilling; Sarah Jovan; Olaf Kuegler

2015-01-01

The air in California’s forests spans a broad range of purity, from virtually no locally generated pollutants to highly elevated levels of pollutants in forests downwind of urban and agricultural source areas. Ten-year remeasurement data from Forest Inventory and Analysis (FIA) plots in California were used in combination with modelled atmospheric nitrogen (N)...

A Genetic Algorithm for the Bi-Level Topological Design of Local Area Networks

PubMed Central

Camacho-Vallejo, José-Fernando; Mar-Ortiz, Julio; López-Ramos, Francisco; Rodríguez, Ricardo Pedraza

2015-01-01

Local access networks (LAN) are commonly used as communication infrastructures which meet the demand of a set of users in the local environment. Usually these networks consist of several LAN segments connected by bridges. The topological LAN design bi-level problem consists on assigning users to clusters and the union of clusters by bridges in order to obtain a minimum response time network with minimum connection cost. Therefore, the decision of optimally assigning users to clusters will be made by the leader and the follower will make the decision of connecting all the clusters while forming a spanning tree. In this paper, we propose a genetic algorithm for solving the bi-level topological design of a Local Access Network. Our solution method considers the Stackelberg equilibrium to solve the bi-level problem. The Stackelberg-Genetic algorithm procedure deals with the fact that the follower’s problem cannot be optimally solved in a straightforward manner. The computational results obtained from two different sets of instances show that the performance of the developed algorithm is efficient and that it is more suitable for solving the bi-level problem than a previous Nash-Genetic approach. PMID:26102502

Rapid increase in cosmogenic 14C in AD 775 measured in New Zealand kauri trees indicates short-lived increase in 14C production spanning both hemispheres

NASA Astrophysics Data System (ADS)

Güttler, D.; Adolphi, F.; Beer, J.; Bleicher, N.; Boswijk, G.; Christl, M.; Hogg, A.; Palmer, J.; Vockenhuber, C.; Wacker, L.; Wunder, J.

2015-02-01

In 2012, Miyake et al. reported a sudden and strong increase of the atmospheric radiocarbon (14C) content in Japanese cedar trees of 1.2% between AD 774 and 775. While their findings were quickly confirmed by a German oak chronology for the Northern Hemisphere (NH), the question remained if the effect was seen in both hemispheres. Here we present the first annually resolved Southern Hemisphere (SH) 14C record spanning the interval AD 760-787, using New Zealand kauri (Agathis australis) chronology wood. An almost identical distinct increase compared to Northern Hemisphere data was observed, suggesting a cosmic event with globally uniform impact as a potential cause for the increase. Deploying a carbon cycle box model a worldwide averaged net 14C production of 2.2 ×108 14C atoms cm-2 was estimated, which is 3.7 times higher than the average annual 14C production. The immediate appearance of the event in tree rings on both hemispheres suggests a short duration event of significantly less than 1 yr.

On the theory of oscillating airfoils of finite span in subsonic compressible flow

NASA Technical Reports Server (NTRS)

Reissner, Eric

1950-01-01

The problem of oscillating lifting surface of finite span in subsonic compressible flow is reduced to an integral equation. The kernel of the integral equation is approximated by a simpler expression, on the basis of the assumption of sufficiently large aspect ratio. With this approximation the double integral occurring in the formulation of the problem is reduced to two single integrals, one of which is taken over the chord and the other over the span of the lifting surface. On the basis of this reduction the three-dimensional problem appears separated into two two-dimensional problems, one of them being effectively the problem of two-dimensional flow and the other being the problem of spanwise circulation distribution. Earlier results concerning the oscillating lifting surface of finite span in incompressible flow are contained in the present more general results.

Distributed MPC based consensus for single-integrator multi-agent systems.

PubMed

Cheng, Zhaomeng; Fan, Ming-Can; Zhang, Hai-Tao

2015-09-01

This paper addresses model predictive control schemes for consensus in multi-agent systems (MASs) with discrete-time single-integrator dynamics under switching directed interaction graphs. The control horizon is extended to be greater than one which endows the closed-loop system with extra degree of freedom. We derive sufficient conditions on the sampling period and the interaction graph to achieve consensus by using the property of infinite products of stochastic matrices. Consensus can be achieved asymptotically if the sampling period is selected such that the interaction graph among agents has a directed spanning tree jointly. Significantly, if the interaction graph always has a spanning tree, one can select an arbitrary large sampling period to guarantee consensus. Finally, several simulations are conducted to illustrate the effectiveness of the theoretical results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Consistent and powerful non-Euclidean graph-based change-point test with applications to segmenting random interfered video data.

PubMed

Shi, Xiaoping; Wu, Yuehua; Rao, Calyampudi Radhakrishna

2018-06-05

The change-point detection has been carried out in terms of the Euclidean minimum spanning tree (MST) and shortest Hamiltonian path (SHP), with successful applications in the determination of authorship of a classic novel, the detection of change in a network over time, the detection of cell divisions, etc. However, these Euclidean graph-based tests may fail if a dataset contains random interferences. To solve this problem, we present a powerful non-Euclidean SHP-based test, which is consistent and distribution-free. The simulation shows that the test is more powerful than both Euclidean MST- and SHP-based tests and the non-Euclidean MST-based test. Its applicability in detecting both landing and departure times in video data of bees' flower visits is illustrated.

A new formation control of multiple underactuated surface vessels

NASA Astrophysics Data System (ADS)

Xie, Wenjing; Ma, Baoli; Fernando, Tyrone; Iu, Herbert Ho-Ching

2018-05-01

This work investigates a new formation control problem of multiple underactuated surface vessels. The controller design is based on input-output linearisation technique, graph theory, consensus idea and some nonlinear tools. The proposed smooth time-varying distributed control law guarantees that the multiple underactuated surface vessels globally exponentially converge to some desired geometric shape, which is especially centred at the initial average position of vessels. Furthermore, the stability analysis of zero dynamics proves that the orientations of vessels tend to some constants that are dependent on the initial values of vessels, and the velocities and control inputs of the vessels decay to zero. All the results are obtained under the communication scenarios of static directed balanced graph with a spanning tree. Effectiveness of the proposed distributed control scheme is demonstrated using a simulation example.

Individual differences in working memory and reasoning-remembering relationships in solving class-inclusion problems.

PubMed

Howe, M L; Rabinowitz, F M; Powell, T L

1998-09-01

In the present experiment, we evaluated the effects of individual differences in reading span and variation in memory demands on class-inclusion performance. One hundred twenty college students whose reading spans ranged from low to medium to high (as indexed by a computerized version of the Daneman and Carpenter [1980] reading-span task) solved 48 class-inclusion problems. Half of the subjects had the solution information available when the problems were presented; the other half performed a detection task between solution information and problem presentation. The results from both standard statistical analyses and from a mathematical model indicated that differences in reading span and memory load had predictable, similar effects. Specifically, the sophistication of reasoning strategies declined when memory demands increased or when reading spans decreased. Surprisingly, these effects were primarily additive. The results were interpreted in terms of global resource models and findings from the developmental literature.

A class of vertex-edge-growth small-world network models having scale-free, self-similar and hierarchical characters

NASA Astrophysics Data System (ADS)

Ma, Fei; Su, Jing; Hao, Yongxing; Yao, Bing; Yan, Guanghui

2018-02-01

The problem of uncovering the internal operating function of network models is intriguing, demanded and attractive in researches of complex networks. Notice that, in the past two decades, a great number of artificial models are built to try to answer the above mentioned task. Based on the different growth ways, these previous models can be divided into two categories, one type, possessing the preferential attachment, follows a power-law P(k) ∼k-γ, 2 < γ < 3. The other has exponential-scaling feature, P(k) ∼α-k. However, there are no models containing above two kinds of growth ways to be presented, even the study of interconnection between these two growth manners in the same model is lacking. Hence, in this paper, we construct a class of planar and self-similar graphs motivated from a new attachment way, vertex-edge-growth network-operation, more precisely, the couple of both them. We report that this model is sparse, small world and hierarchical. And then, not only is scale-free feature in our model, but also lies the degree parameter γ(≈ 3 . 242) out the typical range. Note that, we suggest that the coexistence of multiple vertex growth ways will have a prominent effect on the power-law parameter γ, and the preferential attachment plays a dominate role on the development of networks over time. At the end of this paper, we obtain an exact analytical expression for the total number of spanning trees of models and also capture spanning trees entropy which we have compared with those of their corresponding component elements.

Millennium-scale crossdating and inter-annual climate sensitivities of standing California redwoods.

PubMed

Carroll, Allyson L; Sillett, Stephen C; Kramer, Russell D

2014-01-01

Extremely decay-resistant wood and fire-resistant bark allow California's redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI) helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE) have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood species have numerous scientific applications, including determination of tree ages, accurate dating of fire-return intervals, archaeology, analyses of stable isotopes, long-term climate reconstructions, and quantifying rates of carbon sequestration.

Millennium-Scale Crossdating and Inter-Annual Climate Sensitivities of Standing California Redwoods

PubMed Central

Carroll, Allyson L.; Sillett, Stephen C.; Kramer, Russell D.

2014-01-01

Extremely decay-resistant wood and fire-resistant bark allow California’s redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI) helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE) have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood species have numerous scientific applications, including determination of tree ages, accurate dating of fire-return intervals, archaeology, analyses of stable isotopes, long-term climate reconstructions, and quantifying rates of carbon sequestration. PMID:25029026

The EASTNET Project: Extending the Network of Climate-Sensitive Tree-Ring Chronologies From the Eastern United States for Reconstructing the Spatio-Temporal Characteristics of Climate and Drought Over the Past Millennium

NASA Astrophysics Data System (ADS)

Buckley, B. M.; Cook, E. R.

2002-12-01

Recently, a network of gridded PDSI reconstructions for the contiguous United States was produced, based on the available network of drought-sensitive tree-ring chronologies (Cook et al. 1999). Analyses were constrained to the common period of 1700 - 1979 due to the limitations of the available tree-ring data. While several chronologies from the western U.S. span 1,000 years or more, very few chronologies from the eastern U.S. covered even the past 500 years. The objective of this project, funded by the National Science Foundation's ESH program, is to extend the tree-ring chronology network from the eastern U.S. with chronologies spanning the past 500-1,000 years. This aim is being achieved by sampling in areas that have escaped the effects of development, logging and major disturbance such as fire. The two main target species are Thuja occidentalis (eastern white cedar) and Juniperus virginiana (eastern red cedar). The primary terrain types are on cliffs, rocky outcrops, and other areas that have been difficult to access. We have already developed chronologies from Wisconsin, New Hampshire, Pennsylvania, West Virginia, and Virginia that span from 500 to 1500 years. The temporal depth of these chronologies is being extended through the exploitation of "sub-fossil" wood found at these sites, in the form of standing-dead stems and downed and buried logs. We are also currently pursuing leads in Maine, Vermont, Massachusetts, Connecticut, New York, New Jersey Pennsylvania, Kentucky and North Carolina where old cedar trees have either been reported or where terrain types match criteria developed for this project. In this paper we discuss the current status of the network, and explore the spatio-temporal characteristics of climate and drought across the eastern US for the past 500 years and more. We use our preliminary network to explore the regional expression of climate anomalies such as drought. Our analyses so far demonstrates multicentennial variability suggestive of Medieval Warm Period (MWP) and Little Ice Age (LIA) type signatures from an eastern red cedar chronology from West Virginia that spans the past 1,500 years. This is the oldest chronology so far developed from this project, though we anticipate the development of several more millennial length time-series within the next year. References Cook, E.R., Meko, D.M., Stahle, D.W., and Cleaveland, M.K. 1999. Drought reconstructions for the continental United States. Journal of Climate 12:1145-1162.

STRIDE: Species Tree Root Inference from Gene Duplication Events.

PubMed

Emms, David M; Kelly, Steven

2017-12-01

The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Minimum spanning tree filtering of correlations for varying time scales and size of fluctuations

NASA Astrophysics Data System (ADS)

Kwapień, Jarosław; Oświecimka, Paweł; Forczek, Marcin; DroŻdŻ, Stanisław

2017-05-01

Based on a recently proposed q -dependent detrended cross-correlation coefficient, ρq [J. Kwapień, P. Oświęcimka, and S. Drożdż, Phys. Rev. E 92, 052815 (2015), 10.1103/PhysRevE.92.052815], we generalize the concept of the minimum spanning tree (MST) by introducing a family of q -dependent minimum spanning trees (q MST s ) that are selective to cross-correlations between different fluctuation amplitudes and different time scales of multivariate data. They inherit this ability directly from the coefficients ρq, which are processed here to construct a distance matrix being the input to the MST-constructing Kruskal's algorithm. The conventional MST with detrending corresponds in this context to q =2 . In order to illustrate their performance, we apply the q MSTs to sample empirical data from the American stock market and discuss the results. We show that the q MST graphs can complement ρq in disentangling "hidden" correlations that cannot be observed in the MST graphs based on ρDCCA, and therefore, they can be useful in many areas where the multivariate cross-correlations are of interest. As an example, we apply this method to empirical data from the stock market and show that by constructing the q MSTs for a spectrum of q values we obtain more information about the correlation structure of the data than by using q =2 only. More specifically, we show that two sets of signals that differ from each other statistically can give comparable trees for q =2 , while only by using the trees for q ≠2 do we become able to distinguish between these sets. We also show that a family of q MSTs for a range of q expresses the diversity of correlations in a manner resembling the multifractal analysis, where one computes a spectrum of the generalized fractal dimensions, the generalized Hurst exponents, or the multifractal singularity spectra: the more diverse the correlations are, the more variable the tree topology is for different q 's. As regards the correlation structure of the stock market, our analysis exhibits that the stocks belonging to the same or similar industrial sectors are correlated via the fluctuations of moderate amplitudes, while the largest fluctuations often happen to synchronize in those stocks that do not necessarily belong to the same industry.

Chemically inducing lightwood formation in southern pines

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

Roberts, D.R.; Peters, W.J.

1977-06-01

Chemical induction of lightwood formation promises to be a new method of naval stores production. A broad range of paraquat concentrations and many methods of application induced lightwood formation. Loblolly, slash, and longleaf pines were found to produce increased amounts of turpentine and tall oil in response to paraquat treatment. In one experiment, loblolly pines treated with 8 percent paraquat on a single bark streak yielded, 9 months after treatment, an average of 10 pounds more extractives per tree than did untreated trees. Most of the yield increase was in the lower portion of the tree near the wound, butmore » some increase was noted for heights as great as 27 ft. In another experiment, 8 to 10 inch DBH loblolly, slash, and longleaf pine trees were treated with 0.5, 1.0, and 2.5 percent paraquat applied in ax chops spanning one-third the circumference of the trees. All treated trees yielded more resin acids than did control trees.« less

Rényi indices of financial minimum spanning trees

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao; Song, Fu-Tie; Li, Sai-Ping

2016-02-01

The Rényi index is used here to describe topological structures of minimum spanning trees (MSTs) of financial markets. We categorize the topological structures of MSTs as dragon, star and super-star types. The MST based on Geometric Brownian motion is of dragon type, the MST constructed by One-Factor Model is super-star type, and most MSTs based on real market data belong to the star type. The Rényi index of the MST corresponding to S&P500 is evaluated, and the result shows that the Rényi index varies significantly in different time periods. In particular, it rose during crises and dropped when the S&P500 index rose significantly. A comparison study between the CSI300 index of the Chinese market and the S&P500 index shows that the MST structure of the CSI300 index varies more dramatically than the MST structure of the S&P500.

A tool for filtering information in complex systems

NASA Astrophysics Data System (ADS)

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-07-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. This paper was submitted directly (Track II) to the PNAS office.Abbreviations: MST, minimum spanning tree; PMFG, Planar Maximally Filtered Graph; r-clique, clique of r elements.

Pruning a minimum spanning tree

NASA Astrophysics Data System (ADS)

Sandoval, Leonidas

2012-04-01

This work employs various techniques in order to filter random noise from the information provided by minimum spanning trees obtained from the correlation matrices of international stock market indices prior to and during times of crisis. The first technique establishes a threshold above which connections are considered affected by noise, based on the study of random networks with the same probability density distribution of the original data. The second technique is to judge the strength of a connection by its survival rate, which is the amount of time a connection between two stock market indices endures. The idea is that true connections will survive for longer periods of time, and that random connections will not. That information is then combined with the information obtained from the first technique in order to create a smaller network, in which most of the connections are either strong or enduring in time.

Convergence of Mayer and Virial expansions and the Penrose tree-graph identity

NASA Astrophysics Data System (ADS)

Procacci, Aldo; Yuhjtman, Sergio A.

2017-01-01

We establish new lower bounds for the convergence radius of the Mayer series and the Virial series of a continuous particle system interacting via a stable and tempered pair potential. Our bounds considerably improve those given by Penrose (J Math Phys 4:1312, 1963) and Ruelle (Ann Phys 5:109-120, 1963) for the Mayer series and by Lebowitz and Penrose (J Math Phys 7:841-847, 1964) for the Virial series. To get our results, we exploit the tree-graph identity given by Penrose (Statistical mechanics: foundations and applications. Benjamin, New York, 1967) using a new partition scheme based on minimum spanning trees.

Interpreting the universal phylogenetic tree

NASA Technical Reports Server (NTRS)

Woese, C. R.

2000-01-01

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

From statistics of regular tree-like graphs to distribution function and gyration radius of branched polymers

NASA Astrophysics Data System (ADS)

Grosberg, Alexander Y.; Nechaev, Sergei K.

2015-08-01

We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius R, at large R, obeys, in the scaling sense, Δ S˜ {R}2/({a}2L), with a bond length (or Kuhn segment) and L defined as an average spanning distance. We show that this estimate is valid up to at most the logarithmic correction for any tree. We do so by explicitly computing the largest eigenvalues of Kramers matrices for both regular and ‘sparse’ three-branched trees, uncovering on the way their peculiar mathematical properties.

Model-based conifer crown surface reconstruction from multi-ocular high-resolution aerial imagery

NASA Astrophysics Data System (ADS)

Sheng, Yongwei

2000-12-01

Tree crown parameters such as width, height, shape and crown closure are desirable in forestry and ecological studies, but they are time-consuming and labor intensive to measure in the field. The stereoscopic capability of high-resolution aerial imagery provides a way to crown surface reconstruction. Existing photogrammetric algorithms designed to map terrain surfaces, however, cannot adequately extract crown surfaces, especially for steep conifer crowns. Considering crown surface reconstruction in a broader context of tree characterization from aerial images, we develop a rigorous perspective tree image formation model to bridge image-based tree extraction and crown surface reconstruction, and an integrated model-based approach to conifer crown surface reconstruction. Based on the fact that most conifer crowns are in a solid geometric form, conifer crowns are modeled as a generalized hemi-ellipsoid. Both the automatic and semi-automatic approaches are investigated to optimal tree model development from multi-ocular images. The semi-automatic 3D tree interpreter developed in this thesis is able to efficiently extract reliable tree parameters and tree models in complicated tree stands. This thesis starts with a sophisticated stereo matching algorithm, and incorporates tree models to guide stereo matching. The following critical problems are addressed in the model-based surface reconstruction process: (1) the problem of surface model composition from tree models, (2) the occlusion problem in disparity prediction from tree models, (3) the problem of integrating the predicted disparities into image matching, (4) the tree model edge effect reduction on the disparity map, (5) the occlusion problem in orthophoto production, and (6) the foreshortening problem in image matching, which is very serious for conifer crown surfaces. Solutions to the above problems are necessary for successful crown surface reconstruction. The model-based approach was applied to recover the canopy surface of a dense redwood stand using tri-ocular high-resolution images scanned from 1:2,400 aerial photographs. The results demonstrate the approach's ability to reconstruct complicated stands. The model-based approach proposed in this thesis is potentially applicable to other surfaces recovering problems with a priori knowledge about objects.

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.

Minimal spanning trees at the percolation threshold: a numerical calculation

NASA Astrophysics Data System (ADS)

Sweeney, Sean; Middleton, A. Alan

2013-03-01

Through computer simulations on a hypercubic lattice, we grow minimal spanning trees (MSTs) in up to five dimensions and examine their fractal dimensions. Understanding MSTs is imporant for studying systems with quenched disorder such as spin glasses. We implement a combination of Prim's and Kruskal's algorithms for finding MSTs in order to reduce memory usage and allow for simulation of larger systems than would otherwise be possible. These fractal objects are analyzed in an attempt to numerically verify predictions of the perturbation expansion developed by T. S. Jackson and N. Read for the pathlength fractal dimension ds of MSTs on percolation clusters at criticality [T. S. Jackson and N. Read, Phys. Rev. E 81, 021131 (2010)]. Examining these trees also sparked the development of an analysis technique for dealing with correlated data that could be easily generalized to other systems and should be a robust method for analyzing a wide array of randomly generated fractal structures. This work was made possible in part by NSF Grant No. DMR-1006731 and by the Syracuse University Gravitation and Relativity computing cluster, which is supported in part by NSF Grant No. PHY-0600953.

Similarity measure and topology evolution of foreign exchange markets using dynamic time warping method: Evidence from minimal spanning tree

NASA Astrophysics Data System (ADS)

Wang, Gang-Jin; Xie, Chi; Han, Feng; Sun, Bo

2012-08-01

In this study, we employ a dynamic time warping method to study the topology of similarity networks among 35 major currencies in international foreign exchange (FX) markets, measured by the minimal spanning tree (MST) approach, which is expected to overcome the synchronous restriction of the Pearson correlation coefficient. In the empirical process, firstly, we subdivide the analysis period from June 2005 to May 2011 into three sub-periods: before, during, and after the US sub-prime crisis. Secondly, we choose NZD (New Zealand dollar) as the numeraire and then, analyze the topology evolution of FX markets in terms of the structure changes of MSTs during the above periods. We also present the hierarchical tree associated with the MST to study the currency clusters in each sub-period. Our results confirm that USD and EUR are the predominant world currencies. But USD gradually loses the most central position while EUR acts as a stable center in the MST passing through the crisis. Furthermore, an interesting finding is that, after the crisis, SGD (Singapore dollar) becomes a new center currency for the network.

Functional traits enhance invasiveness of bamboos over co-occurring tree saplings in the semideciduous Atlantic Forest

NASA Astrophysics Data System (ADS)

Montti, Lía; Villagra, Mariana; Campanello, Paula I.; Gatti, M. Genoveva; Goldstein, Guillermo

2014-01-01

Many woody bamboo species are forest understory plants that become invasive after disturbance. They can grow rapidly forming a dense, nearly monospecific understory that inhibits tree regeneration. The principal aim of this study was to understand what functional traits of bamboos allow them to outcompete tree seedlings and saplings and become successful species in the semideciduous Atlantic Forests of northeastern Argentina. We studied leaf and whole-plant functional traits of two bamboo species of the genus Chusquea and five co-occurring saplings of common tree species growing under similar solar radiation and soil nutrient availabilities. Nutrient addition had no effect on bamboo or tree sapling survival and growth after two years. Tree species with high-light requirements had higher growth rates and developed relatively thin leaves with high photosynthetic capacity per unit leaf area and short leaf life-span when growing in gaps, but had lower survival rates in the understory. The opposite pattern was observed in shade-tolerant species that were able to survive in the understory but had lower photosynthetic capacity and growth than light-requiring species in gaps. Bamboos exhibited a high plasticity in functional traits and leaf characteristics that enabled them to grow rapidly in gaps (e.g., higher photosynthetic capacity per unit dry mass and clonal reproduction in gaps than in the understory) but at the same time to tolerate closed-canopy conditions (they had thinner leaves and a relatively longer leaf life-span in the understory compared to gaps). Photosynthetic capacity per unit dry mass was higher in bamboos than in trees. Bamboo plasticity in key functional traits, such as clonal reproduction at the plant level and leaves with a relatively low C cost and high photosynthesis rates, allows them to colonize disturbed forests with consequences at the community and ecosystem levels. Increasing disturbance in some forests worldwide will likely enhance bamboo invasion resulting in profound negative impacts on forest diversity, structure and function in the long term.

Experimental evaluation of the certification-trail method

NASA Technical Reports Server (NTRS)

Sullivan, Gregory F.; Wilson, Dwight S.; Masson, Gerald M.; Itoh, Mamoru; Smith, Warren W.; Kay, Jonathan S.

1993-01-01

Certification trails are a recently introduced and promising approach to fault-detection and fault-tolerance. A comprehensive attempt to assess experimentally the performance and overall value of the method is reported. The method is applied to algorithms for the following problems: huffman tree, shortest path, minimum spanning tree, sorting, and convex hull. Our results reveal many cases in which an approach using certification-trails allows for significantly faster overall program execution time than a basic time redundancy-approach. Algorithms for the answer-validation problem for abstract data types were also examined. This kind of problem provides a basis for applying the certification-trail method to wide classes of algorithms. Answer-validation solutions for two types of priority queues were implemented and analyzed. In both cases, the algorithm which performs answer-validation is substantially faster than the original algorithm for computing the answer. Next, a probabilistic model and analysis which enables comparison between the certification-trail method and the time-redundancy approach were presented. The analysis reveals some substantial and sometimes surprising advantages for ther certification-trail method. Finally, the work our group performed on the design and implementation of fault injection testbeds for experimental analysis of the certification trail technique is discussed. This work employs two distinct methodologies, software fault injection (modification of instruction, data, and stack segments of programs on a Sun Sparcstation ELC and on an IBM 386 PC) and hardware fault injection (control, address, and data lines of a Motorola MC68000-based target system pulsed at logical zero/one values). Our results indicate the viability of the certification trail technique. It is also believed that the tools developed provide a solid base for additional exploration.

On the Complexity of the Metric TSP under Stability Considerations

NASA Astrophysics Data System (ADS)

Mihalák, Matúš; Schöngens, Marcel; Šrámek, Rastislav; Widmayer, Peter

We consider the metric Traveling Salesman Problem (Δ-TSP for short) and study how stability (as defined by Bilu and Linial [3]) influences the complexity of the problem. On an intuitive level, an instance of Δ-TSP is γ-stable (γ> 1), if there is a unique optimum Hamiltonian tour and any perturbation of arbitrary edge weights by at most γ does not change the edge set of the optimal solution (i.e., there is a significant gap between the optimum tour and all other tours). We show that for γ ≥ 1.8 a simple greedy algorithm (resembling Prim's algorithm for constructing a minimum spanning tree) computes the optimum Hamiltonian tour for every γ-stable instance of the Δ-TSP, whereas a simple local search algorithm can fail to find the optimum even if γ is arbitrary. We further show that there are γ-stable instances of Δ-TSP for every 1 < γ< 2. These results provide a different view on the hardness of the Δ-TSP and give rise to a new class of problem instances which are substantially easier to solve than instances of the general Δ-TSP.

Triplet supertree heuristics for the tree of life

PubMed Central

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver

2009-01-01

Background There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogenetic tree that contains all of the taxa in the input trees. The intrinsically hard triplet supertree problem takes a collection of input species trees and seeks a species tree (supertree) that maximizes the number of triplet subtrees that it shares with the input trees. However, the utility of this supertree problem has been limited by a lack of efficient and effective heuristics. Results We introduce fast hill-climbing heuristics for the triplet supertree problem that perform a step-wise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. To realize time efficient heuristics we designed the first nontrivial algorithms for two standard search problems, which greatly improve on the time complexity to the best known (naïve) solutions by a factor of n and n2 (the number of taxa in the supertree). These algorithms enable large-scale supertree analyses based on the triplet supertree problem that were previously not possible. We implemented hill-climbing heuristics that are based on our new algorithms, and in analyses of two published supertree data sets, we demonstrate that our new heuristics outperform other standard supertree methods in maximizing the number of triplets shared with the input trees. Conclusion With our new heuristics, the triplet supertree problem is now computationally more tractable for large-scale supertree analyses, and it provides a potentially more accurate alternative to existing supertree methods. PMID:19208181

Shape matters: improved flight in tapered auto-rotating wings

NASA Astrophysics Data System (ADS)

Liu, Yucen; Vincent, Lionel; Kanso, Eva

2017-11-01

Many plants use gravity and wind to disperse their seeds. The shape of seed pods influence their aerodynamics. For example, Liana seeds form aerodynamic gliders and Sycamore trees release airborne ``helicopters.'' Here, we use carefully-controlled experiments and high-speed photography to examine dispersion by tumbling (auto-rotation) and we focus on the effect of geometry on flight characteristics. We consider four families of shapes: rectangular, elliptic, tapered, and sharp-tip wings, and we vary the span-to-chord ratio. We find that tapered wings exhibit extended flight time and range, that is, better performance. A quasi-steady two-dimensional model is used to highlight the mechanisms by which shape affects flight performance. These findings could have significant implications on linking seedpod designs to seed dispersion patterns as well as on optimizing wing design in active flight problems.

Principles of Dataset Versioning: Exploring the Recreation/Storage Tradeoff

PubMed Central

Bhattacherjee, Souvik; Chavan, Amit; Huang, Silu; Deshpande, Amol; Parameswaran, Aditya

2015-01-01

The relative ease of collaborative data science and analysis has led to a proliferation of many thousands or millions of versions of the same datasets in many scientific and commercial domains, acquired or constructed at various stages of data analysis across many users, and often over long periods of time. Managing, storing, and recreating these dataset versions is a non-trivial task. The fundamental challenge here is the storage-recreation trade-off: the more storage we use, the faster it is to recreate or retrieve versions, while the less storage we use, the slower it is to recreate or retrieve versions. Despite the fundamental nature of this problem, there has been a surprisingly little amount of work on it. In this paper, we study this trade-off in a principled manner: we formulate six problems under various settings, trading off these quantities in various ways, demonstrate that most of the problems are intractable, and propose a suite of inexpensive heuristics drawing from techniques in delay-constrained scheduling, and spanning tree literature, to solve these problems. We have built a prototype version management system, that aims to serve as a foundation to our DataHub system for facilitating collaborative data science. We demonstrate, via extensive experiments, that our proposed heuristics provide efficient solutions in practical dataset versioning scenarios. PMID:28752014

First report of Armillaria sinapina, a cause of armillaria root disease, associated with a variety of forest tree hosts on sites with diverse climates in Alaska

Treesearch

N. B. Klopfenstein; J. E. Lundquist; J. W. Hanna; M.-S. Kim; G. I. McDonald

2009-01-01

In August of 2007, a preliminary survey was conducted in Alaska to evaluate potential impacts of climate change on forest trees. Armillaria sinapina, a root-disease pathogen, was isolated from conifer and hardwood hosts on climatically diverse sites spanning 675 km from the Kenai Peninsula to the Arctic Circle. Seven isolates (NKAK1, NKAK2, NKAK5, NKAK6, NKAK9F, NKAK13...

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

PubMed

Kordi, Misagh; Bansal, Mukul S

2017-01-01

Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.

Diameter-Constrained Steiner Tree

NASA Astrophysics Data System (ADS)

Ding, Wei; Lin, Guohui; Xue, Guoliang

Given an edge-weighted undirected graph G = (V,E,c,w), where each edge e ∈ E has a cost c(e) and a weight w(e), a set S ⊆ V of terminals and a positive constant D 0, we seek a minimum cost Steiner tree where all terminals appear as leaves and its diameter is bounded by D 0. Note that the diameter of a tree represents the maximum weight of path connecting two different leaves in the tree. Such problem is called the minimum cost diameter-constrained Steiner tree problem. This problem is NP-hard even when the topology of Steiner tree is fixed. In present paper we focus on this restricted version and present a fully polynomial time approximation scheme (FPTAS) for computing a minimum cost diameter-constrained Steiner tree under a fixed topology.

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

Using traveling salesman problem algorithms for evolutionary tree construction.

PubMed

Korostensky, C; Gonnet, G H

2000-07-01

The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity. We present a new tree construction method that constructs a tree with minimum score for a given set of sequences, where the score is the amount of evolution measured in PAM distances. To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). The input for the TSP algorithm are the pairwise distances of the sequences and the output is a circular tour through the optimal, unknown tree plus the minimum score of the tree. The circular order and the score can be used to construct the topology of the optimal tree. Our method can be used for any scoring function that correlates to the amount of changes along the branches of an evolutionary tree, for instance it could also be used for parsimony scores, but it cannot be used for least squares fit of distances. A TSP solution reduces the space of all possible trees to 2n. Using this order, we can guarantee that we reconstruct a correct evolutionary tree if the absolute value of the error for each distance measurement is smaller than f2.gif" BORDER="0">, where f3.gif" BORDER="0">is the length of the shortest edge in the tree. For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. Finally simulations and experiments with real data are shown.

Variation in crown light utilization characteristics among tropical canopy trees.

PubMed

Kitajima, Kaoru; Mulkey, Stephen S; Wright, S Joseph

2005-02-01

Light extinction through crowns of canopy trees determines light availability at lower levels within forests. The goal of this paper is the exploration of foliage distribution and light extinction in crowns of five canopy tree species in relation to their shoot architecture, leaf traits (mean leaf angle, life span, photosynthetic characteristics) and successional status (from pioneers to persistent). Light extinction was examined at three hierarchical levels of foliage organization, the whole crown, the outermost canopy and the individual shoots, in a tropical moist forest with direct canopy access with a tower crane. Photon flux density and cumulative leaf area index (LAI) were measured at intervals of 0.25-1 m along multiple vertical transects through three to five mature tree crowns of each species to estimate light extinction coefficients (K). Cecropia longipes, a pioneer species with the shortest leaf life span, had crown LAI <0.5. Among the remaining four species, crown LAI ranged from 2 to 8, and species with orthotropic terminal shoots exhibited lower light extinction coefficients (0.35) than those with plagiotropic shoots (0.53-0.80). Within each type, later successional species exhibited greater maximum LAI and total light extinction. A dense layer of leaves at the outermost crown of a late successional species resulted in an average light extinction of 61% within 0.5 m from the surface. In late successional species, leaf position within individual shoots does not predict the light availability at the individual leaf surface, which may explain their slow decline of photosynthetic capacity with leaf age and weak differentiation of sun and shade leaves. Later-successional tree crowns, especially those with orthotropic branches, exhibit lower light extinction coefficients, but greater total LAI and total light extinction, which contribute to their efficient use of light and competitive dominance.

Consensus seeking in a network of discrete-time linear agents with communication noises

NASA Astrophysics Data System (ADS)

Wang, Yunpeng; Cheng, Long; Hou, Zeng-Guang; Tan, Min; Zhou, Chao; Wang, Ming

2015-07-01

This paper studies the mean square consensus of discrete-time linear time-invariant multi-agent systems with communication noises. A distributed consensus protocol, which is composed of the agent's own state feedback and the relative states between the agent and its neighbours, is proposed. A time-varying consensus gain a[k] is applied to attenuate the effect of noises which inherits in the inaccurate measurement of relative states with neighbours. A polynomial, namely 'parameter polynomial', is constructed. And its coefficients are the parameters in the feedback gain vector of the proposed protocol. It turns out that the parameter polynomial plays an important role in guaranteeing the consensus of linear multi-agent systems. By the proposed protocol, necessary and sufficient conditions for mean square consensus are presented under different topology conditions: (1) if the communication topology graph has a spanning tree and every node in the graph has at least one parent node, then the mean square consensus can be achieved if and only if ∑∞k = 0a[k] = ∞, ∑∞k = 0a2[k] < ∞ and all roots of the parameter polynomial are in the unit circle; (2) if the communication topology graph has a spanning tree and there exits one node without any parent node (the leader-follower case), then the mean square consensus can be achieved if and only if ∑∞k = 0a[k] = ∞, limk → ∞a[k] = 0 and all roots of the parameter polynomial are in the unit circle; (3) if the communication topology graph does not have a spanning tree, then the mean square consensus can never be achieved. Finally, one simulation example on the multiple aircrafts system is provided to validate the theoretical analysis.

A 650-year record of past summer temperatures from Pirin, Bulgaria tree-ring density

NASA Astrophysics Data System (ADS)

Meko, M. D.; Trouet, V.; Panayotov, M.; Frank, D. C.

2017-12-01

New proxy records of past climate provide valuable data essential to enhance spatial and temporal coverage of the global paleoclimate record - the context against which ongoing climate change and climate-model forcing is examined and evaluated. We present a new 650-year record of past summer temperatures in southeastern (SE) Europe derived from tree-ring maximum-latewood-density (MXD) data measured from Bosnian pine (Pinus heldreichii) growing at high elevations in the Pirin Mountains, Bulgaria (PRN). The PRN collection is well-replicated, with 64 trees contributing MXD series ranging in length from 113 to 865 years (median series length = 480 years) spanning the years 1143-2009. The PRN chronology shows a significant (p < 0.05) relationship with summer (JAS) temperatures across a broad geographical area of SE Europe, including the entire Balkan peninsula, southern Italy, and southwestern Anatolia. Our temperature reconstruction, produced by multiple regression utilizing lagged predictors and calibrated against Sofia, Bulgaria meteorological observations, explains nearly 60% of target variance and reveals variability across decadal, centennial, and longer timescales over the 1350-2009 reconstruction interval. Relative to the instrumental 1900-1980 mean, our record shows multidecadal cool anomalies spanning the first half of the 19th century and the late 17th century, and warm periods spanning the 18th century, 16th and early-to-mid 17th centuries, and late 14th to early 15th century. A comparison of the PRN reconstruction with existing reconstructions of Northern Hemisphere temperatures reveal intervals of asynchrony between local and hemisphere-scale decadal temperature variability, with marked asynchrony in the late 16th-early 17th centuries, and unprecedented asynchrony in the late 20th-to early 21st century.

Dynamics of market correlations: taxonomy and portfolio analysis.

PubMed

Onnela, J-P; Chakraborti, A; Kaski, K; Kertész, J; Kanto, A

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the "asset tree" has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for "business as usual" and "crash" periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Manduca rustica (Lepidoptera: Sphingidae) damage on olive (Olea europaea;Lamiales:Oleaceae)trees in Florida

USDA-ARS?s Scientific Manuscript database

The rustic sphinx, Manduca rustica has been identified as an occasional pest for olive, Olea europaea, in Florida. This pest’s distribution spans Florida’s olive growing region from the northern panhandle as far south as Polk County....

Multiple site receptor modeling with a minimal spanning tree combined with a Kohonen neural network

NASA Astrophysics Data System (ADS)

Hopke, Philip K.

1999-12-01

A combination of two pattern recognition methods has been developed that allows the generation of geographical emission maps form multivariate environmental data. In such a projection into a visually interpretable subspace by a Kohonen Self-Organizing Feature Map, the topology of the higher dimensional variables space can be preserved, but parts of the information about the correct neighborhood among the sample vectors will be lost. This can partly be compensated for by an additional projection of Prim's Minimal Spanning Tree into the trained neural network. This new environmental receptor modeling technique has been adapted for multiple sampling sites. The behavior of the method has been studied using simulated data. Subsequently, the method has been applied to mapping data sets from the Southern California Air Quality Study. The projection of a 17 chemical variables measured at up to 8 sampling sites provided a 2D, visually interpretable, geometrically reasonable arrangement of air pollution source sin the South Coast Air Basin.

Stem hydraulic traits and leaf water-stress tolerance are co-ordinated with the leaf phenology of angiosperm trees in an Asian tropical dry karst forest

PubMed Central

Fu, Pei-Li; Jiang, Yan-Juan; Wang, Ai-Ying; Brodribb, Tim J.; Zhang, Jiao-Lin; Zhu, Shi-Dan; Cao, Kun-Fang

2012-01-01

Background and Aims The co-occurring of evergreen and deciduous angiosperm trees in Asian tropical dry forests on karst substrates suggests the existence of different water-use strategies among species. In this study it is hypothesized that the co-occurring evergreen and deciduous trees differ in stem hydraulic traits and leaf water relationships, and there will be correlated evolution in drought tolerance between leaves and stems. Methods A comparison was made of stem hydraulic conductivity, vulnerability curves, wood anatomy, leaf life span, leaf pressure–volume characteristics and photosynthetic capacity of six evergreen and six deciduous tree species co-occurring in a tropical dry karst forest in south-west China. The correlated evolution of leaf and stem traits was examined using both traditional and phylogenetic independent contrasts correlations. Key Results It was found that the deciduous trees had higher stem hydraulic efficiency, greater hydraulically weighted vessel diameter (Dh) and higher mass-based photosynthetic rate (Am); while the evergreen species had greater xylem-cavitation resistance, lower leaf turgor-loss point water potential (π0) and higher bulk modulus of elasticity. There were evolutionary correlations between leaf life span and stem hydraulic efficiency, Am, and dry season π0. Xylem-cavitation resistance was evolutionarily correlated with stem hydraulic efficiency, Dh, as well as dry season π0. Both wood density and leaf density were closely correlated with leaf water-stress tolerance and Am. Conclusions The results reveal the clear distinctions in stem hydraulic traits and leaf water-stress tolerance between the co-occurring evergreen and deciduous angiosperm trees in an Asian dry karst forest. A novel pattern was demonstrated linking leaf longevity with stem hydraulic efficiency and leaf water-stress tolerance. The results show the correlated evolution in drought tolerance between stems and leaves. PMID:22585930

Structural changes of homodimers in the PDB.

PubMed

Koike, Ryotaro; Amemiya, Takayuki; Horii, Tatsuya; Ota, Motonori

2018-04-01

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

3D Visualization of Machine Learning Algorithms with Astronomical Data

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2016-01-01

We present innovative machine learning (ML) methods using unsupervised clustering with minimum spanning trees (MSTs) to study 3D astronomical catalogs. Utilizing Python code to build trees based on galaxy catalogs, we can render the results with the visualization suite Blender to produce interactive 360 degree panoramic videos. The catalogs and their ML results can be explored in a 3D space using mobile devices, tablets or desktop browsers. We compare the statistics of the MST results to a number of machine learning methods relating to optimization and efficiency.

A novel underwater dam crack detection and classification approach based on sonar images

PubMed Central

Shi, Pengfei; Fan, Xinnan; Ni, Jianjun; Khan, Zubair; Li, Min

2017-01-01

Underwater dam crack detection and classification based on sonar images is a challenging task because underwater environments are complex and because cracks are quite random and diverse in nature. Furthermore, obtainable sonar images are of low resolution. To address these problems, a novel underwater dam crack detection and classification approach based on sonar imagery is proposed. First, the sonar images are divided into image blocks. Second, a clustering analysis of a 3-D feature space is used to obtain the crack fragments. Third, the crack fragments are connected using an improved tensor voting method. Fourth, a minimum spanning tree is used to obtain the crack curve. Finally, an improved evidence theory combined with fuzzy rule reasoning is proposed to classify the cracks. Experimental results show that the proposed approach is able to detect underwater dam cracks and classify them accurately and effectively under complex underwater environments. PMID:28640925

A novel underwater dam crack detection and classification approach based on sonar images.

PubMed

Shi, Pengfei; Fan, Xinnan; Ni, Jianjun; Khan, Zubair; Li, Min

2017-01-01

Underwater dam crack detection and classification based on sonar images is a challenging task because underwater environments are complex and because cracks are quite random and diverse in nature. Furthermore, obtainable sonar images are of low resolution. To address these problems, a novel underwater dam crack detection and classification approach based on sonar imagery is proposed. First, the sonar images are divided into image blocks. Second, a clustering analysis of a 3-D feature space is used to obtain the crack fragments. Third, the crack fragments are connected using an improved tensor voting method. Fourth, a minimum spanning tree is used to obtain the crack curve. Finally, an improved evidence theory combined with fuzzy rule reasoning is proposed to classify the cracks. Experimental results show that the proposed approach is able to detect underwater dam cracks and classify them accurately and effectively under complex underwater environments.

Outdoor Illegal Construction Identification Algorithm Based on 3D Point Cloud Segmentation

NASA Astrophysics Data System (ADS)

An, Lu; Guo, Baolong

2018-03-01

Recently, various illegal constructions occur significantly in our surroundings, which seriously restrict the orderly development of urban modernization. The 3D point cloud data technology is used to identify the illegal buildings, which could address the problem above effectively. This paper proposes an outdoor illegal construction identification algorithm based on 3D point cloud segmentation. Initially, in order to save memory space and reduce processing time, a lossless point cloud compression method based on minimum spanning tree is proposed. Then, a ground point removing method based on the multi-scale filtering is introduced to increase accuracy. Finally, building clusters on the ground can be obtained using a region growing method, as a result, the illegal construction can be marked. The effectiveness of the proposed algorithm is verified using a publicly data set collected from the International Society for Photogrammetry and Remote Sensing (ISPRS).

Consensus properties and their large-scale applications for the gene duplication problem.

PubMed

Moon, Jucheol; Lin, Harris T; Eulenstein, Oliver

2016-06-01

Solving the gene duplication problem is a classical approach for species tree inference from gene trees that are confounded by gene duplications. This problem takes a collection of gene trees and seeks a species tree that implies the minimum number of gene duplications. Wilkinson et al. posed the conjecture that the gene duplication problem satisfies the desirable Pareto property for clusters. That is, for every instance of the problem, all clusters that are commonly present in the input gene trees of this instance, called strict consensus, will also be found in every solution to this instance. We prove that this conjecture does not generally hold. Despite this negative result we show that the gene duplication problem satisfies a weaker version of the Pareto property where the strict consensus is found in at least one solution (rather than all solutions). This weaker property contributes to our design of an efficient scalable algorithm for the gene duplication problem. We demonstrate the performance of our algorithm in analyzing large-scale empirical datasets. Finally, we utilize the algorithm to evaluate the accuracy of standard heuristics for the gene duplication problem using simulated datasets.

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.

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.

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

Rivasseau, Vincent, E-mail: vincent.rivasseau@th.u-psud.fr, E-mail: adrian.tanasa@ens-lyon.org; Tanasa, Adrian, E-mail: vincent.rivasseau@th.u-psud.fr, E-mail: adrian.tanasa@ens-lyon.org

The Loop Vertex Expansion (LVE) is a quantum field theory (QFT) method which explicitly computes the Borel sum of Feynman perturbation series. This LVE relies in a crucial way on symmetric tree weights which define a measure on the set of spanning trees of any connected graph. In this paper we generalize this method by defining new tree weights. They depend on the choice of a partition of a set of vertices of the graph, and when the partition is non-trivial, they are no longer symmetric under permutation of vertices. Nevertheless we prove they have the required positivity property tomore » lead to a convergent LVE; in fact we formulate this positivity property precisely for the first time. Our generalized tree weights are inspired by the Brydges-Battle-Federbush work on cluster expansions and could be particularly suited to the computation of connected functions in QFT. Several concrete examples are explicitly given.« less

Imprint of the Atlantic Multidecadal Oscillation on Tree-Ring Widths in Northeastern Asia since 1568

PubMed Central

Wang, Xiaochun; Brown, Peter M.; Zhang, Yanni; Song, Laiping

2011-01-01

We present a new tree-ring reconstruction of the Atlantic Multidecadal Oscillation (AMO) spanning 1568–2007 CE from northeast Asia. Comparison of the instrumental AMO index, an existing tree-ring based AMO reconstruction, and this new record show strongly similar annual to multidecadal patterns of variation over the last 440 years. Warm phases of the AMO are related to increases in growth of Scots pine trees and moisture availability in northeast China and central eastern Siberia. Multi-tape method (MTM) and cross-wavelet analyses indicate that robust multidecadal (∼64–128 years) variability is present throughout the new proxy record. Our results have important implications concerning the influence of North Atlantic sea surface temperatures on East Asian climate, and provide support for the possibility of an AMO signature on global multidecadal climate variability. PMID:21818380

Arctic tree-line reproduction in Canada and Siberia: Possible greenhouse effect?

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

Nichols, H.

1997-12-31

The arctic tree-line is sensitive to climatic changes as indicated by paleo-ecological studies, and it is predicted to respond strongly to global warming. Northern Canadian studies of tree-line reproduction spanning two decades demonstrate a widespread switch from infertility due to cold summers (early 1970`s) to pollen and cone production (1990s), in line with greenhouse warming predictions. Ecotonal cone formation is usually sporadic and localized, but this largescale reproductive shift, along a 1500 km transect, suggests widespread climatic warming since the 1970s. These Siberian studies (at 27 sites) represented only a modest fraction of the Eurasian tree-line, but the widespread fertilitymore » at so many locations, plus the extensive Canadian evidence, suggests that the predicted polar warming may be responsible. Whether this is due to natural or anthropogenic climatic change, and whether it will be short or long-term, is unclear, and merits further study.« less

Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.

PubMed

Korall, Petra; Pryer, Kathleen M; Metzgar, Jordan S; Schneider, Harald; Conant, David S

2006-06-01

Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.

Dynamics of market correlations: Taxonomy and portfolio analysis

NASA Astrophysics Data System (ADS)

Onnela, J.-P.; Chakraborti, A.; Kaski, K.; Kertész, J.; Kanto, A.

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the “asset tree” has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for “business as usual” and “crash” periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

7 CFR 1410.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... State, or (3) Alfalfa and other multi-year grasses and legumes grown in a rotation practice as approved... Deputy Administrator: for alfalfa and other multi-year grasses and legumes planted during 2002 through... approved combinations of certain grasses, legumes, forbs, shrubs and trees with a life span of 10 or more...

Water limitations on forest carbon cycling and conifer traits along a steep climatic gradient in the Cascade Mountains, Oregon

NASA Astrophysics Data System (ADS)

Berner, L. T.; Law, B. E.

2015-11-01

Severe droughts occurred in the western United States during recent decades, and continued human greenhouse gas emissions are expected to exacerbate warming and drying in this region. We investigated the role of water availability in shaping forest carbon cycling and morphological traits in the eastern Cascade Mountains, Oregon, focusing on the transition from low-elevation, dry western juniper (Juniperus occidentalis) woodlands to higher-elevation, wetter ponderosa pine (Pinus ponderosa) and grand fir (Abies grandis) forests. We examined 12 sites in mature forests that spanned a 1300 mm yr-1 gradient in mean growing-year climate moisture index (CMIgy ), computed annually (1964 to 2013) as monthly precipitation minus reference evapotranspiration and summed October to September. Maximum leaf area, annual aboveground productivity, and aboveground live tree biomass increased with CMIgy (r2 = 0.67-0.88, P < 0.05), approximately 50-, 30-, and 10-fold along this drier to wetter gradient. Interannual fluctuations in CMI affected the annual radial growth of 91 % of juniper, 51 % of pine, and 12 % of fir individuals from 1964 to 2013. The magnitude of the site-average growth-CMI correlations decreased with increased CMIgy (r2 = 0.53, P < 0.05). All three species, particularly fir, experienced pronounced declines in radial growth from c. 1985 to 1994, coinciding with a period of sustained below-average CMIgy and extensive insect outbreak. Traits of stress-tolerant juniper included short stature, high wood density for cavitation resistance, and high investment in water transport relative to leaf area. Species occupying wetter areas invested more resources in height growth in response to competition for light relative to investment in hydraulic architecture. Consequently, maximum tree height, leaf area : sapwood area ratio, and stem wood density were all correlated with CMIgy . The tight coupling of forest carbon cycling and species traits with water availability suggests that warmer and drier conditions projected for the 21st century could have significant biogeochemical, ecological, and social consequences in the Pacific Northwest.

Water limitations on forest carbon cycling and conifer traits along a steep climatic gradient in the Cascade Mountains, Oregon

NASA Astrophysics Data System (ADS)

Berner, L. T.; Law, B. E.

2015-09-01

Severe droughts occurred in the western United States during recent decades and continued human greenhouse gas emissions are expected to exacerbate warming and drying in this region. We investigated the role of water availability in shaping forest carbon cycling and morphological traits in the eastern Cascade Mountains, Oregon, focusing on the transition from low-elevation, dry western juniper (Juniperus occidentalis) woodlands to higher-elevation, wetter ponderosa pine (Pinus ponderosa) and grand fir (Abies grandis) forests. We examined 12 sites in mature forests that spanned a 1300 mm yr-1 gradient in mean growing-year climate moisture index (CMIgy ), computed annually (1964 to 2013) as monthly precipitation minus reference evapotranspiration and summed October to September. Maximum leaf area, annual aboveground productivity, and aboveground live tree biomass increased with CMIgy (r2 = 0.58-0.85, P < 0.05), approximately 50-, 30-, and 10-fold along this drier to wetter gradient. Interannual fluctuations in CMI affected the annual radial growth of 91 % of juniper, 51 % of pine, and 12 % of fir from 1964 to 2013. The magnitude of the site-average growth-CMI correlations decreased with increased CMIgy (r2 = 0.65, P < 0.05). All three species, particularly fir, experienced pronounced declines in radial growth from ca. 1985 to 1994, coinciding with a period of sustained below-average CMIgy and extensive insect outbreak. Traits of stress-tolerant juniper included short stature, high wood density for cavitation resistance, and high investment in water transport relative to leaf area. Species occupying wetter areas invested more resources in height growth in response to competition for light relative to investment in hydraulic architecture. Correspondingly, maximum tree height, leaf area:sapwood area ratio, and stem wood density were all correlated with CMIgy . The tight coupling of forest carbon cycling and species traits with water availability suggests that warmer and drier conditions projected for the 21st century could have significant biogeochemical, ecological, and social consequences in the Pacific Northwest.

Study on Multi-stage Logistics System Design Problem with Inventory Considering Demand Change by Hybrid Genetic Algorithm

NASA Astrophysics Data System (ADS)

Inoue, Hisaki; Gen, Mitsuo

The logistics model used in this study is 3-stage model employed by an automobile company, which aims to solve traffic problems at a total minimum cost. Recently, research on the metaheuristics method has advanced as an approximate means for solving optimization problems like this model. These problems can be solved using various methods such as the genetic algorithm (GA), simulated annealing, and tabu search. GA is superior in robustness and adjustability toward a change in the structure of these problems. However, GA has a disadvantage in that it has a slightly inefficient search performance because it carries out a multi-point search. A hybrid GA that combines another method is attracting considerable attention since it can compensate for a fault to a partial solution that early convergence gives a bad influence on a result. In this study, we propose a novel hybrid random key-based GA(h-rkGA) that combines local search and parameter tuning of crossover rate and mutation rate; h-rkGA is an improved version of the random key-based GA (rk-GA). We attempted comparative experiments with spanning tree-based GA, priority based GA and random key-based GA. Further, we attempted comparative experiments with “h-GA by only local search” and “h-GA by only parameter tuning”. We reported the effectiveness of the proposed method on the basis of the results of these experiments.

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

PubMed

Mai, Uyen; Mirarab, Siavash

2018-05-08

Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny. We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled. TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

Combining qualitative and quantitative operational research methods to inform quality improvement in pathways that span multiple settings

PubMed Central

Crowe, Sonya; Brown, Katherine; Tregay, Jenifer; Wray, Jo; Knowles, Rachel; Ridout, Deborah A; Bull, Catherine; Utley, Martin

2017-01-01

Background Improving integration and continuity of care across sectors within resource constraints is a priority in many health systems. Qualitative operational research methods of problem structuring have been used to address quality improvement in services involving multiple sectors but not in combination with quantitative operational research methods that enable targeting of interventions according to patient risk. We aimed to combine these methods to augment and inform an improvement initiative concerning infants with congenital heart disease (CHD) whose complex care pathway spans multiple sectors. Methods Soft systems methodology was used to consider systematically changes to services from the perspectives of community, primary, secondary and tertiary care professionals and a patient group, incorporating relevant evidence. Classification and regression tree (CART) analysis of national audit datasets was conducted along with data visualisation designed to inform service improvement within the context of limited resources. Results A ‘Rich Picture’ was developed capturing the main features of services for infants with CHD pertinent to service improvement. This was used, along with a graphical summary of the CART analysis, to guide discussions about targeting interventions at specific patient risk groups. Agreement was reached across representatives of relevant health professions and patients on a coherent set of targeted recommendations for quality improvement. These fed into national decisions about service provision and commissioning. Conclusions When tackling complex problems in service provision across multiple settings, it is important to acknowledge and work with multiple perspectives systematically and to consider targeting service improvements in response to confined resources. Our research demonstrates that applying a combination of qualitative and quantitative operational research methods is one approach to doing so that warrants further consideration. PMID:28062603

Working memory deficits in children with reading difficulties: memory span and dual task coordination.

PubMed

Wang, Shinmin; Gathercole, Susan E

2013-05-01

The current study investigated the cause of the reported problems in working memory in children with reading difficulties. Verbal and visuospatial simple and complex span tasks, and digit span and reaction times tasks performed singly and in combination, were administered to 46 children with single word reading difficulties and 45 typically developing children matched for age and nonverbal ability. Children with reading difficulties had pervasive deficits in the simple and complex span tasks and had poorer abilities to coordinate two cognitive demanding tasks. These findings indicate that working memory problems in children with reading difficulties may reflect a core deficit in the central executive. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

PubMed Central

Linderman, Michael D.; Simonds, Erin F.; Qiu, Peng; Bruggner, Robert V.; Sheode, Ketaki; Meng, Teresa H.; Plevritis, Sylvia K.; Nolan, Garry P.

2012-01-01

Motivation: Recent advances in flow cytometry enable simultaneous single-cell measurement of 30+ surface and intracellular proteins. CytoSPADE is a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events algorithm for tree-based analysis and visualization of this high-dimensional cytometry data. Availability: Source code and binaries are freely available at http://cytospade.org and via Bioconductor version 2.10 onwards for Linux, OSX and Windows. CytoSPADE is implemented in R, C++ and Java. Contact: michael.linderman@mssm.edu Supplementary Information: Additional documentation available at http://cytospade.org. PMID:22782546

Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees.

PubMed

Hollender, Courtney A; Pascal, Thierry; Tabb, Amy; Hadiarto, Toto; Srinivasan, Chinnathambi; Wang, Wanpeng; Liu, Zhongchi; Scorza, Ralph; Dardick, Chris

2018-05-15

Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325 , having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP , was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications. Copyright © 2018 the Author(s). Published by PNAS.

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

Comparison of Naive Bayes and Decision Tree on Feature Selection Using Genetic Algorithm for Classification Problem

NASA Astrophysics Data System (ADS)

Rahmadani, S.; Dongoran, A.; Zarlis, M.; Zakarias

2018-03-01

This paper discusses the problem of feature selection using genetic algorithms on a dataset for classification problems. The classification model used is the decicion tree (DT), and Naive Bayes. In this paper we will discuss how the Naive Bayes and Decision Tree models to overcome the classification problem in the dataset, where the dataset feature is selectively selected using GA. Then both models compared their performance, whether there is an increase in accuracy or not. From the results obtained shows an increase in accuracy if the feature selection using GA. The proposed model is referred to as GADT (GA-Decision Tree) and GANB (GA-Naive Bayes). The data sets tested in this paper are taken from the UCI Machine Learning repository.

Divergence of species responses to climate change

Treesearch

Songlin Fei; Johanna M. Desprez; Kevin M. Potter; Insu Jo; Jonathan A. Knott; Christopher M. Oswalt

2017-01-01

Climate change can have profound impacts on biodiversity and the sustainability of many ecosystems. Various studies have investigated the impacts of climate change, but large-scale, trait-specific impactsare less understood.Weanalyze abundance data over time for 86 tree species/groups across the eastern United States spanning the last three decades. We show that more...

Cultural Codes as Catalysts for Collective Conscientisation in Environmental Adult Education: Mr. Floatie, Tree Squatting and Save-Our-Surfers

ERIC Educational Resources Information Center

Walter, Pierre

2012-01-01

This study examines how cultural codes in environmental adult education can be used to "frame" collective identity, develop counterhegemonic ideologies, and catalyse "educative-activism" within social movements. Three diverse examples are discussed, spanning environmental movements in urban Victoria, British Columbia, Canada,…

Minimum Covers of Fixed Cardinality in Weighted Graphs.

ERIC Educational Resources Information Center

White, Lee J.

Reported is the result of research on combinatorial and algorithmic techniques for information processing. A method is discussed for obtaining minimum covers of specified cardinality from a given weighted graph. By the indicated method, it is shown that the family of minimum covers of varying cardinality is related to the minimum spanning tree of…

Elevated CO2 or O3 effects on fine-root survivorship in ponderosa pine

EPA Science Inventory

Atmospheric carbon dioxide (CO2) and ozone (O3) concentrations are rising, which may have opposing effects on tree C balance and allocation to fine roots. More information is needed on interactive CO2 and O3 effects on roots, particularly fine-root life span, a critical demograp...

ELEVATED CO2 AND O3 EFFECTS ON FINE-ROOT SURVIVORSHIP IN PONDEROSA PINE MESOCOSMS

EPA Science Inventory

Atmospheric carbon dioxide (CO2) and ozone (O3) concentrations are rising, which may have opposing effects on tree C balance and allocation to fine roots. More information is needed on interactive CO2 and O3 effects on roots, particularly fine-root life span, a critical demograph...

Will the US economy recover in 2010? A minimal spanning tree study

NASA Astrophysics Data System (ADS)

Zhang, Yiting; Lee, Gladys Hui Ting; Wong, Jian Cheng; Kok, Jun Liang; Prusty, Manamohan; Cheong, Siew Ann

2011-06-01

We calculated the cross correlations between the half-hourly times series of the ten Dow Jones US economic sectors over the period February 2000 to August 2008, the two-year intervals 2002-2003, 2004-2005, 2008-2009, and also over 11 segments within the present financial crisis, to construct minimal spanning trees (MSTs) of the US economy at the sector level. In all MSTs, a core-fringe structure is found, with consumer goods, consumer services, and the industrials consistently making up the core, and basic materials, oil & gas, healthcare, telecommunications, and utilities residing predominantly on the fringe. More importantly, we find that the MSTs can be classified into two distinct, statistically robust, topologies: (i) star-like, with the industrials at the center, associated with low-volatility economic growth; and (ii) chain-like, associated with high-volatility economic crisis. Finally, we present statistical evidence, based on the emergence of a star-like MST in Sep 2009, and the MST staying robustly star-like throughout the Greek Debt Crisis, that the US economy is on track to a recovery.

Finding the Optimal Nets for Self-Folding Kirigami

NASA Astrophysics Data System (ADS)

Araújo, N. A. M.; da Costa, R. A.; Dorogovtsev, S. N.; Mendes, J. F. F.

2018-05-01

Three-dimensional shells can be synthesized from the spontaneous self-folding of two-dimensional templates of interconnected panels, called nets. However, some nets are more likely to self-fold into the desired shell under random movements. The optimal nets are the ones that maximize the number of vertex connections, i.e., vertices that have only two of its faces cut away from each other in the net. Previous methods for finding such nets are based on random search, and thus, they do not guarantee the optimal solution. Here, we propose a deterministic procedure. We map the connectivity of the shell into a shell graph, where the nodes and links of the graph represent the vertices and edges of the shell, respectively. Identifying the nets that maximize the number of vertex connections corresponds to finding the set of maximum leaf spanning trees of the shell graph. This method allows us not only to design the self-assembly of much larger shell structures but also to apply additional design criteria, as a complete catalog of the maximum leaf spanning trees is obtained.

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

NASA Astrophysics Data System (ADS)

Hamprecht, Fred A.; Peter, Christine; Daura, Xavier; Thiel, Walter; van Gunsteren, Wilfred F.

2001-02-01

We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms.

Structural changes in the minimal spanning tree and the hierarchical network in the Korean stock market around the global financial crisis

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Maeng, Seong Eun; Ha, Gyeong Gyun; Lee, Jae Woo

2015-04-01

This paper considers stock prices in the Korean stock market during the 2008 global financial crisis by focusing on three time periods: before, during, and after the crisis. Complex networks are extracted from cross-correlation coefficients between the normalized logarithmic return of the stock price time series of firms. The minimal spanning trees (MSTs) and the hierarchical network (HN) are generated from cross-correlation coefficients. Before and after the crisis, securities firms are located at the center of the MST. During the crisis, however, the center of the MST changes to a firm in heavy industry and construction. During the crisis, the MST shrinks in comparison to that before and that after the crisis. This topological change in the MST during the crisis reflects a distinct effect of the global financial crisis. The cophenetic correlation coefficient increases during the crisis, indicating an increase in the hierarchical structure during in this period. When crisis hits the market, firms behave synchronously, and their correlations are higher than those during a normal period.

Balancing building and maintenance costs in growing transport networks

NASA Astrophysics Data System (ADS)

Bottinelli, Arianna; Louf, Rémi; Gherardi, Marco

2017-09-01

The costs associated to the length of links impose unavoidable constraints to the growth of natural and artificial transport networks. When future network developments cannot be predicted, the costs of building and maintaining connections cannot be minimized simultaneously, requiring competing optimization mechanisms. Here, we study a one-parameter nonequilibrium model driven by an optimization functional, defined as the convex combination of building cost and maintenance cost. By varying the coefficient of the combination, the model interpolates between global and local length minimization, i.e., between minimum spanning trees and a local version known as dynamical minimum spanning trees. We show that cost balance within this ensemble of dynamical networks is a sufficient ingredient for the emergence of tradeoffs between the network's total length and transport efficiency, and of optimal strategies of construction. At the transition between two qualitatively different regimes, the dynamics builds up power-law distributed waiting times between global rearrangements, indicating a point of nonoptimality. Finally, we use our model as a framework to analyze empirical ant trail networks, showing its relevance as a null model for cost-constrained network formation.

Robust MST-Based Clustering Algorithm.

PubMed

Liu, Qidong; Zhang, Ruisheng; Zhao, Zhili; Wang, Zhenghai; Jiao, Mengyao; Wang, Guangjing

2018-06-01

Minimax similarity stresses the connectedness of points via mediating elements rather than favoring high mutual similarity. The grouping principle yields superior clustering results when mining arbitrarily-shaped clusters in data. However, it is not robust against noises and outliers in the data. There are two main problems with the grouping principle: first, a single object that is far away from all other objects defines a separate cluster, and second, two connected clusters would be regarded as two parts of one cluster. In order to solve such problems, we propose robust minimum spanning tree (MST)-based clustering algorithm in this letter. First, we separate the connected objects by applying a density-based coarsening phase, resulting in a low-rank matrix in which the element denotes the supernode by combining a set of nodes. Then a greedy method is presented to partition those supernodes through working on the low-rank matrix. Instead of removing the longest edges from MST, our algorithm groups the data set based on the minimax similarity. Finally, the assignment of all data points can be achieved through their corresponding supernodes. Experimental results on many synthetic and real-world data sets show that our algorithm consistently outperforms compared clustering algorithms.

A Model of Desired Performance in Phylogenetic Tree Construction for Teaching Evolution.

ERIC Educational Resources Information Center

Brewer, Steven D.

This research paper examines phylogenetic tree construction-a form of problem solving in biology-by studying the strategies and heuristics used by experts. One result of the research is the development of a model of desired performance for phylogenetic tree construction. A detailed description of the model and the sample problems which illustrate…

Live phylogeny with polytomies: Finding the most compact parsimonious trees.

PubMed

Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

2017-08-01

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

The scientific value and potential of New Zealand swamp kauri

NASA Astrophysics Data System (ADS)

Lorrey, Andrew M.; Boswijk, Gretel; Hogg, Alan; Palmer, Jonathan G.; Turney, Christian S. M.; Fowler, Anthony M.; Ogden, John; Woolley, John-Mark

2018-03-01

New Zealand swamp kauri (Agathis australis) are relic trees that have been buried and preserved in anoxic bog environments of northern New Zealand for centuries through to hundreds of millennia. Kauri are massive in proportion to other native New Zealand trees and they can attain ages greater than 1000 years. The export market for swamp (subfossil) kauri has recently been driven by demand for a high-value workable timber, but there are concerns about the sustainability of the remaining resource, a situation exacerbated in recent years by the rapid extraction of wood. Economic exploitation of swamp kauri presents several unique opportunities for Quaternary science, however the scientific value of this wood is not well understood by the wider research community and public. Here, we summarise the history of scientific research on swamp kauri, and explore the considerable potential of this unique resource. Swamp kauri tree-ring chronologies are temporally unique, and secondary analyses (such as radiocarbon and isotopic analyses) have value for improving our understanding of Earth's recent geologic history and pre-instrumental climate history. Swamp kauri deposits that span the last interglacial-glacial cycle show potential to yield "ultra-long" multi-millennia tree-ring chronologies, and composite records spanning large parts of MIS3 (and most of the Holocene) may be possible. High-precision radiocarbon dating of swamp kauri chronologies can improve the resolution of the global radiocarbon calibration curve, while testing age modelling and chronologic alignment of other independent long-term high-resolution proxy records. Swamp kauri also has the potential to facilitate absolute dating and verification of cosmogenic events found in long Northern Hemisphere tree-ring chronologies. Future efforts to conserve these identified values requires scientists to work closely with swamp kauri industry operators, resource consent authorities, and export regulators to mitigate potential losses to science as this precious material is progressively extracted from the ground and utilized.

Assessing trait-based scaling theory in tropical and temperate forests spanning a broad temperature gradients

NASA Astrophysics Data System (ADS)

Enquist, B. J.

2017-12-01

Tropical and temperate elevation gradients are natural laboratories to assess how changing climate can influence tropical forests. However, there is a need for theory and integrated data collection to scale from traits to ecosystems. We assess predictions of a novel trait-based metabolic scaling theory including whether observed shifts in forest traits across a broad tropical temperature gradient is consistent with local phenotypic optima and adaptive compensation for temperature. We tested a new anaytical theory - Trait Driver Theory - that is capable of scaling from traits to entire stands and ecosystems across several elevation gradients spanning 3300m. Each gradient consists of thousands of tropical and temperate tree trait measures taken from forest plots. In several of these plots, in particular in southern Perú, gross and net primary productivity (GPP and NPP) were measured. We measured multiple traits linked to variation in tree growth and assessed their frequency distributions within and across the elevation gradient. We paired these trait measures across individuals within forests with simultaneous measures of ecosystem net and gross primary productivity. Consistent with theory, variation in forest NPP and GPP primarily scaled with forest biomass but the secondary effect of temperature on productivity was much less than expected. This weak temperature dependency appears to reflect directional shifts in several mean community traits that underlie tree growth with decreases in site temperature. The observed shift in traits of trees that dominant more cold environments appear to reflect `adaptive/acclimatory' compensation for the kinetic effects of temperature on leaf photosynthesis and tree growth. Forest trait distributions across the gradient showed peaked and skewed distributions, consistent with the importance of local filtering of optimal growth traits and recent shifts in species composition and dominance due to warming from climate change. Trait-based metabolic scaling theory provides a basis to predict how shifts in climate have and will influence the trait composition and ecosystem functioning of temperate and tropical forests.

Exploratory and problem-solving consumer behavior across the life span.

PubMed

Lesser, J A; Kunkel, S R

1991-09-01

Different cognitive functioning, social, and personality changes appear to occur systematically during the adult life span. This article synthesizes research on life span changes in order to develop age-specific models of shopping behavior. The models are tested within a naturalistic field study of shoppers.

A field-to-desktop toolchain for X-ray CT densitometry enables tree ring analysis

PubMed Central

De Mil, Tom; Vannoppen, Astrid; Beeckman, Hans; Van Acker, Joris; Van den Bulcke, Jan

2016-01-01

Background and Aims Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. Methods Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. Key Results Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. Conclusions A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species. PMID:27107414

Developing a Method to Mask Trees in Commercial Multispectral Imagery

NASA Astrophysics Data System (ADS)

Becker, S. J.; Daughtry, C. S. T.; Jain, D.; Karlekar, S. S.

2015-12-01

The US Army has an increasing focus on using automated remote sensing techniques with commercial multispectral imagery (MSI) to map urban and peri-urban agricultural and vegetative features; however, similar spectral profiles between trees (i.e., forest canopy) and other vegetation result in confusion between these cover classes. Established vegetation indices, like the Normalized Difference Vegetation Index (NDVI), are typically not effective in reliably differentiating between trees and other vegetation. Previous research in tree mapping has included integration of hyperspectral imagery (HSI) and LiDAR for tree detection and species identification, as well as the use of MSI to distinguish tree crowns from non-vegetated features. This project developed a straightforward method to model and also mask out trees from eight-band WorldView-2 (1.85 meter x 1.85 meter resolution at nadir) satellite imagery at the Beltsville Agricultural Research Center in Beltsville, MD spanning 2012 - 2015. The study site included tree cover, a range of agricultural and vegetative cover types, and urban features. The modeling method exploits the product of the red and red edge bands and defines accurate thresholds between trees and other land covers. Results show this method outperforms established vegetation indices including the NDVI, Soil Adjusted Vegetation Index, Normalized Difference Water Index, Simple Ratio, and Normalized Difference Red Edge Index in correctly masking trees while preserving the other information in the imagery. This method is useful when HSI and LiDAR collection are not possible or when using archived MSI.

Slow growth rates of Amazonian trees: Consequences for carbon cycling

PubMed Central

Vieira, Simone; Trumbore, Susan; Camargo, Plinio B.; Selhorst, Diogo; Chambers, Jeffrey Q.; Higuchi, Niro; Martinelli, Luiz Antonio

2005-01-01

Quantifying age structure and tree growth rate of Amazonian forests is essential for understanding their role in the carbon cycle. Here, we use radiocarbon dating and direct measurement of diameter increment to document unexpectedly slow growth rates for trees from three locations spanning the Brazilian Amazon basin. Central Amazon trees, averaging only ≈1mm/year diameter increment, grow half as fast as those from areas with more seasonal rainfall to the east and west. Slow growth rates mean that trees can attain great ages; across our sites we estimate 17-50% of trees with diameter >10 cm have ages exceeding 300 years. Whereas a few emergent trees that make up a large portion of the biomass grow faster, small trees that are more abundant grow slowly and attain ages of hundreds of years. The mean age of carbon in living trees (60-110 years) is within the range of or slightly longer than the mean residence time calculated from C inventory divided by annual C allocation to wood growth (40-100 years). Faster C turnover is observed in stands with overall higher rates of diameter increment and a larger fraction of the biomass in large, fast-growing trees. As a consequence, forests can recover biomass relatively quickly after disturbance, whereas recovering species composition may take many centuries. Carbon cycle models that apply a single turnover time for carbon in forest biomass do not account for variations in life strategy and therefore may overestimate the carbon sequestration potential of Amazon forests. PMID:16339903

Density-dependent vulnerability of forest ecosystems to drought

USGS Publications Warehouse

Bottero, Alessandra; D'Amato, Anthony W.; Palik, Brian J.; Bradford, John B.; Fraver, Shawn; Battaglia, Mike A.; Asherin, Lance A.

2017-01-01

1. Climate models predict increasing drought intensity and frequency for many regions, which may have negative consequences for tree recruitment, growth and mortality, as well as forest ecosystem services. Furthermore, practical strategies for minimizing vulnerability to drought are limited. Tree population density, a metric of tree abundance in a given area, is a primary driver of competitive intensity among trees, which influences tree growth and mortality. Manipulating tree population density may be a mechanism for moderating drought-induced stress and growth reductions, although the relationship between tree population density and tree drought vulnerability remains poorly quantified, especially across climatic gradients.2. In this study, we examined three long-term forest ecosystem experiments in two widely distributed North American pine species, ponderosa pine Pinus ponderosa (Lawson & C. Lawson) and red pine Pinus resinosa (Aiton), to better elucidate the relationship between tree population density, growth and drought. These experiments span a broad latitude and aridity range and include tree population density treatments that have been purposefully maintained for several decades. We investigated how tree population density influenced resistance (growth during drought) and resilience (growth after drought compared to pre-drought growth) of stand-level growth during and after documented drought events.3. Our results show that relative tree population density was negatively related to drought resistance and resilience, indicating that trees growing at lower densities were less vulnerable to drought. This result was apparent in all three forest ecosystems, and was consistent across species, stand age and drought intensity.4. Synthesis and applications. Our results highlighted that managing pine forest ecosystems at low tree population density represents a promising adaptive strategy for reducing the adverse impacts of drought on forest growth in coming decades. Nonetheless, the broader applicability of our findings to other types of forest ecosystems merits additional investigation.

Interpreting terrestrial organic carbon isotope records across natural and anthropogenic pCO2 change

NASA Astrophysics Data System (ADS)

Schubert, B.; Jahren, H.

2014-12-01

Changes in the net carbon isotope fractionation (Δδ13C) measured in organic carbon from terrestrial substrates results from changes in climate, plant community shifts, and pCO2 level, but separating out these effects in the geologic record can be difficult. Here we present a compilation of 614 Δδ13C measurements on bulk terrestrial organic matter (TOM) and fossil leaves from 23 distinct records within 19 published studies that span the last 30,000 years up to the industrial revolution. To this dataset we add 2735 Δδ13C measurements made on tree ring tissue from 51 records that extend from 1950 to 2010. These records together span the ~80 ppm rise in pCO2 from the Late Glacial to through the Holocene (190-270 ppm; fossil leaves and TOM), and the ~70 ppm rise observed across the last 60 years (310-380 ppm; tree-ring tissue). We find a 2.0‰ relative increase in Δδ13C value across Termination 1 (18,000-11,500 years BP) and a 1.0‰ increase in Δδ13C value recorded in tree rings between 1950 and 2010. We use our recently developed relationship between pCO2 and Δδ13C to show that both increases in Δδ13C value exactly match, in trend and absolute magnitude, the increase in Δδ13C value we predict from our equations in response to rising pCO2 levels. These results have significance for the interpretation of terrestrial organic isotope records spanning both natural and anthropogenic pCO2 changes; we contend that environmental reconstructions based on long-term terrestrial Δδ13C records cannot be accurately interpreted until the isotope data are adjusted for known changes in pCO2 concentration.

Automatic extraction of tree crowns from aerial imagery in urban environment

NASA Astrophysics Data System (ADS)

Liu, Jiahang; Li, Deren; Qin, Xunwen; Yang, Jianfeng

2006-10-01

Traditionally, field-based investigation is the main method to investigate greenbelt in urban environment, which is costly and low updating frequency. In higher resolution image, the imagery structure and texture of tree canopy has great similarity in statistics despite the great difference in configurations of tree canopy, and their surface structures and textures of tree crown are very different from the other types. In this paper, we present an automatic method to detect tree crowns using high resolution image in urban environment without any apriori knowledge. Our method catches unique structure and texture of tree crown surface, use variance and mathematical expectation of defined image window to position the candidate canopy blocks coarsely, then analysis their inner structure and texture to refine these candidate blocks. The possible spans of all the feature parameters used in our method automatically generate from the small number of samples, and HOLE and its distribution as an important characteristics are introduced into refining processing. Also the isotropy of candidate image block and holes' distribution is integrated in our method. After introduction the theory of our method, aerial imageries were used ( with a resolution about 0.3m ) to test our method, and the results indicate that our method is an effective approach to automatically detect tree crown in urban environment.

Single Polygon Counting on Cayley Tree of Order 3

NASA Astrophysics Data System (ADS)

Pah, Chin Hee

2010-07-01

We showed that one form of generalized Catalan numbers is the solution to the problem of finding different connected component with finite vertices containing a fixed root for the semi-infinite Cayley tree of order 3. We give the formula for the full graph, Cayley tree of order 3 which is derived from the generalized Catalan numbers. Using ratios of Gamma functions, two upper bounds are given for problem defined on semi-infinite Cayley tree of order 3 as well as the full graph.

Efficient algorithms for dilated mappings of binary trees

NASA Technical Reports Server (NTRS)

Iqbal, M. Ashraf

1990-01-01

The problem is addressed to find a 1-1 mapping of the vertices of a binary tree onto those of a target binary tree such that the son of a node on the first binary tree is mapped onto a descendent of the image of that node in the second binary tree. There are two natural measures of the cost of this mapping, namely the dilation cost, i.e., the maximum distance in the target binary tree between the images of vertices that are adjacent in the original tree. The other measure, expansion cost, is defined as the number of extra nodes/edges to be added to the target binary tree in order to ensure a 1-1 mapping. An efficient algorithm to find a mapping of one binary tree onto another is described. It is shown that it is possible to minimize one cost of mapping at the expense of the other. This problem arises when designing pipelined arithmetic logic units (ALU) for special purpose computers. The pipeline is composed of ALU chips connected in the form of a binary tree. The operands to the pipeline can be supplied to the leaf nodes of the binary tree which then process and pass the results up to their parents. The final result is available at the root. As each new application may require a distinct nesting of operations, it is useful to be able to find a good mapping of a new binary tree over existing ALU tree. Another problem arises if every distinct required binary tree is known beforehand. Here it is useful to hardwire the pipeline in the form of a minimal supertree that contains all required binary trees.

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The Probabilistic Thinking of Primary School Pupils in Cyprus: The Case of Tree Diagrams

ERIC Educational Resources Information Center

Lamprianou, Iasonas; Lamprianou, Thekla Afantiti

2003-01-01

In this research work we explored the nature of 9-12 year old pupils' responses to probabilistic problems with tree diagrams. It was found that a large percentage of pupils failed to respond correctly even to very simple problems that demanded the identification of "possible routes/paths" in figures with tree diagrams/mazes. The results…

Deer damage in central hardwoods: a potential problem

Treesearch

Nancy G. Tilghman; David A. Marquis

1989-01-01

A major part of the diet of white-tailed deer consists of herbaceous plants, acorns, other tree fruits, and the twigs of trees and shrubs. Deer browsing on young tree seedlings can influence the success of regeneration in forest stands. Excessive deer browsing is not a major problem in the central hardwood forest type, except in parts of Pennsylvania and, to a lesser...

Blended Design Approach of Long Span Structure and Malay Traditional Architecture

NASA Astrophysics Data System (ADS)

Sundari, Titin

2017-12-01

The growing population in the world is so fast, which is followed by the increasing need of some new and large activities. Architects face the problem on how to facilitate buildings with various activities such as for large meeting, conference, indoors gymnasium and sports, and many others. The long span structure of building is one of the solutions to solve that problem. Generally, large buildings which implemented this structure will look as a technological, modern and futuristic ones or even neo futuristic performance. But on the other hand, many people still want to enjoy the specific and unique senses of local traditional architecture. So is the Malay people who want an easy pleasant large facilities which can be fulfilled by implementing modern long span building structure technology. In the same time, their unique sense of Malay traditional architecture can still be maintained. To overcome this double problems of design, it needs a blended design approach of long span structure and Malay Traditional Architecture.

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

PubMed Central

2013-01-01

Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

Reconstructing the temporal ordering of biological samples using microarray data.

PubMed

Magwene, Paul M; Lizardi, Paul; Kim, Junhyong

2003-05-01

Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

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.

SPAN: Ocean science

NASA Technical Reports Server (NTRS)

Thomas, Valerie L.; Koblinsky, Chester J.; Webster, Ferris; Zlotnicki, Victor; Green, James L.

1987-01-01

The Space Physics Analysis Network (SPAN) is a multi-mission, correlative data comparison network which links space and Earth science research and data analysis computers. It provides a common working environment for sharing computer resources, sharing computer peripherals, solving proprietary problems, and providing the potential for significant time and cost savings for correlative data analysis. This is one of a series of discipline-specific SPAN documents which are intended to complement the SPAN primer and SPAN Management documents. Their purpose is to provide the discipline scientists with a comprehensive set of documents to assist in the use of SPAN for discipline specific scientific research.

Estimating Mixed Broadleaves Forest Stand Volume Using Dsm Extracted from Digital Aerial Images

NASA Astrophysics Data System (ADS)

Sohrabi, H.

2012-07-01

In mixed old growth broadleaves of Hyrcanian forests, it is difficult to estimate stand volume at plot level by remotely sensed data while LiDar data is absent. In this paper, a new approach has been proposed and tested for estimating stand forest volume. The approach is based on this idea that forest volume can be estimated by variation of trees height at plots. In the other word, the more the height variation in plot, the more the stand volume would be expected. For testing this idea, 120 circular 0.1 ha sample plots with systematic random design has been collected in Tonekaon forest located in Hyrcanian zone. Digital surface model (DSM) measure the height values of the first surface on the ground including terrain features, trees, building etc, which provides a topographic model of the earth's surface. The DSMs have been extracted automatically from aerial UltraCamD images so that ground pixel size for extracted DSM varied from 1 to 10 m size by 1m span. DSMs were checked manually for probable errors. Corresponded to ground samples, standard deviation and range of DSM pixels have been calculated. For modeling, non-linear regression method was used. The results showed that standard deviation of plot pixels with 5 m resolution was the most appropriate data for modeling. Relative bias and RMSE of estimation was 5.8 and 49.8 percent, respectively. Comparing to other approaches for estimating stand volume based on passive remote sensing data in mixed broadleaves forests, these results are more encouraging. One big problem in this method occurs when trees canopy cover is totally closed. In this situation, the standard deviation of height is low while stand volume is high. In future studies, applying forest stratification could be studied.

Efficient algorithms for a class of partitioning problems

NASA Technical Reports Server (NTRS)

Iqbal, M. Ashraf; Bokhari, Shahid H.

1990-01-01

The problem of optimally partitioning the modules of chain- or tree-like tasks over chain-structured or host-satellite multiple computer systems is addressed. This important class of problems includes many signal processing and industrial control applications. Prior research has resulted in a succession of faster exact and approximate algorithms for these problems. Polynomial exact and approximate algorithms are described for this class that are better than any of the previously reported algorithms. The approach is based on a preprocessing step that condenses the given chain or tree structured task into a monotonic chain or tree. The partitioning of this monotonic take can then be carried out using fast search techniques.

Polynomial reduction and evaluation of tree- and loop-level CHY amplitudes

DOE PAGES

Zlotnikov, Michael

2016-08-24

We develop a polynomial reduction procedure that transforms any gauge fixed CHY amplitude integrand for n scattering particles into a σ-moduli multivariate polynomial of what we call the standard form. We show that a standard form polynomial must have a specific ladder type monomial structure, which has finite size at any n, with highest multivariate degree given by (n – 3)(n – 4)/2. This set of monomials spans a complete basis for polynomials with rational coefficients in kinematic data on the support of scattering equations. Subsequently, at tree and one-loop level, we employ the global residue theorem to derive amore » prescription that evaluates any CHY amplitude by means of collecting simple residues at infinity only. Furthermore, the prescription is then applied explicitly to some tree and one-loop amplitude examples.« less

A pioneer exotic tree search for the Douglas-fir region.

Treesearch

Roy R. Silen; Donald L. Olson

1992-01-01

After three-quarters of a century of introduction of 152 conifer and broadleaf species, no promising candidate exotic was found for the Douglas-fir region. Growth curves spanning 50 years or longer are figured for many species. Firs, pines, larches, spruces, hemlocks, and cedars originating in northwestern North America had superior growth rates to those from other...

Understanding the evidence for historical fire across eastern forests

Treesearch

Charles M. Ruffner

2006-01-01

Evidence for historical fire across the eastern deciduous biome spans several fields, including paleoecology, fire scar analysis, witness tree studies, historical documents and ethnographic sources. In this paper I provide an overview of many of these methods as well as the limitations and examples of each. While the use of any single approach has its cautions and...

Dutch elm disease control: performance and costs

Treesearch

William N., Jr. Cannon; David P. Worley

1976-01-01

Municipal programs to suppress Dutch elm disease have had highly variable results. Performance as measured by tree mortality was unrelated to control strategies. Costs for control programs were 37 to 76 percent less than costs without control programs in the 15-year time-span of the study. Only those municipalities that conducted a high-performance program could be...

Dutch elm disease control: performance and costs

Treesearch

William N., Jr. Cannon; David P. Worley

1980-01-01

Municipal programs to suppress Dutch elm disease have had highly variable results. Performance as measured by tree mortality was unrelated to control strategies. Costs for control programs were 37 to 76 percent less than costs without control programs in the 15-year time-span of the study. Only those municipalities that conducted a high-performance program could be...

Topology of foreign exchange markets using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Naylor, Michael J.; Rose, Lawrence C.; Moyle, Brendan J.

2007-08-01

This paper uses two physics derived hierarchical techniques, a minimal spanning tree and an ultrametric hierarchical tree, to extract a topological influence map for major currencies from the ultrametric distance matrix for 1995-2001. We find that these two techniques generate a defined and robust scale free network with meaningful taxonomy. The topology is shown to be robust with respect to method, to time horizon and is stable during market crises. This topology, appropriately used, gives a useful guide to determining the underlying economic or regional causal relationships for individual currencies and to understanding the dynamics of exchange rate price determination as part of a complex network.

Alpine Holocene Tree Ring Isotope Records - A Synthesis of a Multi-Proxy Approach in Dendroclimatology

NASA Astrophysics Data System (ADS)

Ziehmer, Malin Michelle; Nicolussi, Kurt; Schlüchter, Christian; Leuenberger, Markus

2017-04-01

High-resolution climate reconstructions based on tree-ring proxies are often limited by the individual segment length of living trees selected at the defined sampling sites, which mostly results in relatively short multi-centennial proxy series. A potential extension of living wood records comprise the addition of subfossil and archeological wood remains resulting in chronologies and associated climate reconstructions which are able to cover a few millennia in central Europe (e.g. Büntgen et al., 2011). However, existing multi-millennial tree-ring width chronologies in central Europe rank among the longest continuous chronologies world-wide and span the entire Holocene (Becker et al., 1993; Nicolussi et al. 2009). So far, these chronologies have mainly been used for dating subfossil wood samples, floating chronologies and archeological artifacts, but only in parts for reconstructing climate. Finds of Holocene wood remains in glacier forefields, peat bogs and small lakes allow us not only to establish such long-term tree-ring width records; further they offer the possibility to establish multi-millennial proxy records for the entire Holocene by using a multi-proxy approach which includes both tree-ring width and triple stable isotope ratios. As temperature limits tree growth at the Alpine upper tree line, the existing tree-ring width records are currently limited to reconstruct a single environmental variable. In the framework of the project Alpine Holocene Tree Ring Isotope Records, we combine tree-ring width, cellulose content as well as carbon, oxygen and hydrogen isotope series in a multi-proxy approach which allows the reconstruction of past environments by combining both Holocene wood remains and recent tree samples from two Alpine tree-line species. For this purpose, α-cellulose is prepared from 5-year tree ring blocks following the procedure after Boettger et al. (2007) and subsequently crushed by ultrasonic homogenization (Laumer et al., 2009). The cellulose content is determined for each individual sample and carbon, oxygen and hydrogen isotopic ratios are measured simultaneously (Loader et al., 2015). The isotope records of carbon, oxygen and hydrogen show distinct low-frequency trends for the Early- and Mid-Holocene, but the individual series per proxy are often offset in their isotopic signature. As the sampling sites in our study are distributed along a SW-NE transect, the influence of the site conditions (latitude, longitude, elevation, exposition) and the tree species is tested and subsequently a correction is applied to the individual series. In addition, the tree-ring width records operate as a helpful tool in detecting and attributing the influence of larch budmoth outbreaks on the cellulose content and isotope records. We here present a synthesis of the applied multi-proxy approach and its ability to reconstruct Holocene climate variability for the time span from 9000 to 3500 years b2k covering the Early-Holocene (9000 to 7200 years b2k) and Mid-Holocene (7200 to 4200 years b2k) and the transition to the late Holocene (4200 to 3500 years b2k) as well as the recent 400 years including the modern warming. References Becker, B., & Kromer, B. Palaeogeogr. Palaeoclimatol. Palaeoecol., 1993, 103(1): 67-71 Boettger, T., et al. Anal. Chem., 2007, 79: 4603-4612 Büntgen, U. et al. Science, 2011, 331(6017): 578-582 Laumer, W., et al. Rapid Commun. Mass Spectrom., 2009, 23: 1934-1940 Loader, N.J., et al. Anal. Chem., 2015, 87: 376-380 Nicolussi K., et al. The Holocene, 2009, 19(6): 909-920

Scattering theory for graphs isomorphic to a regular tree at infinity

NASA Astrophysics Data System (ADS)

Colin de Verdière, Yves; Truc, Françoise

2013-06-01

We describe the spectral theory of the adjacency operator of a graph which is isomorphic to a regular tree at infinity. Using some combinatorics, we reduce the problem to a scattering problem for a finite rank perturbation of the adjacency operator on a regular tree. We develop this scattering theory using the classical recipes for Schrödinger operators in Euclidian spaces.

SPACE PROPULSION SYSTEM PHASED-MISSION PROBABILITY ANALYSIS USING CONVENTIONAL PRA METHODS

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

Curtis Smith; James Knudsen

As part of a series of papers on the topic of advance probabilistic methods, a benchmark phased-mission problem has been suggested. This problem consists of modeling a space mission using an ion propulsion system, where the mission consists of seven mission phases. The mission requires that the propulsion operate for several phases, where the configuration changes as a function of phase. The ion propulsion system itself consists of five thruster assemblies and a single propellant supply, where each thruster assembly has one propulsion power unit and two ion engines. In this paper, we evaluate the probability of mission failure usingmore » the conventional methodology of event tree/fault tree analysis. The event tree and fault trees are developed and analyzed using Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE). While the benchmark problem is nominally a "dynamic" problem, in our analysis the mission phases are modeled in a single event tree to show the progression from one phase to the next. The propulsion system is modeled in fault trees to account for the operation; or in this case, the failure of the system. Specifically, the propulsion system is decomposed into each of the five thruster assemblies and fed into the appropriate N-out-of-M gate to evaluate mission failure. A separate fault tree for the propulsion system is developed to account for the different success criteria of each mission phase. Common-cause failure modeling is treated using traditional (i.e., parametrically) methods. As part of this paper, we discuss the overall results in addition to the positive and negative aspects of modeling dynamic situations with non-dynamic modeling techniques. One insight from the use of this conventional method for analyzing the benchmark problem is that it requires significant manual manipulation to the fault trees and how they are linked into the event tree. The conventional method also requires editing the resultant cut sets to obtain the correct results. While conventional methods may be used to evaluate a dynamic system like that in the benchmark, the level of effort required may preclude its use on real-world problems.« less

Comparative analysis of techniques for evaluating the effectiveness of aircraft computing systems

NASA Technical Reports Server (NTRS)

Hitt, E. F.; Bridgman, M. S.; Robinson, A. C.

1981-01-01

Performability analysis is a technique developed for evaluating the effectiveness of fault-tolerant computing systems in multiphase missions. Performability was evaluated for its accuracy, practical usefulness, and relative cost. The evaluation was performed by applying performability and the fault tree method to a set of sample problems ranging from simple to moderately complex. The problems involved as many as five outcomes, two to five mission phases, permanent faults, and some functional dependencies. Transient faults and software errors were not considered. A different analyst was responsible for each technique. Significantly more time and effort were required to learn performability analysis than the fault tree method. Performability is inherently as accurate as fault tree analysis. For the sample problems, fault trees were more practical and less time consuming to apply, while performability required less ingenuity and was more checkable. Performability offers some advantages for evaluating very complex problems.

The inverse Wiener polarity index problem for chemical trees.

PubMed

Du, Zhibin; Ali, Akbar

2018-01-01

The Wiener polarity number (which, nowadays, known as the Wiener polarity index and usually denoted by Wp) was devised by the chemist Harold Wiener, for predicting the boiling points of alkanes. The index Wp of chemical trees (chemical graphs representing alkanes) is defined as the number of unordered pairs of vertices (carbon atoms) at distance 3. The inverse problems based on some well-known topological indices have already been addressed in the literature. The solution of such inverse problems may be helpful in speeding up the discovery of lead compounds having the desired properties. This paper is devoted to solving a stronger version of the inverse problem based on Wiener polarity index for chemical trees. More precisely, it is proved that for every integer t ∈ {n - 3, n - 2,…,3n - 16, 3n - 15}, n ≥ 6, there exists an n-vertex chemical tree T such that Wp(T) = t.

Multi-proxy reconstructions and the power of integration across marine, terrestrial, and freshwater ecosystems. (Invited)

NASA Astrophysics Data System (ADS)

Black, B.

2013-12-01

Over the past decade, dendrochronology (tree-ring analysis) techniques have been increasingly applied to growth increments of various bivalve, fish, and coral species. In particular, the use of crossdating ensures that all increments in a dataset have assigned the correct calendar year of formation and that the resulting chronology is exactly placed in time. Such temporal alignment facilitates direct comparisons among chronologies that span diverse taxa and ecosystems, illustrating the pervasive, synchronizing influence of climate from alpine forests to the continental slope. Such an approach can be particularly beneficial to reconstructions in that each species captures climate signals from its unique 'perspective' of life history and habitat. For example, combinations of tree-ring data and chronologies for the long-lived bivalve Pacific geoduck (Panopea generosa) capture substantially more variance in regional sea surface temperatures than either proxy could explain alone. Just as importantly, networks of chronologies spanning multiple trophic levels can help identify climate variables critical to ecosystem functioning, which can then be targeted to generate most biologically relevant reconstructions possible. Along the west coast of North America, fish and bivalve chronologies in combination with records of seabird reproductive success indicate that winter sea-level pressure is closely associated with California Current productivity, which can be hind-cast over the past six centuries using coastal tree-ring chronologies. Thus, multiple proxies not only increase reconstruction skill, but also help isolate climate variables most closely linked to ecosystem structure and functioning.

Multi-proxy reconstructions and the power of integration across marine, terrestrial, and freshwater ecosystems. (Invited)

NASA Astrophysics Data System (ADS)

Barrett, P. J.

2011-12-01

Over the past decade, dendrochronology (tree-ring analysis) techniques have been increasingly applied to growth increments of various bivalve, fish, and coral species. In particular, the use of crossdating ensures that all increments in a dataset have assigned the correct calendar year of formation and that the resulting chronology is exactly placed in time. Such temporal alignment facilitates direct comparisons among chronologies that span diverse taxa and ecosystems, illustrating the pervasive, synchronizing influence of climate from alpine forests to the continental slope. Such an approach can be particularly beneficial to reconstructions in that each species captures climate signals from its unique 'perspective' of life history and habitat. For example, combinations of tree-ring data and chronologies for the long-lived bivalve Pacific geoduck (Panopea generosa) capture substantially more variance in regional sea surface temperatures than either proxy could explain alone. Just as importantly, networks of chronologies spanning multiple trophic levels can help identify climate variables critical to ecosystem functioning, which can then be targeted to generate most biologically relevant reconstructions possible. Along the west coast of North America, fish and bivalve chronologies in combination with records of seabird reproductive success indicate that winter sea-level pressure is closely associated with California Current productivity, which can be hind-cast over the past six centuries using coastal tree-ring chronologies. Thus, multiple proxies not only increase reconstruction skill, but also help isolate climate variables most closely linked to ecosystem structure and functioning.

Leaf area and light use efficiency patterns of Norway spruce under different thinning regimes and age classes

PubMed Central

Gspaltl, Martin; Bauerle, William; Binkley, Dan; Sterba, Hubert

2013-01-01

Silviculture focuses on establishing forest stand conditions that improve the stand increment. Knowledge about the efficiency of an individual tree is essential to be able to establish stand structures that increase tree resource use efficiency and stand level production. Efficiency is often expressed as stem growth per unit leaf area (leaf area efficiency), or per unit of light absorbed (light use efficiency). We tested the hypotheses that: (1) volume increment relates more closely with crown light absorption than leaf area, since one unit of leaf area can receive different amounts of light due to competition with neighboring trees and self-shading, (2) dominant trees use light more efficiently than suppressed trees and (3) thinning increases the efficiency of light use by residual trees, partially accounting for commonly observed increases in post-thinning growth. We investigated eight even-aged Norway spruce (Picea abies (L.) Karst.) stands at Bärnkopf, Austria, spanning three age classes (mature, immature and pole-stage) and two thinning regimes (thinned and unthinned). Individual leaf area was calculated with allometric equations and absorbed photosynthetically active radiation was estimated for each tree using the three-dimensional crown model Maestra. Absorbed photosynthetically active radiation was only a slightly better predictor of volume increment than leaf area. Light use efficiency increased with increasing tree size in all stands, supporting the second hypothesis. At a given tree size, trees from the unthinned plots were more efficient, however, due to generally larger tree sizes in the thinned stands, an average tree from the thinned treatment was superior (not congruent in all plots, thus only partly supporting the third hypothesis). PMID:25540477

Demographic analysis of tree colonization in a 20-year-old right-of-way.

PubMed

Mercier, C; Brison, J; Bouchard, A

2001-12-01

Past tree colonization dynamics of a powerline-right-of-way (ROW) corridor in the Haut-Saint-Laurent region of Quebec was studied based on the present age distribution of its tree populations. This colonization study spans 20 years, from 1977 (ROW clearance) to 1996. The sampled quadrats were classified into six vegetation types. Tree colonization dynamics were interpreted in each type, and three distinct patterns were identified. (1) Communities adapted to acidic conditions were heavily colonized by Acer rubrum, at least for the last 12 years. (2) Communities adapted to mesic or to hydric conditions were more intensely colonized in the period 1985-1987 than in the following 9 years; this past success in tree colonization may have been caused by herbicide treatments, which could have facilitated tree establishment by damaging the herbaceous and shrub vegetation. (3) Cattail, vine-raspberry, and reed-dominated communities contained few tree individuals, with almost all trees establishing between 1979 and 1990; those three vegetation types appear as the most resistant to tree invasion in the ROW studied. This study supports the need for an integrated approach in ROW vegetation management, in which the selection of vegetation treatment methods would depend on the tree colonization dynamics in each vegetation type. Minimizing disturbances inflicted on ROW herbaceous and shrub covers should be the central strategy because disturbances jeopardize natural resistance to future tree invasion, except in communities adapted to acidic conditions where the existing vegetation does not prevent invasion by A. rubrum. Many trees are surviving the successive cutting operations by producing new sprouts each time, particularly in communities adapted to mesic and hydric conditions. In these cases, mechanical cutting should be replaced by a one-time stump-killing operation, to avoid repeated and unsuccessful treatments of the same individuals over time.

Evaluation of growth disturbances of Picea abies (L.) Karst. to disturbances caused by landslide movements

NASA Astrophysics Data System (ADS)

Šilhán, Karel

2017-01-01

Dendrogeomorphic methods are frequently used in landslide analyses. Although methods of landslide dating based on tree rings are well developed, they still indicated many questions. The aim of this study was to evaluate the frequently used theoretical scheme based on the event-response relationship. Seventy-four individuals of Norway spruce (Picea abies (L.) Karst.) exhibiting visible external disturbance, were sampled on the Girová landslide (the largest historical flow-like landslide in the Czech Republic). This landslide reactivated in May 2010, and post-landslide tree growth responses were studied in detail. These growth responses were compared with the intensity and occurrence of visible external tree disturbance: tilted stems, damaged root systems, and decapitation. Twenty-nine trees (39.2%) died within one to four years following the 2010 landslide movement. The trees that died following the landslide movement were significantly younger and displayed significantly greater stem tilting than the live trees. Abrupt growth suppression was a more-frequent response among the dead trees, whereas growth release dominated among the live trees. Only two trees (2.7%) created no reaction wood in response to the landslide movement. Forty-four percent of the trees started to produce reaction wood structure after a delay, which generally spanned one year. Some eccentric growth was evident in the tree rings of the landslide year and was significant in the first years following the landslide movement. Missing rings were observed only on the upper sides of the stems, and no false tree rings were observed. The results confirm the general validity of event-response relationship, nevertheless this study points out the limitations and uncertainties of this generally accepted working scheme.

Economic costs of electrical system instability and power outages caused by snakes on the Island of Guam

USGS Publications Warehouse

Fritts, T.H.

2002-01-01

The Brown Tree Snake, Boiga irregularis, is an introduced species on Guam where it causes frequent electrical power outages. The snake's high abundance, its propensity for climbing, and use of disturbed habitats all contribute to interruption of Guam's electrical service and the activities that depend on electrical power. Snakes have caused more than 1600 power outages in the 20-yr period of 1978-1997 and most recently nearly 200 outages per year. Single outages spanning the entire island and lasting 8 or more hours are estimated to cost in excess of $3,000,000 in lost productivity, but the costs of outages that involve only parts of the island or those of shorter durations are more difficult to quantify. Costs to the island's economy have exceeded $4.5 M per year over a 7-yr period without considering repair costs, damage to electrical equipment, and lost revenues. Snakes pose the greatest problem on high voltage transmission lines, on transformers, and inside electrical substations.

No evidence that elevated CO2 gives tropical lianas an advantage over tropical trees.

PubMed

Marvin, David C; Winter, Klaus; Burnham, Robyn J; Schnitzer, Stefan A

2015-05-01

Recent studies indicate that lianas are increasing in size and abundance relative to trees in neotropical forests. As a result, forest dynamics and carbon balance may be altered through liana-induced suppression of tree growth and increases in tree mortality. Increasing atmospheric CO2 is hypothesized to be responsible for the increase in neotropical lianas, yet no study has directly compared the relative response of tropical lianas and trees to elevated CO2 . We explicitly tested whether tropical lianas had a larger response to elevated CO2 than co-occurring tropical trees and whether seasonal drought alters the response of either growth form. In two experiments conducted in central Panama, one spanning both wet and dry seasons and one restricted to the dry season, we grew liana (n = 12) and tree (n = 10) species in open-top growth chambers maintained at ambient or twice-ambient CO2 levels. Seedlings of eight individuals (four lianas, four trees) were grown in the ground in each chamber for at least 3 months during each season. We found that both liana and tree seedlings had a significant and positive response to elevated CO2 (in biomass, leaf area, leaf mass per area, and photosynthesis), but that the relative response to elevated CO2 for all variables was not significantly greater for lianas than trees regardless of the season. The lack of differences in the relative response between growth forms does not support the hypothesis that elevated CO2 is responsible for increasing liana size and abundance across the neotropics. © 2014 John Wiley & Sons Ltd.

Span of control matters.

PubMed

Cathcart, Deb; Jeska, Susan; Karnas, Joan; Miller, Sue E; Pechacek, Judy; Rheault, Lolita

2004-09-01

Prompted by manager concerns about span of control, a large, integrated health system set out to determine if span of control really mattered. Was there something to it, or was it just an excuse for poor performance? A team of middle managers studied the problem and ultimately demonstrated a strong relationship between span of control and employee engagement. Consequently, it was decided to add 4 management positions to note the effect. One year later, positive changes were observed in employee engagement scores in all 4 areas. This study suggests careful review of manager spans of control to address the untoward effects of large spans of control on employee engagement.

Tree planting - strip-mined area in Maryland

Treesearch

Fred L. Bagley

1980-01-01

This report is written to elucidate some of the problems encountered in the planting of trees on strip-mined areas in Maryland. When problems are recognized, normally a solution (or at least, an improvement) can be instituted to alleviate the problem. The methods cited herein are those of experienced foresters engaged in strip-mine planting during the past seventeen...

Working Memory Deficits in Children with Reading Difficulties: Memory Span and Dual Task Coordination

ERIC Educational Resources Information Center

Wang, Shinmin; Gathercole, Susan E.

2013-01-01

The current study investigated the cause of the reported problems in working memory in children with reading difficulties. Verbal and visuospatial simple and complex span tasks, and digit span and reaction times tasks performed singly and in combination, were administered to 46 children with single word reading difficulties and 45 typically…

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest.

PubMed

Schilling, Erik M; Waring, Bonnie G; Schilling, Jonathan S; Powers, Jennifer S

2016-09-01

We investigated how forest composition, litter quality, and rainfall interact to affect leaf litter decomposition across three successional tropical dry forests in Costa Rica. We monitored litter stocks and bulk litter turnover in 18 plots that exhibit substantial variation in soil characteristics, tree community structure, fungal communities (including forests dominated by ecto- or arbuscular mycorrhizal host trees), and forest age. Simultaneously, we decomposed three standard litter substrates over a 6-month period spanning an unusually intense drought. Decay rates of standard substrates depended on the interaction between litter identity and forest type. Decomposition rates were correlated with tree and soil fungal community composition as well as soil fertility, but these relationships differed among litter types. In low fertility soils dominated by ectomycorrhizal oak trees, bulk litter turnover rates were low, regardless of soil moisture. By contrast, in higher fertility soils that supported mostly arbuscular mycorrhizal trees, bulk litter decay rates were strongly dependent on seasonal water availability. Both measures of decomposition increased with forest age, as did the frequency of termite-mediated wood decay. Taken together, our results demonstrate that soils and forest age exert strong control over decomposition dynamics in these tropical dry forests, either directly through effects on microclimate and nutrients, or indirectly by affecting tree and microbial community composition and traits, such as litter quality.

A field-to-desktop toolchain for X-ray CT densitometry enables tree ring analysis.

PubMed

De Mil, Tom; Vannoppen, Astrid; Beeckman, Hans; Van Acker, Joris; Van den Bulcke, Jan

2016-06-01

Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Environment and paleoecology of a 12 ka mid-North American Younger Dryas forest chronicled in tree rings

USGS Publications Warehouse

Panyushkina, Irina P.; Leavitt, Steven W.; Thompson, Todd A.; Schneider, Allan F.; Lange, Todd

2008-01-01

Until now, availability of wood from the Younger Dryas abrupt cooling event (YDE) in N. America ca. 12.9 to 11.6 ka has been insufficient to develop high-resolution chronologies for refining our understanding of YDE conditions. Here we present a multi-proxy tree-ring chronology (ring widths, “events” evidenced by microanatomy and macro features, stable isotopes) from a buried black spruce forest in the Great Lakes area (Liverpool East site), spanning 116 yr at ca. 12,000 cal yr BP. During this largely cold and wet period, the proxies convey a coherent and precise forest history including frost events, tilting, drowning and burial in estuarine sands as the Laurentide Ice Sheet deteriorated. In the middle of the period, a short mild interval appears to have launched the final and largest episode of tree recruitment. Ultimately the tops of the trees were sheared off after death, perhaps by wind-driven ice floes, culminating an interval of rising water and sediment deposition around the base of the trees. Although relative influences of the continental ice sheet and local effects from ancestral Lake Michigan are indeterminate, the tree-ring proxies provide important insight into environment and ecology of a N. American YDE boreal forest stand.

Magnetic record associated with tree ring density: Possible climate proxy

PubMed Central

Kletetschka, Gunther; Pruner, Petr; Venhodova, Daniela; Kadlec, Jaroslav

2007-01-01

A magnetic signature of tree rings was tested as a potential paleo-climatic indicator. We examined wood from sequoia tree, located in Mountain Home State Forest, California, whose tree ring record spans over the period 600 – 1700 A.D. We measured low and high-field magnetic susceptibility, the natural remanent magnetization (NRM), saturation isothermal remanent magnetization (SIRM), and stability against thermal and alternating field (AF) demagnetization. Magnetic investigation of the 200 mm long sequoia material suggests that magnetic efficiency of natural remanence may be a sensitive paleoclimate indicator because it is substantially higher (in average >1%) during the Medieval Warm Epoch (700–1300 A.D.) than during the Little Ice Age (1300–1850 A.D.) where it is <1%. Diamagnetic behavior has been noted to be prevalent in regions with higher tree ring density. The mineralogical nature of the remanence carrier was not directly detected but maghemite is suggested due to low coercivity and absence of Verwey transition. Tree ring density, along with the wood's magnetic remanence efficiency, records the Little Ice Age (LIA) well documented in Europe. Such a record suggests that the European LIA was a global phenomenon. Magnetic analysis of the thermal stability reveals the blocking temperatures near 200 degree C. This phenomenon suggests that the remanent component in this tree may be thermal in origin and was controlled by local thermal condition. PMID:17381844

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm.

PubMed

Majumdar, Satya N

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm

NASA Astrophysics Data System (ADS)

Majumdar, Satya N.

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Considering Student Retention as a Complex System: A Possible Way forward for Enhancing Student Retention

ERIC Educational Resources Information Center

Forsman, Jonas; van den Bogaard, Maartje; Linder, Cedric; Fraser, Duncan

2015-01-01

This study uses multilayer minimum spanning tree analysis to develop a model for student retention from a complex system perspective, using data obtained from first-year engineering students at a large well-regarded institution in the European Union. The results show that the elements of the system of student retention are related to one another…

Correlation networks among currencies

NASA Astrophysics Data System (ADS)

Mizuno, Takayuki; Takayasu, Hideki; Takayasu, Misako

2006-05-01

By analyzing the foreign exchange market data of various currencies, we derive a hierarchical taxonomy of currencies constructing minimal-spanning trees. Clustered structure of the currencies and the key currency in each cluster are found. The clusters match nicely with the geographical regions of corresponding countries in the world such as Asia or East Europe, the key currencies are generally given by major economic countries as expected.

History and current condition of longleaf pine in the Southern United States

Treesearch

Christopher M. Oswalt; Jason A. Cooper; Dale G. Brockway; Horace W. Brooks; Joan L. Walker; Kristina F. Connor; Sonja N. Oswalt; Roger C. Conner

2012-01-01

Longleaf pine (Pinus palustris Mill.) was once one of the most ecologically important tree species in the Southern United States. Longleaf pine and its accompanying forest ecosystems covered vast swaths of the Southern United States, spanning an estimated 92 million acres. Although once one of the most extensive forest ecosystems in North America, only a fraction of...

Predicting surface fuel models and fuel metrics using lidar and CIR imagery in a dense mixed conifer forest

Treesearch

Marek K. Jakubowksi; Qinghua Guo; Brandon Collins; Scott Stephens; Maggi Kelly

2013-01-01

We compared the ability of several classification and regression algorithms to predict forest stand structure metrics and standard surface fuel models. Our study area spans a dense, topographically complex Sierra Nevada mixed-conifer forest. We used clustering, regression trees, and support vector machine algorithms to analyze high density (average 9 pulses/m

What tree-ring reconstruction tells us about conifer defoliator outbreaks

Treesearch

Ann M. Lynch

2012-01-01

Our ability to understand the dynamics of forest insect outbreaks is limited by the lack of long-term data describing the temporal and spatial trends of outbreaks, the size and long life span of host plants, and the impracticability of manipulative experiments at relevant temporal and spatial scales. Population responses can be studied across varying site and stand...

Dynamics of a temperate deciduous forest under landscape-scale management: Implications for adaptability to climate change

Treesearch

Matthew G. Olson; Benjamin O. Knapp; John M. Kabrick

2017-01-01

Landscape forest management is an approach to meeting diverse objectives that collectively span multiple spatial scales. It is critical that we understand the long-term effects of landscape management on the structure and composition of forest tree communities to ensure that these practices are sustainable. Furthermore, it is increasingly important to also consider...

Development of forest regeneration imputation models using permanent plots in Oregon and Washington

Treesearch

Karin Kralicek; Andrew Sánchez Meador; Leah Rathbun

2015-01-01

Imputation models were developed and tested to estimate tree regeneration on Forest Service land in Oregon and Washington. The models were based on Forest Inventory and Analysis and Pacific Northwest Regional NFS Monitoring data. The data was processed into sets of tables containing estimates of regeneration by broad plant associations and spanning a large variety in...

Growth data for 29 elevational transect years from the California study of ponderosa pine

Treesearch

M. Thompson Conkle

1973-01-01

Ponderosa pine progenies from parents restricted in latitude but spanning 7.000 feet of elevation show significant growth differences in plantations at low-, mid-, and high-elevation test sites. At low- and mid-elevation sites tree heights and diameters of progenies from high-elevation parents were the smallest; those from the low-elevation parents, intermediate; and...

Stock market network’s topological stability: Evidence from planar maximally filtered graph and minimal spanning tree

NASA Astrophysics Data System (ADS)

Yan, Xin-Guo; Xie, Chi; Wang, Gang-Jin

2015-08-01

We study the topological stability of stock market network by investigating the topological robustness, namely the ability of the network to resist structural or topological changes. The stock market network is extracted by minimal spanning tree (MST) and planar maximally filtered graph (PMFG). We find that the specific delisting thresholds of the listed companies exist in both MST and PMFG networks. In comparison with MST, PMFG provides more information and is better for the aim of exploring stock market network’s robustness. The PMFG before the US sub-prime crisis (i.e., from June 2005 to May 2007) has a stronger robustness against the intentional topological damage than the other two sub-periods (i.e., from June 2007 to May 2009 and from June 2009 to May 2011). We also find that the nonfractal property exists in MSTs of S&P 500, i.e., the highly connected nodes link with each other directly, which indicates that the MSTs are vulnerable to the removal of such important nodes. Moreover, the financial institutions and high technology companies are important in maintaining the stability of S&P 500 network.

Health and disease phenotyping in old age using a cluster network analysis.

PubMed

Valenzuela, Jesus Felix; Monterola, Christopher; Tong, Victor Joo Chuan; Ng, Tze Pin; Larbi, Anis

2017-11-15

Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree. We show, by way of a correspondence analysis between the two sets of clusters, that they correspond to coarse-grained and fine-grained structure of the network relationships. The clusters obtained from the minimum spanning tree mapped to various conceptual domains and corresponded to physiological and syndromic states. Hierarchical ordering of these clusters identified six common themes based on interactions with physiological systems and common underlying substrates of age-associated morbidity and disease chronicity, functional disability, and quality of life. These findings provide a starting point for indepth analyses of ageing that incorporate immunologic, metabolomic and proteomic biomarkers, and ultimately offer low-level-based typologies of healthy and unhealthy ageing.

Radial growth of Qilian juniper on the Northeast Tibetan Plateau and potential climate associations.

PubMed

Qin, Chun; Yang, Bao; Melvin, Thomas M; Fan, Zexin; Zhao, Yan; Briffa, Keith R

2013-01-01

There is controversy regarding the limiting climatic factor for tree radial growth at the alpine treeline on the northeastern Tibetan Plateau. In this study, we collected 594 increment cores from 331 trees, grouped within four altitude belts spanning the range 3550 to 4020 m.a.s.l. on a single hillside. We have developed four equivalent ring-width chronologies and shown that there are no significant differences in their growth-climate responses during 1956 to 2011 or in their longer-term growth patterns during the period AD 1110-2011. The main climate influence on radial growth is shown to be precipitation variability. Missing ring analysis shows that tree radial growth at the uppermost treeline location is more sensitive to climate variation than that at other elevations, and poor tree radial growth is particularly linked to the occurrence of serious drought events. Hence water limitation, rather than temperature stress, plays the pivotal role in controlling the radial growth of Sabina przewalskii Kom. at the treeline in this region. This finding contradicts any generalisation that tree-ring chronologies from high-elevation treeline environments are mostly indicators of temperature changes.

Radial Growth of Qilian Juniper on the Northeast Tibetan Plateau and Potential Climate Associations

PubMed Central

Qin, Chun; Yang, Bao; Melvin, Thomas M.; Fan, Zexin; Zhao, Yan; Briffa, Keith R.

2013-01-01

There is controversy regarding the limiting climatic factor for tree radial growth at the alpine treeline on the northeastern Tibetan Plateau. In this study, we collected 594 increment cores from 331 trees, grouped within four altitude belts spanning the range 3550 to 4020 m.a.s.l. on a single hillside. We have developed four equivalent ring-width chronologies and shown that there are no significant differences in their growth-climate responses during 1956 to 2011 or in their longer-term growth patterns during the period AD 1110–2011. The main climate influence on radial growth is shown to be precipitation variability. Missing ring analysis shows that tree radial growth at the uppermost treeline location is more sensitive to climate variation than that at other elevations, and poor tree radial growth is particularly linked to the occurrence of serious drought events. Hence water limitation, rather than temperature stress, plays the pivotal role in controlling the radial growth of Sabina przewalskii Kom. at the treeline in this region. This finding contradicts any generalisation that tree-ring chronologies from high-elevation treeline environments are mostly indicators of temperature changes. PMID:24244488

Simultaneous measurements of L- and S-band tree shadowing for space-Earth communications

NASA Technical Reports Server (NTRS)

Vogel, Wolfhard J.; Torrence, Geoffrey W.; Lin, Hsin P.

1995-01-01

We present results from simultaneous L- and S-Band slant-path fade measurements through trees. One circularly-polarized antenna was used at each end of the dual-frequency link to provide information on the correlation of tree shadowing at 1620 and 2500 MHz. Fades were measured laterally in the shadow region with 5 cm spacing. Fade differences between L- and S-Band had a normal distribution with low means and standard deviations from 5.2 to 7.5 dB. Spatial variations occurred with periods larger than 1-2 wavelengths. Swept measurements over 160 MHz spans showed that the stdv. of power as function of frequency increased from approximately 1-6 dB at locations with mean fades of 4 and 20 dB, respectively. At a 5 dB fade, the central 90% of fade slopes were within a range of 0.7 (1.9) dB/MHz at L-(S-) Band.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

PubMed Central

Parks, Matthew B; Wickett, Norman J; Alverson, Andrew J

2018-01-01

Abstract Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available. PMID:29040712

Phylogenomic analyses data of the avian phylogenomics project.

PubMed

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Narula, Nitish; Liu, Liang; Burt, Dave; Ellegren, Hans; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas Pius; Zhang, Guojie

2015-01-01

Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

Environmental Impact Research Program. Restoration of Problem Soil Materials at Corps of Engineers Construction Sites.

DTIC Science & Technology

1985-05-01

the total weight of a given population of organisms. Browse: Twigs or shoots, with or without attached leaves, of shrubs , trees, or woody vines ...volunteer woody plants, or the fsuccessful establishment, later on, of planted shrubs , trees, and ground covers. 184. Some problem soils absolutely...properly prepared seedbed. Woody plants, such as shrubs and trees, are established by seedling transplants. However, some woody species can be seeded

Clarifying the effects of dwarfing rootstock on vegetative and reproductive growth during tree development: a study on apple trees.

PubMed

Costes, E; García-Villanueva, E

2007-08-01

Despite the widespread use of dwarfing rootstocks in the fruit-tree industry, their impact on tree architectural development and possible role in the within-tree balance between growth and flowering are still poorly understood, in particular during the early years of growth. The present study addressed this question in apple trees, through a detailed analysis of shoot populations, i.e. both vegetative and flowering shoots, during tree development. Architectural databases were constructed for trees of two cultivars that were either own-rooted or grafted on dwarfing rootstock. Within-tree shoot demographics and annual shoot characteristics, i.e. their dimensions, number of laterals and flowering, were observed from the first to the fifth year of growth and compared among scion/root system combinations. Differences in axis demographics appeared among scion/root system combinations after the second year of growth. Differences were found (a) in the number of long axes and (b) the number of medium axes. Dwarfing rootstock reduced the total number of axes developed in a tree, and this reduction resulted from proportionally more medium axes and spurs than long axes. The life span of spurs was also shortened. These phenomena appeared after an increase in flowering that started in the second year of growth and involved both axillary and terminal positions. Flowering regularity was also increased in grafted trees. These results confirm that the number of long shoots and flowering potential depend on the cultivar. They indicate that tree architectural plasticity in response to its root system mainly derives from the number of medium shoots developed and follows priorities within the whole tree axis population. There was also evidence for dwarfing rootstock involvement in adjusting the flowering abundance and that differences in flowering occurrence take precedence over those regarding vegetative growth during tree development.

Symptoms and circumstances associated with bites by the brown tree snake (Colubridae: Boiga irregularis) on Guam

USGS Publications Warehouse

Fritts, T.H.; McCoid, M.J.; Haddock, R.L.

1994-01-01

A review of 94 cases of snakebite by the brown tree snake, Boiga irregularis, in Guam spanning a two year period shows a high proportion (80%) involve victims bitten while sleeping in their homes at night. Some bites apparently involve attempts to feed on small children. Of all children less than 1 yr old that were bitten in a two year period, infants 1-3 mo old comprised 82%. The symptoms exhibited by children are more severe than those experienced by adults. The snake is a rear-fanged (i.e., has enlarged and grooved teeth on the posterior maxillae) colubrid with a moderately large Duvernoy's gland.

Fermionic Field Theory for Trees and Forests

NASA Astrophysics Data System (ADS)

Caracciolo, Sergio; Jacobsen, Jesper Lykke; Saleur, Hubert; Sokal, Alan D.; Sportiello, Andrea

2004-08-01

We prove a generalization of Kirchhoff’s matrix-tree theorem in which a large class of combinatorial objects are represented by non-Gaussian Grassmann integrals. As a special case, we show that unrooted spanning forests, which arise as a q→0 limit of the Potts model, can be represented by a Grassmann theory involving a Gaussian term and a particular bilocal four-fermion term. We show that this latter model can be mapped, to all orders in perturbation theory, onto the N-vector model at N=-1 or, equivalently, onto the σ model taking values in the unit supersphere in R1|2. It follows that, in two dimensions, this fermionic model is perturbatively asymptotically free.

Instruction-matrix-based genetic programming.

PubMed

Li, Gang; Wang, Jin Feng; Lee, Kin Hong; Leung, Kwong-Sak

2008-08-01

In genetic programming (GP), evolving tree nodes separately would reduce the huge solution space. However, tree nodes are highly interdependent with respect to their fitness. In this paper, we propose a new GP framework, namely, instruction-matrix (IM)-based GP (IMGP), to handle their interactions. IMGP maintains an IM to evolve tree nodes and subtrees separately. IMGP extracts program trees from an IM and updates the IM with the information of the extracted program trees. As the IM actually keeps most of the information of the schemata of GP and evolves the schemata directly, IMGP is effective and efficient. Our experimental results on benchmark problems have verified that IMGP is not only better than those of canonical GP in terms of the qualities of the solutions and the number of program evaluations, but they are also better than some of the related GP algorithms. IMGP can also be used to evolve programs for classification problems. The classifiers obtained have higher classification accuracies than four other GP classification algorithms on four benchmark classification problems. The testing errors are also comparable to or better than those obtained with well-known classifiers. Furthermore, an extended version, called condition matrix for rule learning, has been used successfully to handle multiclass classification problems.

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

PubMed

Zaccaria, Simone; El-Kebir, Mohammed; Klau, Gunnar W; Raphael, Benjamin J

2018-04-16

Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.

Fault Tree in the Trenches, A Success Story

NASA Technical Reports Server (NTRS)

Long, R. Allen; Goodson, Amanda (Technical Monitor)

2000-01-01

Getting caught up in the explanation of Fault Tree Analysis (FTA) minutiae is easy. In fact, most FTA literature tends to address FTA concepts and methodology. Yet there seems to be few articles addressing actual design changes resulting from the successful application of fault tree analysis. This paper demonstrates how fault tree analysis was used to identify and solve a potentially catastrophic mechanical problem at a rocket motor manufacturer. While developing the fault tree given in this example, the analyst was told by several organizations that the piece of equipment in question had been evaluated by several committees and organizations, and that the analyst was wasting his time. The fault tree/cutset analysis resulted in a joint-redesign of the control system by the tool engineering group and the fault tree analyst, as well as bragging rights for the analyst. (That the fault tree found problems where other engineering reviews had failed was not lost on the other engineering groups.) Even more interesting was that this was the analyst's first fault tree which further demonstrates how effective fault tree analysis can be in guiding (i.e., forcing) the analyst to take a methodical approach in evaluating complex systems.

Variations in leaf growth parameters within the tree structure of adult Coffea arabica in relation to seasonal growth, water availability and air carbon dioxide concentration.

PubMed

Rakocevic, Miroslava; Matsunaga, Fabio Takeshi

2018-04-05

Dynamics in branch and leaf growth parameters, such as the phyllochron, duration of leaf expansion, leaf life span and bud mortality, determine tree architecture and canopy foliage distribution. We aimed to estimate leaf growth parameters in adult Arabica coffee plants based on leaf supporter axis order and position along the vertical profile, considering their modifications related to seasonal growth, air [CO2] and water availability. Growth and mortality of leaves and terminal buds of adult Arabica coffee trees were followed in two independent field experiments in two sub-tropical climate regions of Brazil, Londrina-PR (Cfa) and Jaguariúna-SP (Cwa). In the Cwa climate, coffee trees were grown under a FACE (free air CO2 enrichment) facility, where half of those had been irrigated. Plants were observed at a 15-30 d frequency for 1 year. Leaf growth parameters were estimated on five axes orders and expressed as functions of accumulated thermal time (°Cd per leaf). The phyllochron and duration of leaf expansion increased with axis order, from the seond to the fourth. The phyllochron and life span during the reduced vegetative seasonal growth were greater than during active growth. It took more thermal time for leaves from the first- to fourth-order axes to expand their blades under irrigation compared with rainfed conditions. The compensation effects of high [CO2] for low water availability were observed on leaf retention on the second and third axes orders, and duration of leaf expansion on the first- and fourth-order axes. The second-degree polynomials modelled leaf growth parameter distribution in the vertical tree profile, and linear regressions modelled the proportion of terminal bud mortality. Leaf growth parameters in coffee plants were determined by axis order. The duration of leaf expansion contributed to phyllochron determination. Leaf growth parameters varied according the position of the axis supporter along the vertical profile, suggesting an effect of axes age and micro-environmental light modulations.

Seeing Central African forests through their largest trees

PubMed Central

Bastin, J.-F.; Barbier, N.; Réjou-Méchain, M.; Fayolle, A.; Gourlet-Fleury, S.; Maniatis, D.; de Haulleville, T.; Baya, F.; Beeckman, H.; Beina, D.; Couteron, P.; Chuyong, G.; Dauby, G.; Doucet, J.-L.; Droissart, V.; Dufrêne, M.; Ewango, C.; Gillet, J.F.; Gonmadje, C.H.; Hart, T.; Kavali, T.; Kenfack, D.; Libalah, M.; Malhi, Y.; Makana, J.-R.; Pélissier, R.; Ploton, P.; Serckx, A.; Sonké, B.; Stevart, T.; Thomas, D.W.; De Cannière, C.; Bogaert, J.

2015-01-01

Large tropical trees and a few dominant species were recently identified as the main structuring elements of tropical forests. However, such result did not translate yet into quantitative approaches which are essential to understand, predict and monitor forest functions and composition over large, often poorly accessible territories. Here we show that the above-ground biomass (AGB) of the whole forest can be predicted from a few large trees and that the relationship is proved strikingly stable in 175 1-ha plots investigated across 8 sites spanning Central Africa. We designed a generic model predicting AGB with an error of 14% when based on only 5% of the stems, which points to universality in forest structural properties. For the first time in Africa, we identified some dominant species that disproportionally contribute to forest AGB with 1.5% of recorded species accounting for over 50% of the stock of AGB. Consequently, focusing on large trees and dominant species provides precise information on the whole forest stand. This offers new perspectives for understanding the functioning of tropical forests and opens new doors for the development of innovative monitoring strategies. PMID:26279193

Seeing Central African forests through their largest trees.

PubMed

Bastin, J-F; Barbier, N; Réjou-Méchain, M; Fayolle, A; Gourlet-Fleury, S; Maniatis, D; de Haulleville, T; Baya, F; Beeckman, H; Beina, D; Couteron, P; Chuyong, G; Dauby, G; Doucet, J-L; Droissart, V; Dufrêne, M; Ewango, C; Gillet, J F; Gonmadje, C H; Hart, T; Kavali, T; Kenfack, D; Libalah, M; Malhi, Y; Makana, J-R; Pélissier, R; Ploton, P; Serckx, A; Sonké, B; Stevart, T; Thomas, D W; De Cannière, C; Bogaert, J

2015-08-17

Large tropical trees and a few dominant species were recently identified as the main structuring elements of tropical forests. However, such result did not translate yet into quantitative approaches which are essential to understand, predict and monitor forest functions and composition over large, often poorly accessible territories. Here we show that the above-ground biomass (AGB) of the whole forest can be predicted from a few large trees and that the relationship is proved strikingly stable in 175 1-ha plots investigated across 8 sites spanning Central Africa. We designed a generic model predicting AGB with an error of 14% when based on only 5% of the stems, which points to universality in forest structural properties. For the first time in Africa, we identified some dominant species that disproportionally contribute to forest AGB with 1.5% of recorded species accounting for over 50% of the stock of AGB. Consequently, focusing on large trees and dominant species provides precise information on the whole forest stand. This offers new perspectives for understanding the functioning of tropical forests and opens new doors for the development of innovative monitoring strategies.

Seasonal variations of isoprene emissions from deciduous trees

NASA Astrophysics Data System (ADS)

Xiaoshan, Zhang; Yujing, Mu; Wenzhi, Song; Yahui, Zhuang

Isoprene emission fluxes were investigated for 12 tree species in and around Beijing city. Bag-enclosure method was used to collect the air sample and GC-PID was used to directly analyze isoprene. Ginkgo and Magnolia denudata had negligible isoprene emissions, while significant emissions were observed for Platanus orientalis, Pendula loud, Populus simonii, and Salix matsudana koidz, and other remaining trees showed no sign of isoprene emission. Variations in isoprene emission with changes in light, temperature and season were investigated for Platanus orientalis and Pendula loud. Isoprene emission rates strongly depended on light, temperature and leaf age. The maximum emission rates for the two trees were observed in summer with values of about 232 and 213 μg g -1 dw h -1, respectively. The measured emission fluxes were used to evaluate "Guenther" emission algorithm. The emission fluxes predicted by the algorithm were in relatively good agreement with field measurements. However, there were large differences for the calculated median emission factors during spring, summer and fall. The 25-75 percentiles span of the emission factor data sets ranged from -33 to +15% of the median values.

Increase of radiocarbon concentration in tree rings from Kujawy (SE Poland) around AD 774-775

NASA Astrophysics Data System (ADS)

Rakowski, Andrzej Z.; Krąpiec, Marek; Huels, Mathias; Pawlyta, Jacek; Dreves, Alexander; Meadows, John

2015-10-01

Evidence of a rapid increase in atmospheric radiocarbon (14C) content in AD 774-775 was presented by Miyake et al. (2012), who observed an increase of about 12‰ in the 14C content in annual tree rings from Japanese cedar. Usoskin et al. (2013) report a similar 14C spike in German oak, and attribute it to exceptional solar activity. If this phenomenon is global in character, such rapid changes in 14C concentration may affect the accuracy of calibrated dates, as the existing calibration curve is composed mainly of decadal samples. Single-year samples of dendro-chronologically dated tree rings of deciduous oak (Quercus robur) from Kujawy, a village near Krakow (SE Poland), spanning the years AD 765-796, were collected and their 14C content was measured using the AMS system in the Leibniz Laboratory. The results clearly show a rapid increase of 9.2 ± 2.1‰ in the 14C concentration in tree rings between AD 774 and AD 775, with maximum Δ14C = 4.1 ± 2.3‰ noted in AD 776.

Improved representation of plant functional types and physiology in the Joint UK Land Environment Simulator (JULES v4.2) using plant trait information

NASA Astrophysics Data System (ADS)

Harper, Anna B.; Cox, Peter M.; Friedlingstein, Pierre; Wiltshire, Andy J.; Jones, Chris D.; Sitch, Stephen; Mercado, Lina M.; Groenendijk, Margriet; Robertson, Eddy; Kattge, Jens; Bönisch, Gerhard; Atkin, Owen K.; Bahn, Michael; Cornelissen, Johannes; Niinemets, Ülo; Onipchenko, Vladimir; Peñuelas, Josep; Poorter, Lourens; Reich, Peter B.; Soudzilovskaia, Nadjeda A.; van Bodegom, Peter

2016-07-01

Dynamic global vegetation models are used to predict the response of vegetation to climate change. They are essential for planning ecosystem management, understanding carbon cycle-climate feedbacks, and evaluating the potential impacts of climate change on global ecosystems. JULES (the Joint UK Land Environment Simulator) represents terrestrial processes in the UK Hadley Centre family of models and in the first generation UK Earth System Model. Previously, JULES represented five plant functional types (PFTs): broadleaf trees, needle-leaf trees, C3 and C4 grasses, and shrubs. This study addresses three developments in JULES. First, trees and shrubs were split into deciduous and evergreen PFTs to better represent the range of leaf life spans and metabolic capacities that exists in nature. Second, we distinguished between temperate and tropical broadleaf evergreen trees. These first two changes result in a new set of nine PFTs: tropical and temperate broadleaf evergreen trees, broadleaf deciduous trees, needle-leaf evergreen and deciduous trees, C3 and C4 grasses, and evergreen and deciduous shrubs. Third, using data from the TRY database, we updated the relationship between leaf nitrogen and the maximum rate of carboxylation of Rubisco (Vcmax), and updated the leaf turnover and growth rates to include a trade-off between leaf life span and leaf mass per unit area.Overall, the simulation of gross and net primary productivity (GPP and NPP, respectively) is improved with the nine PFTs when compared to FLUXNET sites, a global GPP data set based on FLUXNET, and MODIS NPP. Compared to the standard five PFTs, the new nine PFTs simulate a higher GPP and NPP, with the exception of C3 grasses in cold environments and C4 grasses that were previously over-productive. On a biome scale, GPP is improved for all eight biomes evaluated and NPP is improved for most biomes - the exceptions being the tropical forests, savannahs, and extratropical mixed forests where simulated NPP is too high. With the new PFTs, the global present-day GPP and NPP are 128 and 62 Pg C year-1, respectively. We conclude that the inclusion of trait-based data and the evergreen/deciduous distinction has substantially improved productivity fluxes in JULES, in particular the representation of GPP. These developments increase the realism of JULES, enabling higher confidence in simulations of vegetation dynamics and carbon storage.

Coordinated changes in photosynthesis, water relations and leaf nutritional traits of canopy trees along a precipitation gradient in lowland tropical forest.

PubMed

Santiago, Louis S; Kitajima, Kaoru; Wright, S Joseph; Mulkey, Stephen S

2004-05-01

We investigated leaf physiological traits of dominant canopy trees in four lowland Panamanian forests with contrasting mean annual precipitation (1,800, 2,300, 3,100 and 3,500 mm). There was near complete turn-over of dominant canopy tree species among sites, resulting in greater dominance of evergreen species with long-lived leaves as precipitation increased. Mean structural and physiological traits changed along this gradient as predicted by cost-benefit theories of leaf life span. Nitrogen content per unit mass (Nmass) and light- and CO2-saturated photosynthetic rates per unit mass (Pmass) of upper canopy leaves decreased with annual precipitation, and these changes were partially explained by increasing leaf thickness and decreasing specific leaf area (SLA). Comparison of 1,800 mm and 3,100 mm sites, where canopy access was available through the use of construction cranes, revealed an association among extended leaf longevity, greater structural defense, higher midday leaf water potential, and lower Pmass, Nmass, and SLA at wetter sites. Shorter leaf life spans and more enriched foliar delta15N values in drier sites suggest greater resorption and re-metabolism of leaf N in drier forest. Greater dominance of short-lived leaves with relatively high Pmass in drier sites reflects a strategy to maximize photosynthesis when water is available and to minimize water loss and respiration costs during rainless periods. Overall, our study links coordinated change in leaf functional traits that affect productivity and nutrient cycling to seasonality in lowland tropical forests. Copyright 2004 Springer-Verlag

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

PubMed Central

2010-01-01

Background The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations. PMID:20525185

The weight distribution of coarse particulate organic matter exported from an alpine headwater stream

NASA Astrophysics Data System (ADS)

Turowski, Jens; Badoux, Alexandre; Bunte, Kristin; Rickli, Christian; Federspiel, Nicole

2013-04-01

Coarse particulate organic matter (CPOM) spans sizes from 1 mm particles, weighing less than 1 mg, to large logs and whole trees, which may weigh several hundred kilograms. Different size and weight classes play different roles in stream environments, from being the prime source of energy in stream ecosystems to macroscopically determining channel morphology and local hydraulics. We show that a single scaling exponent can describe the weight distribution of CPOM transported in a mountain stream. This exponent is independent of discharge and valid for particle weights spanning almost seven orders of magnitude. Together with a rating curve of CPOM transport rates with discharge, we discuss the importance of the scaling exponent for measuring strategies, natural hazard mitigation and ecosystems.

Stand- and landscape-scale selection of large trees by fishers in the Rocky Mountains of Montana and Idaho

Treesearch

Michael K. Schwartz; Nicholas J. DeCesare; Benjamin S. Jimenez; Jeffrey P. Copeland; Wayne E. Melquist

2013-01-01

The fisher (Pekania pennanti; formerly known as Martes pennanti) is a North American endemic mustelid with a geographic distribution that spans much of the boreal forests of North America. In the Northern Rocky Mountain (NRM) fishers have been the focus of Endangered Species Act (ESA) listing decisions. Habitat studies of West Coast fishers in California have...

Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback

PubMed Central

Sánchez-Rangel, Diana; Hernández-Domínguez, Eric; Pérez-Torres, Claudia-Anahí; Ortiz-Castro, Randy; Villafán, Emanuel; Alonso-Sánchez, Alexandro; Rodríguez-Haas, Benjamín; López-Buenfil, Abel; García-Avila, Clemente; Ramírez-Pool, José-Abrahán

2017-01-01

ABSTRACT Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes. PMID:28860245

Water availability limits tree productivity, carbon stocks, and carbon residence time in mature forests across the western US

NASA Astrophysics Data System (ADS)

Berner, Logan T.; Law, Beverly E.; Hudiburg, Tara W.

2017-01-01

Water availability constrains the structure and function of terrestrial ecosystems and is projected to change in many parts of the world over the coming century. We quantified the response of tree net primary productivity (NPP), live biomass (BIO), and mean carbon residence time (CRT = BIO / NPP) to spatial variation in water availability in the western US. We used forest inventory measurements from 1953 mature stands (> 100 years) in Washington, Oregon, and California (WAORCA) along with satellite and climate data sets covering the western US. We summarized forest structure and function in both domains along a 400 cm yr-1 hydrologic gradient, quantified with a climate moisture index (CMI) based on the difference between precipitation and reference evapotranspiration summed over the water year (October-September) and then averaged annually from 1985 to 2014 (CMIwy). Median NPP, BIO, and CRT computed at 10 cm yr-1 intervals along the CMIwy gradient increased monotonically with increasing CMIwy across both WAORCA (rs = 0.93-0.96, p < 0.001) and the western US (rs = 0.93-0.99, p < 0.001). Field measurements from WAORCA showed that median NPP increased from 2.2 to 5.6 Mg C ha-1 yr-1 between the driest and wettest 5 % of sites, while BIO increased from 26 to 281 Mg C ha-1 and CRT increased from 11 to 49 years. The satellite data sets revealed similar changes over the western US, though these data sets tended to plateau in the wettest areas, suggesting that additional efforts are needed to better quantify NPP and BIO from satellites in high-productivity, high-biomass forests. Our results illustrate that long-term average water availability is a key environmental constraint on tree productivity, carbon storage, and carbon residence time in mature forests across the western US, underscoring the need to assess potential ecosystem response to projected warming and drying over the coming century.

On estimation in k-tree sampling

Treesearch

Christoph Kleinn; Frantisek Vilcko

2007-01-01

The plot design known as k-tree sampling involves taking the k nearest trees from a selected sample point as sample trees. While this plot design is very practical and easily applied in the field for moderate values of k, unbiased estimation remains a problem. In this article, we give a brief introduction to the...

Mathematical form models of tree trunks

Treesearch

Rudolfs Ozolins

2000-01-01

Assortment structure analysis of tree trunks is a characteristic and proper problem that can be solved by using mathematical modeling and standard computer programs. Mathematical form model of tree trunks consists of tapering curve equations and their parameters. Parameters for nine species were obtained by processing measurements of 2,794 model trees and studying the...

Phase synchronization based minimum spanning trees for analysis of financial time series with nonlinear correlations

NASA Astrophysics Data System (ADS)

Radhakrishnan, Srinivasan; Duvvuru, Arjun; Sultornsanee, Sivarit; Kamarthi, Sagar

2016-02-01

The cross correlation coefficient has been widely applied in financial time series analysis, in specific, for understanding chaotic behaviour in terms of stock price and index movements during crisis periods. To better understand time series correlation dynamics, the cross correlation matrices are represented as networks, in which a node stands for an individual time series and a link indicates cross correlation between a pair of nodes. These networks are converted into simpler trees using different schemes. In this context, Minimum Spanning Trees (MST) are the most favoured tree structures because of their ability to preserve all the nodes and thereby retain essential information imbued in the network. Although cross correlations underlying MSTs capture essential information, they do not faithfully capture dynamic behaviour embedded in the time series data of financial systems because cross correlation is a reliable measure only if the relationship between the time series is linear. To address the issue, this work investigates a new measure called phase synchronization (PS) for establishing correlations among different time series which relate to one another, linearly or nonlinearly. In this approach the strength of a link between a pair of time series (nodes) is determined by the level of phase synchronization between them. We compare the performance of phase synchronization based MST with cross correlation based MST along selected network measures across temporal frame that includes economically good and crisis periods. We observe agreement in the directionality of the results across these two methods. They show similar trends, upward or downward, when comparing selected network measures. Though both the methods give similar trends, the phase synchronization based MST is a more reliable representation of the dynamic behaviour of financial systems than the cross correlation based MST because of the former's ability to quantify nonlinear relationships among time series or relations among phase shifted time series.

Constructing Student Problems in Phylogenetic Tree Construction.

ERIC Educational Resources Information Center

Brewer, Steven D.

Evolution is often equated with natural selection and is taught from a primarily functional perspective while comparative and historical approaches, which are critical for developing an appreciation of the power of evolutionary theory, are often neglected. This report describes a study of expert problem-solving in phylogenetic tree construction.…

Thread Graphs, Linear Rank-Width and Their Algorithmic Applications

NASA Astrophysics Data System (ADS)

Ganian, Robert

The introduction of tree-width by Robertson and Seymour [7] was a breakthrough in the design of graph algorithms. A lot of research since then has focused on obtaining a width measure which would be more general and still allowed efficient algorithms for a wide range of NP-hard problems on graphs of bounded width. To this end, Oum and Seymour have proposed rank-width, which allows the solution of many such hard problems on a less restricted graph classes (see e.g. [3,4]). But what about problems which are NP-hard even on graphs of bounded tree-width or even on trees? The parameter used most often for these exceptionally hard problems is path-width, however it is extremely restrictive - for example the graphs of path-width 1 are exactly paths.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.

Combining qualitative and quantitative operational research methods to inform quality improvement in pathways that span multiple settings.

PubMed

Crowe, Sonya; Brown, Katherine; Tregay, Jenifer; Wray, Jo; Knowles, Rachel; Ridout, Deborah A; Bull, Catherine; Utley, Martin

2017-08-01

Improving integration and continuity of care across sectors within resource constraints is a priority in many health systems. Qualitative operational research methods of problem structuring have been used to address quality improvement in services involving multiple sectors but not in combination with quantitative operational research methods that enable targeting of interventions according to patient risk. We aimed to combine these methods to augment and inform an improvement initiative concerning infants with congenital heart disease (CHD) whose complex care pathway spans multiple sectors. Soft systems methodology was used to consider systematically changes to services from the perspectives of community, primary, secondary and tertiary care professionals and a patient group, incorporating relevant evidence. Classification and regression tree (CART) analysis of national audit datasets was conducted along with data visualisation designed to inform service improvement within the context of limited resources. A 'Rich Picture' was developed capturing the main features of services for infants with CHD pertinent to service improvement. This was used, along with a graphical summary of the CART analysis, to guide discussions about targeting interventions at specific patient risk groups. Agreement was reached across representatives of relevant health professions and patients on a coherent set of targeted recommendations for quality improvement. These fed into national decisions about service provision and commissioning. When tackling complex problems in service provision across multiple settings, it is important to acknowledge and work with multiple perspectives systematically and to consider targeting service improvements in response to confined resources. Our research demonstrates that applying a combination of qualitative and quantitative operational research methods is one approach to doing so that warrants further consideration. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

TimeTree2: species divergence times on the iPhone.

PubMed

Kumar, Sudhir; Hedges, S Blair

2011-07-15

Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K-12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature. TimeTree2 is accessible from the URL http://www.timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo).

The coalescent of a sample from a binary branching process.

PubMed

Lambert, Amaury

2018-04-25

At time 0, start a time-continuous binary branching process, where particles give birth to a single particle independently (at a possibly time-dependent rate) and die independently (at a possibly time-dependent and age-dependent rate). A particular case is the classical birth-death process. Stop this process at time T>0. It is known that the tree spanned by the N tips alive at time T of the tree thus obtained (called a reduced tree or coalescent tree) is a coalescent point process (CPP), which basically means that the depths of interior nodes are independent and identically distributed (iid). Now select each of the N tips independently with probability y (Bernoulli sample). It is known that the tree generated by the selected tips, which we will call the Bernoulli sampled CPP, is again a CPP. Now instead, select exactly k tips uniformly at random among the N tips (a k-sample). We show that the tree generated by the selected tips is a mixture of Bernoulli sampled CPPs with the same parent CPP, over some explicit distribution of the sampling probability y. An immediate consequence is that the genealogy of a k-sample can be obtained by the realization of k random variables, first the random sampling probability Y and then the k-1 node depths which are iid conditional on Y=y. Copyright © 2018. Published by Elsevier Inc.

Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East.

PubMed

Kaniewski, David; Van Campo, Elise; Boiy, Tom; Terral, Jean-Frédéric; Khadari, Bouchaïb; Besnard, Guillaume

2012-11-01

Our knowledge of the origins of olive tree domestication in the Middle East and on the processes governing its extension and persistence in different vegetation types from prehistory through antiquity to modern times derives from diverse sources, spanning the biological sciences to the humanities. Nonetheless, it lacks a robust overview that may lead to floating interpretations. This is especially true in the Middle East, considered as the cradle of agriculture, and where the evolutionary history of this emblematic tree is intertwined with that of civilizations. Olive fruit, oil and wood have been, since Prehistoric times, characteristic products of the lands bordering the Mediterranean Sea. In the domestic economy of these countries, the olive tree gradually became a traditional tree crop since the first oil extraction, through the emergence of regional commerce that accompanied the rise and fall of early Near-Middle Eastern urbanism, until the development of modern trade, with an oil production estimated at circa 3000000 tons per year. The rising importance of the olive tree in human life has turned the tree into an endless source of fascination in the Aegean and Eastern Mediterranean, a symbol and a sacred tree, widely cited in the Bibles, the Koran, and in ancient literature. Here we argue that advances in radiocarbon chronology, palaeobotany, genetics, and archaeology-history have profoundly refined the history of olive trees in the Middle East. This review shows that the heartland of primary olive domestication must be enlarged to the Levant and not only focus on the Jordan Valley. The domestication of the olive tree is a long and ongoing process, linked to the early production of oil and the development of the olive trade. We also suggest that the olive tree became a particular icon, a sacred tree, during the Biblical period in the Levant. © 2012 The Author. Biological Reviews © 2012 Cambridge Philosophical Society.

The Tree-Ring Mercury Record of Gold Mining in the Klondike, Central Yukon Territory

NASA Astrophysics Data System (ADS)

Clackett, S.; Porter, T. J.; Lehnherr, I.

2016-12-01

Mercury (Hg) is an atmospherically mixed pollutant of global concern with the potential to become toxic methyl-Hg (MeHg) is some environments. Accurate projections of future health impacts caused by Hg pollution will partly depend on changes in the atmospheric Hg pool, but knowledge of natural Hg variability is limited by a lack of long term monitoring data, which precludes a robust analysis of how it may evolve in the future. Natural archives such as lake sediments, ice cores and tree-rings have the potential to fill this knowledge gap. Tree-rings may be ideally suited for this purpose since they are annually resolved, they span multiple centuries in some areas, and cover large portions of the Earth's surface. Few studies have evaluated tree-ring Hg, and generally agree tree-rings are a passive archive for local Hg emissions. However, further studies are needed to validate this hypothesis. An ideal site to test this proxy is Bear Creek in the Klondike where the Hg amalgamation method was used during the period 1918-1966 to recover fine gold from placer ore. Gaseous Hg was lost to the local environment during operations, as is confirmed by high soil Hg concentrations at the site today. Local trees would have been exposed to the elevated Hg emissions. We measured tree-ring Hg at Bear Creek to determine if historical Hg trends are preserved. Our preliminary results from a single tree reveal that: (1) peak tree-ring Hg coincides with Bear Creek operations; (2) the lowest tree-ring Hg is observed during the pre-industrial control period (1870-1880); and (3) post-Bear Creek operations (1970-2010) coincides with intermediate tree-ring Hg levels, presumably due to higher Hg global backgrounds in recent decades. Additional trees are being analysed to determine if this result is robust, and will provide important insights on the reliability of this proxy for reconstructing long-term atmospheric Hg at local and potentially broader spatial scales.

Photosynthetic capacity peaks at intermediate size in temperate deciduous trees.

PubMed

Thomas, Sean C

2010-05-01

Studies of age-related changes in leaf functional biology have generally been based on dichotomous comparisons of young and mature individuals (e.g., saplings and mature canopy trees), with little data available to describe changes through the entire ontogeny of trees, particularly of broadleaf angiosperms. Leaf-level gas-exchange and morphological parameters were quantified in situ in the upper canopy of trees acclimated to high light conditions, spanning a wide range of ontogenetic stages from saplings (approximately 1 cm in stem diameter) to trees >60 cm d.b.h. and nearing their maximum lifespan, in three temperate deciduous tree species in central Ontario, Canada. Traits associated with growth performance, including leaf photosynthetic capacity (expressed on either an area, mass or leaf N basis), stomatal conductance, leaf size and leaf N content, generally showed a unimodal ('hump-shaped') pattern, with peak values at an intermediate ontogenetic stage. In contrast, leaf mass per area (LMA) and related morphological parameters (leaf thickness, leaf tissue density, leaf C content) increased monotonically with tree size, as did water-use efficiency; these monotonic relationships were well described by simple allometric functions of the form Y = aX(b). For traits showing unimodal patterns, tree size corresponding to the trait maximum differed markedly among traits: all three species showed a similar pattern in which the peak for leaf size occurred in trees approximately 2-6 cm d.b.h., followed by leaf chemical traits and photosynthetic capacity on a mass or leaf N basis and finally by photosynthetic capacity on a leaf area basis, which peaked approximately at the size of reproductive onset. It is argued that ontogenetic increases in photosynthetic capacity and related traits early in tree ontogeny are general among relatively shade-tolerant tree species that have a low capacity for leaf-level acclimation, as are declines in this set of traits late in tree ontogeny.

Cluster analyses of 20th century growth patterns in high elevation Great Basin bristlecone pine in the Snake Mountain Range, Nevada, USA

NASA Astrophysics Data System (ADS)

Tran, T. J.; Bruening, J. M.; Bunn, A. G.; Salzer, M. W.; Weiss, S. B.

2015-12-01

Great Basin bristlecone pine (Pinus longaeva) is a useful climate proxy because of the species' long lifespan (up to 5000 years) and the climatic sensitivity of its annually-resolved rings. Past studies have shown that growth of individual trees can be limited by temperature, soil moisture, or a combination of the two depending on biophysical setting at the scale of tens of meters. We extend recent research suggesting that trees vary in their growth response depending on their position on the landscape to analyze how growth patterns vary over time. We used hierarchical cluster analysis to examine the growth of 52 bristlecone pine trees near the treeline of Mount Washington, Nevada, USA. We classified growth of individual trees over the instrumental climate record into one of two possible scenarios: trees belonging to a temperature-sensitive cluster and trees belonging to a precipitation-sensitive cluster. The number of trees in the precipitation-sensitive cluster outnumbered the number of trees in the temperature-sensitive cluster, with trees in colder locations belonging to the temperature-sensitive cluster. When we separated the temporal range into two sections (1895-1949 and 1950-2002) spanning the length of the instrumental climate record, we found that most of the 52 trees remained loyal to their cluster membership (e.g., trees in the temperature-sensitive cluster in 1895-1949 were also in the temperature sensitive cluster in 1950-2002), though not without exception. Of those trees that do not remain consistent in cluster membership, the majority changed from temperature-sensitive to precipitation-sensitive as time progressed. This could signal a switch from temperature limitation to water limitation with warming climate. We speculate that topographic complexity in high mountain environments like Mount Washington might allow for climate refugia where growth response could remain constant over the Holocene.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

PubMed

Springer, Mark S; Gatesy, John

2018-02-26

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful enough to infer the correct species tree for difficult phylogenetic problems in the anomaly zone, where concatenation is expected to fail because of ILS, then there should be a decreasing probability of inferring the correct species tree using longer loci with many intralocus recombination breakpoints (i.e., increased levels of concatenation).

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets

PubMed Central

Springer, Mark S.; Gatesy, John

2018-01-01

Summary coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset—the ‘recombination ratchet’—is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d’etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful enough to infer the correct species tree for difficult phylogenetic problems in the anomaly zone, where concatenation is expected to fail because of ILS, then there should be a decreasing probability of inferring the correct species tree using longer loci with many intralocus recombination breakpoints (i.e., increased levels of concatenation). PMID:29495400

STUDYING FOREST ROOT SYSTEMS - AN OVERVIEW OF METHODOLOGICAL PROBLEMS

EPA Science Inventory

The study of tree root systems is central to understanding forest ecosystem carbon and nutrient cycles, nutrient and water uptake, C allocation patterns by trees, soil microbial populations, adaptation of trees to stress, soil organic matter production, etc. Methodological probl...

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.

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.

Escape problem under stochastic volatility: The Heston model

NASA Astrophysics Data System (ADS)

Masoliver, Jaume; Perelló, Josep

2008-11-01

We solve the escape problem for the Heston random diffusion model from a finite interval of span L . We obtain exact expressions for the survival probability (which amounts to solving the complete escape problem) as well as for the mean exit time. We also average the volatility in order to work out the problem for the return alone regardless of volatility. We consider these results in terms of the dimensionless normal level of volatility—a ratio of the three parameters that appear in the Heston model—and analyze their form in several asymptotic limits. Thus, for instance, we show that the mean exit time grows quadratically with large spans while for small spans the growth is systematically slower, depending on the value of the normal level. We compare our results with those of the Wiener process and show that the assumption of stochastic volatility, in an apparently paradoxical way, increases survival and prolongs the escape time. We finally observe that the model is able to describe the main exit-time statistics of the Dow-Jones daily index.

Machine Learning Through Signature Trees. Applications to Human Speech.

ERIC Educational Resources Information Center

White, George M.

A signature tree is a binary decision tree used to classify unknown patterns. An attempt was made to develop a computer program for manipulating signature trees as a general research tool for exploring machine learning and pattern recognition. The program was applied to the problem of speech recognition to test its effectiveness for a specific…

Phylogenetic prediction of Alternaria leaf blight resistance in wild and cultivated species of carrots (Daucus, Apiaceae)

USDA-ARS?s Scientific Manuscript database

Plant scientists make inferences and predictions from phylogenetic trees to solve scientific problems. Crop losses due to disease damage is an important problem that many plant breeders would like to solve, so the ability to predict traits like disease resistance from phylogenetic trees derived from...

What shakes the FX tree? Understanding currency dominance, dependence, and dynamics (Keynote Address)

NASA Astrophysics Data System (ADS)

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

2005-05-01

There is intense interest in understanding the stochastic and dynamical properties of the global Foreign Exchange (FX) market, whose daily transactions exceed one trillion US dollars. This is a formidable task since the FX market is characterized by a web of fluctuating exchange rates, with subtle inter-dependencies which may change in time. In practice, traders talk of particular currencies being 'in play' during a particular period of time -- yet there is no established machinery for detecting such important information. Here we apply the construction of Minimum Spanning Trees (MSTs) to the FX market, and show that the MST can capture important features of the global FX dynamics. Moreover, we show that the MST can help identify momentarily dominant and dependent currencies.

North Pacific decadal climate variability since 1661

USGS Publications Warehouse

Biondi, Franco; Gershunov, Alexander; Cayan, Daniel R.

2001-01-01

Climate in the North Pacific and North American sectors has experienced interdecadal shifts during the twentieth century. A network of recently developed tree-ring chronologies for Southern and Baja California extends the instrumental record and reveals decadal-scale variability back to 1661. The Pacific decadal oscillation (PDO) is closely matched by the dominant mode of tree-ring variability that provides a preliminary view of multiannual climate fluctuations spanning the past four centuries. The reconstructed PDO index features a prominent bidecadal oscillation, whose amplitude weakened in the late l700s to mid-1800s. A comparison with proxy records of ENSO suggests that the greatest decadal-scale oscillations in Pacific climate between 1706 and 1977 occurred around 1750, 1905, and 1947.

The Proposal of a Evolutionary Strategy Generating the Data Structures Based on a Horizontal Tree for the Tests

NASA Astrophysics Data System (ADS)

Żukowicz, Marek; Markiewicz, Michał

2016-09-01

The aim of the article is to present a mathematical definition of the object model, that is known in computer science as TreeList and to show application of this model for design evolutionary algorithm, that purpose is to generate structures based on this object. The first chapter introduces the reader to the problem of presenting data using the TreeList object. The second chapter describes the problem of testing data structures based on TreeList. The third one shows a mathematical model of the object TreeList and the parameters, used in determining the utility of structures created through this model and in evolutionary strategy, that generates these structures for testing purposes. The last chapter provides a brief summary and plans for future research related to the algorithm presented in the article.

Percolating Contact Subnetworks on the Edge of Isostaticity

DTIC Science & Technology

2011-01-01

pressure, and cyclic loading of photoelastic disks under constant vol- ume. D. M. Walker · A. Tordesillas (B) Department of Mathematics and Statistics ...Complex networks · Spanning trees · Force chains · Force cycles · Isostatic 1 Introduction Ioannis Vardoulakis and his collaborators brought soil ...57, 706–727 (2009) 2. Vardoulakis, I.: Shear-banding and liquefaction in granular mate- rials on the basis of a Cosserat continuum theory. Ingenieur

Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback.

PubMed

Ibarra-Laclette, Enrique; Sánchez-Rangel, Diana; Hernández-Domínguez, Eric; Pérez-Torres, Claudia-Anahí; Ortiz-Castro, Randy; Villafán, Emanuel; Alonso-Sánchez, Alexandro; Rodríguez-Haas, Benjamín; López-Buenfil, Abel; García-Avila, Clemente; Ramírez-Pool, José-Abrahán

2017-08-31

Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes. Copyright © 2017 Ibarra-Laclette et al.

Analyzing systemic risk using non-linear marginal expected shortfall and its minimum spanning tree

NASA Astrophysics Data System (ADS)

Song, Jae Wook; Ko, Bonggyun; Chang, Woojin

2018-02-01

The aim of this paper is to propose a new theoretical framework for analyzing the systemic risk using the marginal expected shortfall (MES) and its correlation-based minimum spanning tree (MST). At first, we develop two parametric models of MES with their closed-form solutions based on the Capital Asset Pricing Model. Our models are derived from the non-symmetric quadratic form, which allows them to consolidate the non-linear relationship between the stock and market returns. Secondly, we discover the evidences related to the utility of our models and the possible association in between the non-linear relationship and the emergence of severe systemic risk by considering the US financial system as a benchmark. In this context, the evolution of MES also can be regarded as a reasonable proxy of systemic risk. Lastly, we analyze the structural properties of the systemic risk using the MST based on the computed series of MES. The topology of MST conveys the presence of sectoral clustering and strong co-movements of systemic risk leaded by few hubs during the crisis. Specifically, we discover that the Depositories are the majority sector leading the connections during the Non-Crisis period, whereas the Broker-Dealers are majority during the Crisis period.

Scaffold explorer: an interactive tool for organizing and mining structure-activity data spanning multiple chemotypes.

PubMed

Agrafiotis, Dimitris K; Wiener, John J M

2010-07-08

We introduce Scaffold Explorer, an interactive tool that allows medicinal chemists to define hierarchies of chemical scaffolds and use them to explore their project data. Scaffold Explorer allows the user to construct a tree, where each node corresponds to a specific scaffold. Each node can have multiple children, each of which represents a more refined substructure relative to its parent node. Once the tree is defined, it can be mapped onto any collection of compounds and be used as a navigational tool to explore structure-activity relationships (SAR) across different chemotypes. The rich visual analytics of Scaffold Explorer afford the user a "bird's-eye" view of the chemical space spanned by a particular data set, map any physicochemical property or biological activity of interest onto the individual scaffold nodes, serve as an aggregator for the properties of the compounds represented by these nodes, and quickly distinguish promising chemotypes from less interesting or problematic ones. Unlike previous approaches, which focused on automated extraction and classification of scaffolds, the utility of the new tool rests on its interactivity and ability to accommodate the medicinal chemists' intuition by allowing the use of arbitrary substructures containing variable atoms, bonds, and/or substituents such as those employed in substructure search.

Local population extinction and vitality of an epiphytic lichen in fragmented old-growth forest.

PubMed

Ockinger, Erik; Nilsson, Sven G

2010-07-01

The population dynamics of organisms living in short-lived habitats will largely depend on the turnover of habitat patches. It has been suggested that epiphytes, whose host plants can be regarded as habitat patches, often form such patch-tracking populations. However, very little is known about the long-term fate of epiphyte individuals and populations. We estimated life span and assessed environmental factors influencing changes in vitality, fertility, abundance, and distribution of the epiphytic lichen species Lobaria pulmonaria on two spatial scales, individual trees and forest patches, over a period of approximately 10 years in 66 old-growth forest fragments. The lichen had gone extinct from 7 of the 66 sites (13.0%) where it was found 10 years earlier, even though the sites remained unchanged. The risk of local population extinction increased with decreasing population size. In contrast to the decrease in the number of occupied trees and sites, the mean area of the lichen per tree increased by 43.0%. The number of trees with fertile ramets of L. pulmonaria increased from 7 (approximately 1%) to 61 (approximately 10%) trees, and the number of forest fragments with fertile ramets increased from 4 to 23 fragments. The mean annual rate of L. pulmonaria extinction at the tree level was estimated to be 2.52%, translating into an expected lifetime of 39.7 years. This disappearance rate is higher than estimated mortality rates for potential host trees. The risk of extinction at the tree level was significantly positively related to tree circumference and differed between tree species. The probability of presence of fertile ramets increased significantly with local population size. Our results show a long expected lifetime of Lobaria pulmonaria ramets on individual trees and a recent increase in vitality, probably due to decreasing air pollution. The population is, however, declining slowly even though remaining stands are left uncut, which we interpret as an extinction debt.

Savanna tree density, herbivores, and the herbaceous community: bottom-up vs. top-down effects.

PubMed

Riginos, Corinna; Grace, James B

2008-08-01

Herbivores choose their habitats both to maximize forage intake and to minimize their risk of predation. For African savanna herbivores, the available habitats range in woody cover from open areas with few trees to dense, almost-closed woodlands. This variation in woody cover or density can have a number of consequences for herbaceous species composition, cover, and productivity, as well as for ease of predator detection and avoidance. Here, we consider two alternative possibilities: first, that tree density affects the herbaceous vegetation, with concomitant "bottom-up" effects on herbivore habitat preferences; or, second, that tree density affects predator visibility, mediating "top-down" effects of predators on herbivore habitat preferences. We sampled sites spanning a 10-fold range of tree densities in an Acacia drepanolobium-dominated savanna in Laikipia, Kenya, for variation in (1) herbaceous cover, composition, and species richness; (2) wild and domestic herbivore use; and (3) degree of visibility obstruction by the tree layer. We then used structural equation modeling to consider the potential influences that tree density may have on herbivores and herbaceous community properties. Tree density was associated with substantial variation in herbaceous species composition and richness. Cattle exhibited a fairly uniform use of the landscape, whereas wild herbivores, with the exception of elephants, exhibited a strong preference for areas of low tree density. Model results suggest that this was not a response to variation in herbaceous-community characteristics, but rather a response to the greater visibility associated with more open places. Elephants, in contrast, preferred areas with higher densities of trees, apparently because of greater forage availability. These results suggest that, for all but the largest species, top-down behavioral effects of predator avoidance on herbivores are mediated by tree density. This, in turn, appears to have cascading effects on the herbaceous vegetation. These results shed light on one of the major features of the "landscape of fear" in which African savanna herbivores exist.

Lianas always outperform tree seedlings regardless of soil nutrients: results from a long-term fertilization experiment.

PubMed

Pasquini, Sarah C; Wright, S Joseph; Santiago, Louis S

2015-07-01

Lianas are a prominent growth form in tropical forests, and there is compelling evidence that they are increasing in abundance throughout the Neotropics. While recent evidence shows that soil resources limit tree growth even in deep shade, the degree to which soil resources limit lianas in forest understories, where they coexist with trees for decades, remains unknown. Regardless, the physiological underpinnings of soil resource limitation in deeply shaded tropical habitats remain largely unexplored for either trees or lianas. Theory predicts that lianas should be more limited by soil resources than trees because they occupy the quick-return end of the "leaf economic spectrum," characterized by high rates of photosynthesis, high specific leaf area, short leaf life span, affinity to high-nutrient sites, and greater foliar nutrient concentrations. To address these issues, we asked whether soil resources (nitrogen, phosphorus, and potassium), alone or in combination, applied experimentally for more than a decade would cause significant changes in the morphology or physiology of tree and liana seedlings in a lowland tropical forest. We found evidence for the first time that phosphorus limits the photosynthetic performance of both trees and lianas in deeply shaded understory habitats. More importantly, lianas always showed significantly greater photosynthetic capacity, quenching, and saturating light levels compared to trees across all treatments. We found little evidence for nutrient x growth form interactions, indicating that lianas were not disproportionately favored in nutrient-rich habitats. Tree and liana seedlings differed markedly for six key morphological traits, demonstrating that architectural differences occurred very early in ontogeny prior to lianas finding a trellis (all seedlings were self-supporting). Overall, our results do not support nutrient loading as a mechanism of increasing liana abundance in the Neotropics. Rather, our finding that lianas always outperform trees, in terms of photosynthetic processes and under contrasting rates of resource supply of macronutrients, will allow lianas to increase in abundance if disturbance and tree turnover rates are increasing in Neotropical forests as has been suggested.

Barking up the Right Tree

ERIC Educational Resources Information Center

Houston, Paul D.

2006-01-01

There is a childhood saying about a confused dog who thinks he sees a possum in a tree. The problem is that the possum is actually in a different tree so the dog barks up the wrong tree. American education is constantly playing both dog and possum. Sometimes they are the prey, and sometimes they are just confused about what and where the prey is.…

Algorithms and Complexity Results for Genome Mapping Problems.

PubMed

Rajaraman, Ashok; Zanetti, Joao Paulo Pereira; Manuch, Jan; Chauve, Cedric

2017-01-01

Genome mapping algorithms aim at computing an ordering of a set of genomic markers based on local ordering information such as adjacencies and intervals of markers. In most genome mapping models, markers are assumed to occur uniquely in the resulting map. We introduce algorithmic questions that consider repeats, i.e., markers that can have several occurrences in the resulting map. We show that, provided with an upper bound on the copy number of repeated markers and with intervals that span full repeat copies, called repeat spanning intervals, the problem of deciding if a set of adjacencies and repeat spanning intervals admits a genome representation is tractable if the target genome can contain linear and/or circular chromosomal fragments. We also show that extracting a maximum cardinality or weight subset of repeat spanning intervals given a set of adjacencies that admits a genome realization is NP-hard but fixed-parameter tractable in the maximum copy number and the number of adjacent repeats, and tractable if intervals contain a single repeated marker.

Spatial and temporal oxygen isotope trends at the northern tree-line in Eurasia

NASA Astrophysics Data System (ADS)

Saurer, Matthias; Schweingruber, Fritz; Vaganov, Eugene A.; Shiyatov, Stepan G.; Siegwolf, Rolf

2002-05-01

The oxygen isotope ratio of ice cores and sea-sediments is an extremely useful source of information on long-term climatic changes. A similar approach has been applied to the oxygen isotope ratio of tree rings to enable a pattern-based reconstruction of the isotope variations on the continents. We present an oxygen isotope map for northern Eurasia spanning from Norway to Siberia, that reflects the isotope distribution in the late 19th century, and compare it with an equivalent map for the present-day situation. The average isotope values of 130 trees show a large east-to-west gradient and are highly correlated with the isotope distribution of precipitation. Surprisingly, the 18O/16O ratio of the wood has been decreasing in the interior of the continent since the late 19th century, in contrast to the strong temperature increase recorded by meteorological data. From this isotope trend over time a change in the seasonality of precipitation can be inferred.

An IPv6 routing lookup algorithm using weight-balanced tree based on prefix value for virtual router

NASA Astrophysics Data System (ADS)

Chen, Lingjiang; Zhou, Shuguang; Zhang, Qiaoduo; Li, Fenghua

2016-10-01

Virtual router enables the coexistence of different networks on the same physical facility and has lately attracted a great deal of attention from researchers. As the number of IPv6 addresses is rapidly increasing in virtual routers, designing an efficient IPv6 routing lookup algorithm is of great importance. In this paper, we present an IPv6 lookup algorithm called weight-balanced tree (WBT). WBT merges Forwarding Information Bases (FIBs) of virtual routers into one spanning tree, and compresses the space cost. WBT's average time complexity and the worst case time complexity of lookup and update process are both O(logN) and space complexity is O(cN) where N is the size of routing table and c is a constant. Experiments show that WBT helps reduce more than 80% Static Random Access Memory (SRAM) cost in comparison to those separation schemes. WBT also achieves the least average search depth comparing with other homogeneous algorithms.

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.

Radiofrequency radiation injures trees around mobile phone base stations.

PubMed

Waldmann-Selsam, Cornelia; Balmori-de la Puente, Alfonso; Breunig, Helmut; Balmori, Alfonso

2016-12-01

In the last two decades, the deployment of phone masts around the world has taken place and, for many years, there has been a discussion in the scientific community about the possible environmental impact from mobile phone base stations. Trees have several advantages over animals as experimental subjects and the aim of this study was to verify whether there is a connection between unusual (generally unilateral) tree damage and radiofrequency exposure. To achieve this, a detailed long-term (2006-2015) field monitoring study was performed in the cities of Bamberg and Hallstadt (Germany). During monitoring, observations and photographic recordings of unusual or unexplainable tree damage were taken, alongside the measurement of electromagnetic radiation. In 2015 measurements of RF-EMF (Radiofrequency Electromagnetic Fields) were carried out. A polygon spanning both cities was chosen as the study site, where 144 measurements of the radiofrequency of electromagnetic fields were taken at a height of 1.5m in streets and parks at different locations. By interpolation of the 144 measurement points, we were able to compile an electromagnetic map of the power flux density in Bamberg and Hallstadt. We selected 60 damaged trees, in addition to 30 randomly selected trees and 30 trees in low radiation areas (n=120) in this polygon. The measurements of all trees revealed significant differences between the damaged side facing a phone mast and the opposite side, as well as differences between the exposed side of damaged trees and all other groups of trees in both sides. Thus, we found that side differences in measured values of power flux density corresponded to side differences in damage. The 30 selected trees in low radiation areas (no visual contact to any phone mast and power flux density under 50μW/m 2 ) showed no damage. Statistical analysis demonstrated that electromagnetic radiation from mobile phone masts is harmful for trees. These results are consistent with the fact that damage afflicted on trees by mobile phone towers usually start on one side, extending to the whole tree over time. Copyright © 2016 Elsevier B.V. All rights reserved.

Economic costs of electrical system instability and power outages caused by snakes on the Island of Guam

USGS Publications Warehouse

Fritts, T.H.

2002-01-01

The Brown Tree Snake, Boiga irregularis, is an introduced species on Guam where it causes frequent electrical power outages. The snake's high abundance, its propensity for climbing, and use of disturbed habitats all contribute to interruption of Guam's electrical service and the activities that depend on electrical power. Snakes have caused more than 1600 power outages in the 20-yr period of 1978–1997 and most recently nearly 200 outages per year. Single outages spanning the entire island and lasting 8 or more hours are estimated to cost in excess of $3,000,000 in lost productivity, but the costs of outages that involve only parts of the island or those of shorter durations are more difficult to quantify. Costs to the island's economy have exceeded $4.5 M $4.5M"> per year over a 7-yr period without considering repair costs, damage to electrical equipment, and lost revenues. Snakes pose the greatest problem on high voltage transmission lines, on transformers, and inside electrical substations.

Improving the Held and Karp Approach with Constraint Programming

NASA Astrophysics Data System (ADS)

Benchimol, Pascal; Régin, Jean-Charles; Rousseau, Louis-Martin; Rueher, Michel; van Hoeve, Willem-Jan

Held and Karp have proposed, in the early 1970s, a relaxation for the Traveling Salesman Problem (TSP) as well as a branch-and-bound procedure that can solve small to modest-size instances to optimality [4, 5]. It has been shown that the Held-Karp relaxation produces very tight bounds in practice, and this relaxation is therefore applied in TSP solvers such as Concorde [1]. In this short paper we show that the Held-Karp approach can benefit from well-known techniques in Constraint Programming (CP) such as domain filtering and constraint propagation. Namely, we show that filtering algorithms developed for the weighted spanning tree constraint [3, 8] can be adapted to the context of the Held and Karp procedure. In addition to the adaptation of existing algorithms, we introduce a special-purpose filtering algorithm based on the underlying mechanisms used in Prim's algorithm [7]. Finally, we explored two different branching schemes to close the integrality gap. Our initial experimental results indicate that the addition of the CP techniques to the Held-Karp method can be very effective.

Distributed Fault-Tolerant Control of Networked Uncertain Euler-Lagrange Systems Under Actuator Faults.

PubMed

Chen, Gang; Song, Yongduan; Lewis, Frank L

2016-05-03

This paper investigates the distributed fault-tolerant control problem of networked Euler-Lagrange systems with actuator and communication link faults. An adaptive fault-tolerant cooperative control scheme is proposed to achieve the coordinated tracking control of networked uncertain Lagrange systems on a general directed communication topology, which contains a spanning tree with the root node being the active target system. The proposed algorithm is capable of compensating for the actuator bias fault, the partial loss of effectiveness actuation fault, the communication link fault, the model uncertainty, and the external disturbance simultaneously. The control scheme does not use any fault detection and isolation mechanism to detect, separate, and identify the actuator faults online, which largely reduces the online computation and expedites the responsiveness of the controller. To validate the effectiveness of the proposed method, a test-bed of multiple robot-arm cooperative control system is developed for real-time verification. Experiments on the networked robot-arms are conduced and the results confirm the benefits and the effectiveness of the proposed distributed fault-tolerant control algorithms.

Convergence analysis of directed signed networks via an M-matrix approach

NASA Astrophysics Data System (ADS)

Meng, Deyuan

2018-04-01

This paper aims at solving convergence problems on directed signed networks with multiple nodes, where interactions among nodes are described by signed digraphs. The convergence analysis is achieved by matrix-theoretic and graph-theoretic tools, in which M-matrices play a central role. The fundamental digon sign-symmetry assumption upon signed digraphs can be removed with the proposed analysis approach. Furthermore, necessary and sufficient conditions are established for semi-positive and positive stabilities of Laplacian matrices of signed digraphs, respectively. A benefit of this result is that given strong connectivity, a directed signed network can achieve bipartite consensus (or state stability) if and only if the signed digraph associated with it is structurally balanced (or unbalanced). If the interactions between nodes are described by a signed digraph only with spanning trees, a directed signed network can achieve interval bipartite consensus (or state stability) if and only if the signed digraph contains a structurally balanced (or unbalanced) rooted subgraph. Simulations are given to illustrate the developed results by considering signed networks associated with digon sign-unsymmetric signed digraphs.

Aftershock identification problem via the nearest-neighbor analysis for marked point processes

NASA Astrophysics Data System (ADS)

Gabrielov, A.; Zaliapin, I.; Wong, H.; Keilis-Borok, V.

2007-12-01

The centennial observations on the world seismicity have revealed a wide variety of clustering phenomena that unfold in the space-time-energy domain and provide most reliable information about the earthquake dynamics. However, there is neither a unifying theory nor a convenient statistical apparatus that would naturally account for the different types of seismic clustering. In this talk we present a theoretical framework for nearest-neighbor analysis of marked processes and obtain new results on hierarchical approach to studying seismic clustering introduced by Baiesi and Paczuski (2004). Recall that under this approach one defines an asymmetric distance D in space-time-energy domain such that the nearest-neighbor spanning graph with respect to D becomes a time- oriented tree. We demonstrate how this approach can be used to detect earthquake clustering. We apply our analysis to the observed seismicity of California and synthetic catalogs from ETAS model and show that the earthquake clustering part is statistically different from the homogeneous part. This finding may serve as a basis for an objective aftershock identification procedure.

On the use of cartographic projections in visualizing phylo-genetic tree space

PubMed Central

2010-01-01

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets. PMID:20529355

Adaptable Constrained Genetic Programming: Extensions and Applications

NASA Technical Reports Server (NTRS)

Janikow, Cezary Z.

2005-01-01

An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.

Extended Full Computation-Tree Logic with Sequence Modal Operator: Representing Hierarchical Tree Structures

NASA Astrophysics Data System (ADS)

Kamide, Norihiro; Kaneiwa, Ken

An extended full computation-tree logic, CTLS*, is introduced as a Kripke semantics with a sequence modal operator. This logic can appropriately represent hierarchical tree structures where sequence modal operators in CTLS* are applied to tree structures. An embedding theorem of CTLS* into CTL* is proved. The validity, satisfiability and model-checking problems of CTLS* are shown to be decidable. An illustrative example of biological taxonomy is presented using CTLS* formulas.

Tanglegrams: A Reduction Tool for Mathematical Phylogenetics.

PubMed

Matsen, Frederick A; Billey, Sara C; Kas, Arnold; Konvalinka, Matjaz

2018-01-01

Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.

Isolation of Cryptococcus gattii from Oregon soil and tree bark, 2010-2011.

PubMed

DeBess, Emilio; Lockhart, Shawn R; Iqbal, Naureen; Cieslak, Paul R

2014-12-21

In Oregon, human and animal infections by C. gattii were first identified in 2004. Cryptococcus gattii is considered to be an emerging non-zoonotic infection affecting animals and humans in Oregon. We report a longitudinal environmental isolation of C. gattii after an Oregon dog was diagnosed with the disease in 2009. Cryptococcus gattii was isolated twice from the same location with a span of one year between isolation dates. Cryptococcus gattii molecular types VGIIa and VGI were isolated in 2010 from soil and tree bark near the home of a 9-month-old dog which three months previously had an infection caused by C. gattii genotype VGIIa. The environment featured heavy growth of Douglas Fir trees. In 2011, a second set of soil and tree bark samples was collected in the same area and C. gattii VGIIa was again identified from the environment, along with genotypes VGIIb and VGIIc. The use of animal surveillance data to identify environmental niches of C. gattii should be considered to expand the understanding of this emerging pathogen. Understanding the ecology and how the environment and other factors might modify the existing niches is important for assessing risk and for designing measures to protect human and animal health.

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.

Applied Swarm-based medicine: collecting decision trees for patterns of algorithms analysis.

PubMed

Panje, Cédric M; Glatzer, Markus; von Rappard, Joscha; Rothermundt, Christian; Hundsberger, Thomas; Zumstein, Valentin; Plasswilm, Ludwig; Putora, Paul Martin

2017-08-16

The objective consensus methodology has recently been applied in consensus finding in several studies on medical decision-making among clinical experts or guidelines. The main advantages of this method are an automated analysis and comparison of treatment algorithms of the participating centers which can be performed anonymously. Based on the experience from completed consensus analyses, the main steps for the successful implementation of the objective consensus methodology were identified and discussed among the main investigators. The following steps for the successful collection and conversion of decision trees were identified and defined in detail: problem definition, population selection, draft input collection, tree conversion, criteria adaptation, problem re-evaluation, results distribution and refinement, tree finalisation, and analysis. This manuscript provides information on the main steps for successful collection of decision trees and summarizes important aspects at each point of the analysis.

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 Riparian Approach to Dendrochronological Flow Reconstruction, Yellowstone River, Montana

NASA Astrophysics Data System (ADS)

Schook, D. M.; Rathburn, S. L.; Friedman, J. M.

2015-12-01

Tree ring-based flow reconstructions can reveal river discharge variability over durations far exceeding the gauged record, building perspective for both the measured record and future flows. We use plains cottonwood (Populus deltoides subsp. monilifera) tree rings collected from four rivers to reconstruct flow history of the Yellowstone River near its confluence with the Missouri River. Upland trees in dry regions are typically used in flow reconstruction because their annual growth is controlled by the same precipitation that drives downstream flow, but our study improves flow reconstruction by including floodplain trees that are directly affected by the river. Cores from over 1000 cottonwoods along the Yellowstone, Powder, Little Missouri, and Redwater Rivers were collected from within a 170 km radius to reconstruct flows using the Age Curve Standardization technique in a multiple regression analysis. The large sample from trees spanning many age classes allows us to use only the rings that were produced when each tree was less than 50 years old and growth was most strongly correlated to river discharge. Using trees from a range of rivers improves our ability to differentiate between growth resulting from local precipitation and river flow, and we show that cottonwood growth differs across these neighboring rivers having different watersheds. Using the program Seascorr, tree growth is found to better correlated to seasonal river discharge (R = 0.69) than to local precipitation (R = 0.45). Our flow reconstruction reveals that the most extreme multi-year or multi-decade drought periods of the last 250 years on either the Yellowstone (1817-1821) or Powder (1846-1865) Rivers are missed by the gauged discharge record. Across all sites, we document increased growth in the 20th century compared to the 19th, a finding unattainable with conventional methods but having important implications for flow management.

Application of Composite Structures in Bridge Engineering. Problems of Construction Process and Strength Analysis

NASA Astrophysics Data System (ADS)

Flaga, Kazimierz; Furtak, Kazimierz

2015-03-01

Steel-concrete composite structures have been used in bridge engineering from decades. This is due to rational utilisation of the strength properties of the two materials. At the same time, the reinforced concrete (or prestressed) deck slab is more favourable than the orthotropic steel plate used in steel bridges (higher mass, better vibration damping, longer life). The most commonly found in practice are composite girder bridges, particularly in highway bridges of small and medium spans, but the spans may reach over 200 m. In larger spans steel truss girders are applied. Bridge composite structures are also employed in cable-stayed bridge decks of the main girder spans of the order of 600, 800 m. The aim of the article is to present the cionstruction process and strength analysis problems concerning of this type of structures. Much attention is paid to the design and calculation of the shear connectors characteristic for the discussed objects. The authors focused mainly on the issues of single composite structures. The effect of assembly states on the stresses and strains in composite members are highlighted. A separate part of problems is devoted to the influence of rheological factors, i.e. concrete shrinkage and creep, as well as thermal factors on the stresses and strains and redistribution of internal forces.

Attention problems in very preterm children from childhood to adulthood: the Bavarian Longitudinal Study.

PubMed

Breeman, Linda D; Jaekel, Julia; Baumann, Nicole; Bartmann, Peter; Wolke, Dieter

2016-02-01

Very preterm (VP; gestational age <32 weeks) and very low birth weight (VLBW; <1500 grams) is related to attention problems in childhood and adulthood. The stability of these problems into adulthood is not known. The Bavarian Longitudinal Study is a prospective cohort study that followed 260 VP/VLBW and 229 term-born individuals from birth to adulthood. Data on attention were collected at 6, 8, and 26 years of age, using parent reports, expert behavior observations, and clinical ADHD diagnoses. At each assessment, VP/VLBW individuals had significantly more attention problems, shorter attention span, and were more frequently diagnosed with ADHD than term-born comparisons. In both VP/VLBW and term-born individuals, overall, attention span increased and attention problems decreased from childhood to adulthood. Attention problems and attention span were more stable over time for VP/VLBW than term-born individuals. Similarly, ADHD diagnoses showed moderate stability from childhood to adulthood in VP/VLBW, but not in term-born individuals. However, when those with severe disabilities were excluded, differences between VP/VLBW and term-born individuals reduced. Despite improvement in attention regulation from childhood to adulthood, children born very preterm remained at increased risk for attention problems in adulthood. In contrast, term-born children with clinical attention problems outgrew these by adulthood. As inattentive behavior of VP/VLBW children may be overlooked by teachers, it may be necessary to raise awareness for school intervention programs that reduce attention problems in VP/VLBW children. © 2015 Association for Child and Adolescent Mental Health.

What is the danger of the anomaly zone for empirical phylogenetics?

PubMed

Huang, Huateng; Knowles, L Lacey

2009-10-01

The increasing number of observations of gene trees with discordant topologies in phylogenetic studies has raised awareness about the problems of incongruence between species trees and gene trees. Moreover, theoretical treatments focusing on the impact of coalescent variance on phylogenetic study have also identified situations where the most probable gene trees are ones that do not match the underlying species tree (i.e., anomalous gene trees [AGTs]). However, although the theoretical proof of the existence of AGTs is alarming, the actual risk that AGTs pose to empirical phylogenetic study is far from clear. Establishing the conditions (i.e., the branch lengths in a species tree) for which AGTs are possible does not address the critical issue of how prevalent they might be. Furthermore, theoretical characterization of the species trees for which AGTs may pose a problem (i.e., the anomaly zone or the species histories for which AGTs are theoretically possible) is based on consideration of just one source of variance that contributes to species tree and gene tree discord-gene lineage coalescence. Yet, empirical data contain another important stochastic component-mutational variance. Estimated gene trees will differ from the underlying gene trees (i.e., the actual genealogy) because of the random process of mutation. Here, we take a simulation approach to investigate the prevalence of AGTs, among estimated gene trees, thereby characterizing the boundaries of the anomaly zone taking into account both coalescent and mutational variances. We also determine the frequency of realized AGTs, which is critical to putting the theoretical work on AGTs into a realistic biological context. Two salient results emerge from this investigation. First, our results show that mutational variance can indeed expand the parameter space (i.e., the relative branch lengths in a species tree) where AGTs might be observed in empirical data. By exploring the underlying cause for the expanded anomaly zone, we identify aspects of empirical data relevant to avoiding the problems that AGTs pose for species tree inference from multilocus data. Second, for the empirical species histories where AGTs are possible, unresolved trees-not AGTs-predominate the pool of estimated gene trees. This result suggests that the risk of AGTs, while they exist in theory, may rarely be realized in practice. By considering the biological realities of both mutational and coalescent variances, the study has refined, and redefined, what the actual challenges are for empirical phylogenetic study of recently diverged taxa that have speciated rapidly-AGTs themselves are unlikely to pose a significant danger to empirical phylogenetic study.

Food Allergy

MedlinePlus

... trigger allergic reactions include fish, shellfish, peanuts, and tree nuts, such as walnuts. Problem foods for children can include eggs, milk, peanuts, tree nuts, soy, and wheat. The allergic reaction may ...

A modified tree classification for use in growth studies and timber marking in Black Hills ponderosa pine

Treesearch

E. M. Hornibrook

1939-01-01

A satisfactory silvicultural management of ponderosa pine stands requires a judicious selection of trees to be left in the reserve stand. The timber marker must know what type of tree has the greatest growth potentialities and what type of tree will respond but slightly upon being released. The silvicultural problem in marking therefore is one of recognizing the...

Cost-effectiveness Analysis with Influence Diagrams.

PubMed

Arias, M; Díez, F J

2015-01-01

Cost-effectiveness analysis (CEA) is used increasingly in medicine to determine whether the health benefit of an intervention is worth the economic cost. Decision trees, the standard decision modeling technique for non-temporal domains, can only perform CEA for very small problems. To develop a method for CEA in problems involving several dozen variables. We explain how to build influence diagrams (IDs) that explicitly represent cost and effectiveness. We propose an algorithm for evaluating cost-effectiveness IDs directly, i.e., without expanding an equivalent decision tree. The evaluation of an ID returns a set of intervals for the willingness to pay - separated by cost-effectiveness thresholds - and, for each interval, the cost, the effectiveness, and the optimal intervention. The algorithm that evaluates the ID directly is in general much more efficient than the brute-force method, which is in turn more efficient than the expansion of an equivalent decision tree. Using OpenMarkov, an open-source software tool that implements this algorithm, we have been able to perform CEAs on several IDs whose equivalent decision trees contain millions of branches. IDs can perform CEA on large problems that cannot be analyzed with decision trees.

Identifying failure in a tree network of a parallel computer

DOEpatents

Archer, Charles J.; Pinnow, Kurt W.; Wallenfelt, Brian P.

2010-08-24

Methods, parallel computers, and products are provided for identifying failure in a tree network of a parallel computer. The parallel computer includes one or more processing sets including an I/O node and a plurality of compute nodes. For each processing set embodiments include selecting a set of test compute nodes, the test compute nodes being a subset of the compute nodes of the processing set; measuring the performance of the I/O node of the processing set; measuring the performance of the selected set of test compute nodes; calculating a current test value in dependence upon the measured performance of the I/O node of the processing set, the measured performance of the set of test compute nodes, and a predetermined value for I/O node performance; and comparing the current test value with a predetermined tree performance threshold. If the current test value is below the predetermined tree performance threshold, embodiments include selecting another set of test compute nodes. If the current test value is not below the predetermined tree performance threshold, embodiments include selecting from the test compute nodes one or more potential problem nodes and testing individually potential problem nodes and links to potential problem nodes.

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

TimeTree2: species divergence times on the iPhone

PubMed Central

Kumar, Sudhir; Hedges, S. Blair

2011-01-01

Summary: Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K–12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature. Availability: TimeTree2 is accessible from the URL http://www.timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo). Contact: sbh1@psu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21622662

An assessment of correlations between chlorinated VOC concentrations in tree tissue and groundwater for phytoscreening applications.

PubMed

Duncan, Candice M; Brusseau, Mark L

2018-03-01

The majority of prior phytoscreening applications have employed the method as a tool to qualitatively determine the presence of contamination in the subsurface. Although qualitative data is quite useful, this study explores the potential for using phytoscreening quantitatively. The existence of site-specific and non-site-specific (master) correlations between VOC concentrations in tree tissue and groundwater is investigated using data collected from several phytoscreening studies. The aggregated data comprise 100 measurements collected from 12 sites that span a wide range of site conditions. Significant site-specific correlations are observed between tetrachloroethene (PCE) and trichloroethene (TCE) concentrations measured for tree tissue and those measured in groundwater for three sites. A moderately significant correlation (r 2 =0.56) exists for the entire aggregate data set. Parsing the data by groundwater depth produced a highly significant correlation (r 2 =0.88) for sites with shallow (<4m) groundwater. Such a significant correlation for data collected by different investigators from multiple sites with a wide range of tree species and subsurface conditions indicates that groundwater concentration is the predominant factor mediating tree-tissue concentrations for these sites. This may be a result of trees likely directly tapping groundwater for these shallow groundwater conditions. This master correlation may provide reasonable order-of-magnitude estimates of VOC concentrations in groundwater for such sites, thereby allowing the use of phytoscreening in a more quantitative mode. Copyright © 2017 Elsevier B.V. All rights reserved.

The Decision Tree: A Tool for Achieving Behavioral Change.

ERIC Educational Resources Information Center

Saren, Dru

1999-01-01

Presents a "Decision Tree" process for structuring team decision making and problem solving about specific student behavioral goals. The Decision Tree involves a sequence of questions/decisions that can be answered in "yes/no" terms. Questions address reasonableness of the goal, time factors, importance of the goal, responsibilities, safety,…

On the Integration of Logic Programming and Functional Programming.

DTIC Science & Technology

1985-06-01

be performed with simple handtools and devices. However, if the problem is more complex, say involving the cylinders, camshaft , or drive train, then...f(x,x) with f(y, g(y)), and would bind x to g(x) (Ref. 7]. The problem, of course, is that the attempt to prune the search tree allows circularity...combinatorial-explosion, since the search trees generated can grow very unpredictably (Re£. 19: p. 2293. Somewhat akin to the halting problem, it means that a

Geographic Distribution and Ecology of Potential Malaria Vectors in the Republic of Korea

DTIC Science & Technology

2009-05-01

species . Figure 4 shows a minimal spanning tree of the non- metric multidimensional scaling analysis of the means of the Þrst 15 principal components...to develop ecological niche models (ENMs) of the potential geographic distribution for eight anopheline species known to occur there. The areas...predicted suitable for the Hyrcanus Group species were the most extensive for Anopheles sinensis Wiedemann, An. kleini Rueda, An. belenrae Rueda, and An

On the Kirchhoff Index of Graphs

NASA Astrophysics Data System (ADS)

Das, Kinkar C.

2013-09-01

Let G be a connected graph of order n with Laplacian eigenvalues μ1 ≥ μ2 ≥ ... ≥ μn-1 > mn = 0. The Kirchhoff index of G is defined as [xxx] In this paper. we give lower and upper bounds on Kf of graphs in terms on n, number of edges, maximum degree, and number of spanning trees. Moreover, we present lower and upper bounds on the Nordhaus-Gaddum-type result for the Kirchhoff index.

Translations on Western Europe, Number 1063

DTIC Science & Technology

1977-05-05

other. When the national committee of the Center Party had its big dinner at Ystad in June of last year, one of the speeches was given by the...build tall greenhouses of the span type . Arboriculture: The growing of citrus trees should be protected and attention should be paid to the...that was established by the United Nations . K.B. Andersen praised the Industrial Council for its recent initiative by means of a publication

Leonardo's Tree Theory.

ERIC Educational Resources Information Center

Werner, Suzanne K.

2003-01-01

Describes a series of activities exploring Leonardo da Vinci's tree theory that are designed to strengthen 8th grade students' data collection and problem solving skills in physical science classes. (KHR)

Integrated Network Decompositions and Dynamic Programming for Graph Optimization (INDDGO)

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

The INDDGO software package offers a set of tools for finding exact solutions to graph optimization problems via tree decompositions and dynamic programming algorithms. Currently the framework offers serial and parallel (distributed memory) algorithms for finding tree decompositions and solving the maximum weighted independent set problem. The parallel dynamic programming algorithm is implemented on top of the MADNESS task-based runtime.

On the Complexity of the Asymmetric VPN Problem

NASA Astrophysics Data System (ADS)

Rothvoß, Thomas; Sanità, Laura

We give the first constant factor approximation algorithm for the asymmetric Virtual Private Network (textsc{Vpn}) problem with arbitrary concave costs. We even show the stronger result, that there is always a tree solution of cost at most 2·OPT and that a tree solution of (expected) cost at most 49.84·OPT can be determined in polynomial time.

Suitability of live and fire-killed small-diameter ponderosa and lodgepole pine trees for manufacturing a new structural wood composite

Treesearch

J.M. Linton; H.M. Barnes; R.D. Seale; P.D. Jones; E. Lowell; S.S. Hummel

2010-01-01

Finding alternative uses for raw material from small-diameter trees is a critical problem throughout the United States. In western states, a lack of markets for small-diameter ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta ) can contribute to problems associated with overstocking. To test the feasibility of...

DeepSAT: A Deep Learning Approach to Tree-Cover Delineation in 1-m NAIP Imagery for the Continental United States

NASA Technical Reports Server (NTRS)

Ganguly, Sangram; Basu, Saikat; Nemani, Ramakrishna R.; Mukhopadhyay, Supratik; Michaelis, Andrew; Votava, Petr

2016-01-01

High resolution tree cover classification maps are needed to increase the accuracy of current land ecosystem and climate model outputs. Limited studies are in place that demonstrates the state-of-the-art in deriving very high resolution (VHR) tree cover products. In addition, most methods heavily rely on commercial softwares that are difficult to scale given the region of study (e.g. continents to globe). Complexities in present approaches relate to (a) scalability of the algorithm, (b) large image data processing (compute and memory intensive), (c) computational cost, (d) massively parallel architecture, and (e) machine learning automation. In addition, VHR satellite datasets are of the order of terabytes and features extracted from these datasets are of the order of petabytes. In our present study, we have acquired the National Agriculture Imagery Program (NAIP) dataset for the Continental United States at a spatial resolution of 1-m. This data comes as image tiles (a total of quarter million image scenes with 60 million pixels) and has a total size of 65 terabytes for a single acquisition. Features extracted from the entire dataset would amount to 8-10 petabytes. In our proposed approach, we have implemented a novel semi-automated machine learning algorithm rooted on the principles of "deep learning" to delineate the percentage of tree cover. Using the NASA Earth Exchange (NEX) initiative, we have developed an end-to-end architecture by integrating a segmentation module based on Statistical Region Merging, a classification algorithm using Deep Belief Network and a structured prediction algorithm using Conditional Random Fields to integrate the results from the segmentation and classification modules to create per-pixel class labels. The training process is scaled up using the power of GPUs and the prediction is scaled to quarter million NAIP tiles spanning the whole of Continental United States using the NEX HPC supercomputing cluster. An initial pilot over the state of California spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles has produced true positive rates of around 88 percent for fragmented forests and 74 percent for urban tree cover areas, with false positive rates lower than 2 percent for both landscapes.

DeepSAT: A Deep Learning Approach to Tree-cover Delineation in 1-m NAIP Imagery for the Continental United States

NASA Astrophysics Data System (ADS)

Ganguly, S.; Basu, S.; Nemani, R. R.; Mukhopadhyay, S.; Michaelis, A.; Votava, P.

2016-12-01

High resolution tree cover classification maps are needed to increase the accuracy of current land ecosystem and climate model outputs. Limited studies are in place that demonstrates the state-of-the-art in deriving very high resolution (VHR) tree cover products. In addition, most methods heavily rely on commercial softwares that are difficult to scale given the region of study (e.g. continents to globe). Complexities in present approaches relate to (a) scalability of the algorithm, (b) large image data processing (compute and memory intensive), (c) computational cost, (d) massively parallel architecture, and (e) machine learning automation. In addition, VHR satellite datasets are of the order of terabytes and features extracted from these datasets are of the order of petabytes. In our present study, we have acquired the National Agriculture Imagery Program (NAIP) dataset for the Continental United States at a spatial resolution of 1-m. This data comes as image tiles (a total of quarter million image scenes with 60 million pixels) and has a total size of 65 terabytes for a single acquisition. Features extracted from the entire dataset would amount to 8-10 petabytes. In our proposed approach, we have implemented a novel semi-automated machine learning algorithm rooted on the principles of "deep learning" to delineate the percentage of tree cover. Using the NASA Earth Exchange (NEX) initiative, we have developed an end-to-end architecture by integrating a segmentation module based on Statistical Region Merging, a classification algorithm using Deep Belief Network and a structured prediction algorithm using Conditional Random Fields to integrate the results from the segmentation and classification modules to create per-pixel class labels. The training process is scaled up using the power of GPUs and the prediction is scaled to quarter million NAIP tiles spanning the whole of Continental United States using the NEX HPC supercomputing cluster. An initial pilot over the state of California spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles has produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes.

Simulated parallel annealing within a neighborhood for optimization of biomechanical systems.

PubMed

Higginson, J S; Neptune, R R; Anderson, F C

2005-09-01

Optimization problems for biomechanical systems have become extremely complex. Simulated annealing (SA) algorithms have performed well in a variety of test problems and biomechanical applications; however, despite advances in computer speed, convergence to optimal solutions for systems of even moderate complexity has remained prohibitive. The objective of this study was to develop a portable parallel version of a SA algorithm for solving optimization problems in biomechanics. The algorithm for simulated parallel annealing within a neighborhood (SPAN) was designed to minimize interprocessor communication time and closely retain the heuristics of the serial SA algorithm. The computational speed of the SPAN algorithm scaled linearly with the number of processors on different computer platforms for a simple quadratic test problem and for a more complex forward dynamic simulation of human pedaling.

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

PubMed

Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

2014-10-01

One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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

Zlotnikov, Michael

We develop a polynomial reduction procedure that transforms any gauge fixed CHY amplitude integrand for n scattering particles into a σ-moduli multivariate polynomial of what we call the standard form. We show that a standard form polynomial must have a specific ladder type monomial structure, which has finite size at any n, with highest multivariate degree given by (n – 3)(n – 4)/2. This set of monomials spans a complete basis for polynomials with rational coefficients in kinematic data on the support of scattering equations. Subsequently, at tree and one-loop level, we employ the global residue theorem to derive amore » prescription that evaluates any CHY amplitude by means of collecting simple residues at infinity only. Furthermore, the prescription is then applied explicitly to some tree and one-loop amplitude examples.« less

Binary space partitioning trees and their uses

NASA Technical Reports Server (NTRS)

Bell, Bradley N.

1989-01-01

Binary Space Partitioning (BSP) trees have some qualities that make them useful in solving many graphics related problems. The purpose is to describe what a BSP tree is, and how it can be used to solve the problem of hidden surface removal, and constructive solid geometry. The BSP tree is based on the idea that a plane acting as a divider subdivides space into two parts with one being on the positive side and the other on the negative. A polygonal solid is then represented as the volume defined by the collective interior half spaces of the solid's bounding surfaces. The nature of how the tree is organized lends itself well for sorting polygons relative to an arbitrary point in 3 space. The speed at which the tree can be traversed for depth sorting is fast enough to provide hidden surface removal at interactive speeds. The fact that a BSP tree actually represents a polygonal solid as a bounded volume also makes it quite useful in performing the boolean operations used in constructive solid geometry. Due to the nature of the BSP tree, polygons can be classified as they are subdivided. The ability to classify polygons as they are subdivided can enhance the simplicity of implementing constructive solid geometry.

Allelochemicals and activities in a replanted Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) tree ecosystem.

PubMed

Kong, C H; Chen, L C; Xu, X H; Wang, P; Wang, S L

2008-12-24

Autotoxicity is a major reason for replant problems in managed tree ecosystems. Studies have related phenolics-based allelochemicals to autotoxicity. We selected a 20-year-old replanted Chinese fir [Cunninghamia lancealata (Lamb.) Hook] tree ecosystem to isolate, identify, determine the biological activity of, and quantify soil phytotoxins. Eight common phenolics (coumarin, vanillin, isovanillin, and p-hydroxybenzoic, vanillic, benzoic, cinnamic, and ferulic acids), friedelin, and a novel cyclic dipeptide (6-hydroxy-1,3-dimethyl-8-nonadecyl-[1,4]-diazocane-2,5-diketone) were obtained by using the bioassay-guided isolation technique from toxic soil of the replanted Chinese fir tree ecosystem. Chemical structures were determined by spectroscopic means, including 2D-NMR (COSY, HMQC, HMBC, and NOESY) experiments. High concentrations of soil phenolics and friedelin were observed in the natural evergreen broadleaf forest (CK) rather than in the Chinese fir tree ecosystem. The phenolics and friedelin were not phytotoxic to Chinese fir trees. However, the cyclic dipeptide inhibited Chinese fir growth at soil concentrations determined in the replanted Chinese fir tree ecosystem. There was a significantly higher soil concentration of cyclic dipeptide in the replanted Chinese fir tree ecosystem than in a fresh Chinese fir tree ecosystem. The results suggest that phenolics and friedelin are not key allelochemicals since they are weakly phytotoxic and are detected in low concentrations in the replanted Chinese fir tree ecosystem, while cyclic dipeptide is a highly active allelochemical with a phytotoxic effect that limits offspring growth in the replanted Chinese fir tree ecosystem. The discovery of cyclic dipeptide, as well as a further understanding of its potential action mechanism in the replanted Chinese fir tree ecosystem, may contribute to solving the replant problems in managed tree ecosystems.

Role of tree size in moist tropical forest carbon cycling and water deficit responses.

PubMed

Meakem, Victoria; Tepley, Alan J; Gonzalez-Akre, Erika B; Herrmann, Valentine; Muller-Landau, Helene C; Wright, S Joseph; Hubbell, Stephen P; Condit, Richard; Anderson-Teixeira, Kristina J

2017-06-06

Drought disproportionately affects larger trees in tropical forests, but implications for forest composition and carbon (C) cycling in relation to dry season intensity remain poorly understood. In order to characterize how C cycling is shaped by tree size and drought adaptations and how these patterns relate to spatial and temporal variation in water deficit, we analyze data from three forest dynamics plots spanning a moisture gradient in Panama that have experienced El Niño droughts. At all sites, aboveground C cycle contributions peaked below 50-cm stem diameter, with stems ≥ 50 cm accounting for on average 59% of live aboveground biomass, 45% of woody productivity and 49% of woody mortality. The dominance of drought-avoidance strategies increased interactively with stem diameter and dry season intensity. Although size-related C cycle contributions did not vary systematically across the moisture gradient under nondrought conditions, woody mortality of larger trees was disproportionately elevated under El Niño drought stress. Thus, large (> 50 cm) stems, which strongly mediate but do not necessarily dominate C cycling, have drought adaptations that compensate for their more challenging hydraulic environment, particularly in drier climates. However, these adaptations do not fully buffer the effects of severe drought, and increased large tree mortality dominates ecosystem-level drought responses. © 2017 Smithsonian. Institute New Phytologist © 2017 New Phytologist Trust.

Recent advances in long-term climate and moisture reconstructions from the Baltic region: Exploring the potential for a new multi-millennial tree-ring chronology

NASA Astrophysics Data System (ADS)

Edvardsson, Johannes; Corona, Christophe; Mažeika, Jonas; Pukienė, Rutile; Stoffel, Markus

2016-01-01

This study presents the first results from an ongoing initiative to develop a multi-millennial Baltic tree-ring width (TRW) chronology consisting of 12 floating records from subfossil Scots pines (Pinus sylvestris L.) extracted from three Lithuanian peat-mining areas. The floating series have been complemented with absolutely dated TRW chronologies which were obtained from living trees growing in unmanaged and unexploited peatland areas adjacent to each of the above study sites. The subfossil material has been dated by radiocarbon and shows a temporal spread over the last 6000 years, with assemblages of trees during the Holocene Thermal Maximum (HTM; 8000-4000 BP) and the onset of the Medieval Warm Period (MWP, AD 900-1350). Annual tree growth and sample replication of peatland pines reflect moisture variations and long-term climate variability. The importance of extending the TRW chronologies should not therefore be underestimated as (1) climate records of comparable length and resolution do not exist for the Baltic region, but also as (2) a result of a widespread lack of detailed moisture proxies spanning several millennia. Our data clearly show that a 6000-yr, continuous pine chronology from the Baltic region is a realistic objective, and would doubtlessly fill a major geographic gap in an ecologically sensitive region located at the interface between the temperate and boreal vegetation zones.

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.

Disentangling the effects of acidic air pollution, atmospheric CO2 , and climate change on recent growth of red spruce trees in the Central Appalachian Mountains.

PubMed

Mathias, Justin M; Thomas, Richard B

2018-05-20

In the 45 years after legislation of the Clean Air Act, there has been tremendous progress in reducing acidic air pollutants in the eastern United States, yet limited evidence exists that cleaner air has improved forest health. Here, we investigate the influence of recent environmental changes on the growth and physiology of red spruce (Picea rubens Sarg.) trees, a key indicator species of forest health, spanning three locations along a 100 km transect in the Central Appalachian Mountains. We incorporated a multiproxy approach using 75-year tree ring chronologies of basal tree growth, carbon isotope discrimination (∆ 13 C, a proxy for leaf gas exchange), and δ 15 N (a proxy for ecosystem N status) to examine tree and ecosystem level responses to environmental change. Results reveal the two most important factors driving increased tree growth since ca. 1989 are reductions in acidic sulfur pollution and increases in atmospheric CO 2 , while reductions in pollutant emissions of NO x and warmer springs played smaller, but significant roles. Tree ring ∆ 13 C signatures increased significantly since 1989, concurrently with significant declines in tree ring δ 15 N signatures. These isotope chronologies provide strong evidence that simultaneous changes in C and N cycling, including greater photosynthesis and stomatal conductance of trees and increases in ecosystem N retention, were related to recent increases in red spruce tree growth and are consequential to ecosystem recovery from acidic pollution. Intrinsic water use efficiency (iWUE) of the red spruce trees increased by ~51% across the 75-year chronology, and was driven by changes in atmospheric CO 2 and acid pollution, but iWUE was not linked to recent increases in tree growth. This study documents the complex environmental interactions that have contributed to the recovery of red spruce forest ecosystems from pervasive acidic air pollution beginning in 1989, about 15 years after acidic pollutants started to decline in the United States. © 2018 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Control of deer damage with chemical repellents in regenerating hardwood stands

Treesearch

Brian J. MacGowan; Larry Severeid; Fred, Jr. Skemp

2004-01-01

Wildlife damage can be a major problem in natural tree regeneration or tree plantings. In the North Central Hardwoods region, white-tailed deer (Odocoileus virginianus) are a significant cause of damage to hardwood seedlings. We evaluated the use of a combination of chemical repellents (Hinder®, Tree Guard®, chicken eggs, and...

Links to Literature--Huge Trees, Small Drawings: Ideas of Relative Sizes.

ERIC Educational Resources Information Center

Burton, Gail

1996-01-01

Discusses a unit integrating science, mathematics, and environmental education centered around "The Great Kapok Tree," by Lynne Cherry (1990). Ratios are used to make scale drawings of trees in a rain forest. Other activities include a terrarium and problem-solving activities based on eating habits of rain forest animals. (KMC)

From forest to freezer: a comprehensive seed collection of the Kentucky coffeetree, Gymnocladus dioicus (L.) K

Treesearch

A.P. Schmitz; J.D. Carstens

2017-01-01

Kentucky coffeetree, Gymnocladus dioicus, is a picturesque shade tree adaptable to urban conditions and drought, with no serious insect or disease problems. These traits make G. dioicus a promising candidate among diverse tree genera to replace ash (Fraxinus) trees affected by the emerald ash borer (Agrilus...

Introduction to the Space Physics Analysis Network (SPAN)

NASA Technical Reports Server (NTRS)

Green, J. L. (Editor); Peters, D. J. (Editor)

1985-01-01

The Space Physics Analysis Network or SPAN is emerging as a viable method for solving an immediate communication problem for the space scientist. SPAN provides low-rate communication capability with co-investigators and colleagues, and access to space science data bases and computational facilities. The SPAN utilizes up-to-date hardware and software for computer-to-computer communications allowing binary file transfer and remote log-on capability to over 25 nationwide space science computer systems. SPAN is not discipline or mission dependent with participation from scientists in such fields as magnetospheric, ionospheric, planetary, and solar physics. Basic information on the network and its use are provided. It is anticipated that SPAN will grow rapidly over the next few years, not only from the standpoint of more network nodes, but as scientists become more proficient in the use of telescience, more capability will be needed to satisfy the demands.

Using decision trees to characterize verbal communication during change and stuck episodes in the therapeutic process

PubMed Central

Masías, Víctor H.; Krause, Mariane; Valdés, Nelson; Pérez, J. C.; Laengle, Sigifredo

2015-01-01

Methods are needed for creating models to characterize verbal communication between therapists and their patients that are suitable for teaching purposes without losing analytical potential. A technique meeting these twin requirements is proposed that uses decision trees to identify both change and stuck episodes in therapist-patient communication. Three decision tree algorithms (C4.5, NBTree, and REPTree) are applied to the problem of characterizing verbal responses into change and stuck episodes in the therapeutic process. The data for the problem is derived from a corpus of 8 successful individual therapy sessions with 1760 speaking turns in a psychodynamic context. The decision tree model that performed best was generated by the C4.5 algorithm. It delivered 15 rules characterizing the verbal communication in the two types of episodes. Decision trees are a promising technique for analyzing verbal communication during significant therapy events and have much potential for use in teaching practice on changes in therapeutic communication. The development of pedagogical methods using decision trees can support the transmission of academic knowledge to therapeutic practice. PMID:25914657

Using decision trees to characterize verbal communication during change and stuck episodes in the therapeutic process.

PubMed

Masías, Víctor H; Krause, Mariane; Valdés, Nelson; Pérez, J C; Laengle, Sigifredo

2015-01-01

Methods are needed for creating models to characterize verbal communication between therapists and their patients that are suitable for teaching purposes without losing analytical potential. A technique meeting these twin requirements is proposed that uses decision trees to identify both change and stuck episodes in therapist-patient communication. Three decision tree algorithms (C4.5, NBTree, and REPTree) are applied to the problem of characterizing verbal responses into change and stuck episodes in the therapeutic process. The data for the problem is derived from a corpus of 8 successful individual therapy sessions with 1760 speaking turns in a psychodynamic context. The decision tree model that performed best was generated by the C4.5 algorithm. It delivered 15 rules characterizing the verbal communication in the two types of episodes. Decision trees are a promising technique for analyzing verbal communication during significant therapy events and have much potential for use in teaching practice on changes in therapeutic communication. The development of pedagogical methods using decision trees can support the transmission of academic knowledge to therapeutic practice.

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

PubMed Central

2014-01-01

Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates. PMID:24678701

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines.

PubMed

DeGiorgio, Michael; Syring, John; Eckert, Andrew J; Liston, Aaron; Cronn, Richard; Neale, David B; Rosenberg, Noah A

2014-03-29

As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each "strategy" for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.

Examining unusual digit span performance in a population of postsecondary students assessed for academic difficulties.

PubMed

Harrison, Allyson G; Rosenblum, Yoni; Currie, Shannon

2010-09-01

Methods of identifying poor test-related motivation using the Wechsler Adult Intelligence Scale Digit Span subtest are based on identification of performance patterns that are implausible if the test taker is investing full effort. No studies to date, however, have examined the specificity of such measures, particularly when evaluating persons with either known or suspected learning or attention disorders. This study investigated performance of academically challenged students on three measures embedded in the Wechsler Adult Intelligence Scale-III, namely, low Digit Span, high Vocabulary-Digit span (Voc-DS), and low Reliable Digit Span scores. Evaluating subjects believed to be investing full effort in testing, it was found that both Digit Span and Reliable Digit Span had high specificity, although both showed relatively lower sensitivity. In contrast, VOC-DS was especially weak in both sensitivity and specificity, with an apparent false positive rate of 28%. Use of VOC-DS is therefore not appropriate for those with a history of learning or attention problems.

Measuring Human Performance on Clustering Problems: Some Potential Objective Criteria and Experimental Research Opportunities

ERIC Educational Resources Information Center

Brusco, Michael J.

2007-01-01

The study of human performance on discrete optimization problems has a considerable history that spans various disciplines. The two most widely studied problems are the Euclidean traveling salesperson problem and the quadratic assignment problem. The purpose of this paper is to outline a program of study for the measurement of human performance on…

Dynamic Changes in Anger, Externalizing and Internalizing Problems: Attention and Regulation

ERIC Educational Resources Information Center

Kim, Jungmeen; Deater-Deckard, Kirby

2011-01-01

Background: Low levels of dispositional anger and a good attention span are critical to healthy social emotional development, with attention control reflecting effective cognitive self-regulation of negative emotions such as anger. Using a longitudinal design, we examined attention span as a moderator of reciprocal links between changes in anger…

A dynamic fault tree model of a propulsion system

NASA Technical Reports Server (NTRS)

Xu, Hong; Dugan, Joanne Bechta; Meshkat, Leila

2006-01-01

We present a dynamic fault tree model of the benchmark propulsion system, and solve it using Galileo. Dynamic fault trees (DFT) extend traditional static fault trees with special gates to model spares and other sequence dependencies. Galileo solves DFT models using a judicious combination of automatically generated Markov and Binary Decision Diagram models. Galileo easily handles the complexities exhibited by the benchmark problem. In particular, Galileo is designed to model phased mission systems.

Impact of urban environmental pollution on growth, leaf damage, and chemical constituents of Warsaw urban trees

Treesearch

Waldemar Chmielewski; Wojciech Dmuchowski; Stanislaw Suplat

1998-01-01

In the last 10 years, 3.5 percent of the tree population died annually in PolandÕs largest and most polluted cities, which is a problem of economic importance. Dieback of streetside trees in Warsaw is a long term process. It is an effect of biological reactions of trees to unfavorable conditions in the urban environment, particularly air and soil pollution and water...

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

Chuang, Chihpin; Singh, Dileep; Kenesei, Peter

The size and morphology of the graphite particles play a crucial role in determining various mechanical and thermal properties of cast iron. In the present study, we utilized high-energy synchrotron X-ray tomography to perform quantitative 3D-characterization of the distribution of graphite particles in high-strength compacted graphite iron (CGI). The size, shape, and spatial connectivity of graphite were examined. The analysis reveals that the compacted graphite can grow with a coral-tree-like morphology and span several hundred microns in the iron matrix.

Eigentime identities for on weighted polymer networks

NASA Astrophysics Data System (ADS)

Dai, Meifeng; Tang, Hualong; Zou, Jiahui; He, Di; Sun, Yu; Su, Weiyi

2018-01-01

In this paper, we first analytically calculate the eigenvalues of the transition matrix of a structure with very complex architecture and their multiplicities. We call this structure polymer network. Based on the eigenvalues obtained in the iterative manner, we then calculate the eigentime identity. We highlight two scaling behaviors (logarithmic and linear) for this quantity, strongly depending on the value of the weight factor. Finally, by making use of the obtained eigenvalues, we determine the weighted counting of spanning trees.

Resource-constrained Data Collection and Fusion for Identifying Weak Distributed Patterns in Networks

DTIC Science & Technology

2013-10-15

statistic,” in Artifical Intelligence and Statistics (AISTATS), 2013. [6] ——, “Detecting activity in graphs via the Graph Ellipsoid Scan Statistic... Artifical Intelligence and Statistics (AISTATS), 2013. [8] ——, “Near-optimal anomaly detection in graphs using Lovász Extended Scan Statistic,” in Neural...networks,” in Artificial Intelligence and Statistics (AISTATS), 2010. 11 [11] D. Aldous, “The random walk construction of uniform spanning trees and

The dynamic response of housing values to a forest invasive disease: evidence from a sudden oak death infestation

Treesearch

Kent Kovacs; Thomas P Holmes; Jeffrey E Englin; Janice Alexander

2011-01-01

“Sudden Oak Death” (Phytophthora ramorum) is a non-indigenous forest pathogen which causes substantial mortality of coast live oak (Quercus agrifolia) and several other oak tree species on the Pacific Coast of the United States. We estimated the time path of residential property values subject to oak mortality using a dataset that spans more than two decades—including...

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

Bedrock composition regulates mountain ecosystems and landscape evolution

PubMed Central

Hahm, W. Jesse; Riebe, Clifford S.; Lukens, Claire E.; Araki, Sayaka

2014-01-01

Earth’s land surface teems with life. Although the distribution of ecosystems is largely explained by temperature and precipitation, vegetation can vary markedly with little variation in climate. Here we explore the role of bedrock in governing the distribution of forest cover across the Sierra Nevada Batholith, California. Our sites span a narrow range of elevations and thus a narrow range in climate. However, land cover varies from Giant Sequoia (Sequoiadendron giganteum), the largest trees on Earth, to vegetation-free swaths that are visible from space. Meanwhile, underlying bedrock spans nearly the entire compositional range of granitic bedrock in the western North American cordillera. We explored connections between lithology and vegetation using measurements of bedrock geochemistry and forest productivity. Tree-canopy cover, a proxy for forest productivity, varies by more than an order of magnitude across our sites, changing abruptly at mapped contacts between plutons and correlating with bedrock concentrations of major and minor elements, including the plant-essential nutrient phosphorus. Nutrient-poor areas that lack vegetation and soil are eroding more than two times slower on average than surrounding, more nutrient-rich, soil-mantled bedrock. This suggests that bedrock geochemistry can influence landscape evolution through an intrinsic limitation on primary productivity. Our results are consistent with widespread bottom-up lithologic control on the distribution and diversity of vegetation in mountainous terrain. PMID:24516144

Optimization of incremental structure from motion combining a random k-d forest and pHash for unordered images in a complex scene

NASA Astrophysics Data System (ADS)

Zhan, Zongqian; Wang, Chendong; Wang, Xin; Liu, Yi

2018-01-01

On the basis of today's popular virtual reality and scientific visualization, three-dimensional (3-D) reconstruction is widely used in disaster relief, virtual shopping, reconstruction of cultural relics, etc. In the traditional incremental structure from motion (incremental SFM) method, the time cost of the matching is one of the main factors restricting the popularization of this method. To make the whole matching process more efficient, we propose a preprocessing method before the matching process: (1) we first construct a random k-d forest with the large-scale scale-invariant feature transform features in the images and combine this with the pHash method to obtain a value of relatedness, (2) we then construct a connected weighted graph based on the relatedness value, and (3) we finally obtain a planned sequence of adding images according to the principle of the minimum spanning tree. On this basis, we attempt to thin the minimum spanning tree to reduce the number of matchings and ensure that the images are well distributed. The experimental results show a great reduction in the number of matchings with enough object points, with only a small influence on the inner stability, which proves that this method can quickly and reliably improve the efficiency of the SFM method with unordered multiview images in complex scenes.

Space physics analysis network node directory (The Yellow Pages): Fourth edition

NASA Technical Reports Server (NTRS)

Peters, David J.; Sisson, Patricia L.; Green, James L.; Thomas, Valerie L.

1989-01-01

The Space Physics Analysis Network (SPAN) is a component of the global DECnet Internet, which has over 17,000 host computers. The growth of SPAN from its implementation in 1981 to its present size of well over 2,500 registered SPAN host computers, has created a need for users to acquire timely information about the network through a central source. The SPAN Network Information Center (SPAN-NIC) an online facility managed by the National Space Science Data Center (NSSDC) was developed to meet this need for SPAN-wide information. The remote node descriptive information in this document is not currently contained in the SPAN-NIC database, but will be incorporated in the near future. Access to this information is also available to non-DECnet users over a variety of networks such as Telenet, the NASA Packet Switched System (NPSS), and the TCP/IP Internet. This publication serves as the Yellow Pages for SPAN node information. The document also provides key information concerning other computer networks connected to SPAN, nodes associated with each SPAN routing center, science discipline nodes, contacts for primary SPAN nodes, and SPAN reference information. A section on DECnet Internetworking discusses SPAN connections with other wide-area DECnet networks (many with thousands of nodes each). Another section lists node names and their disciplines, countries, and institutions in the SPAN Network Information Center Online Data Base System. All remote sites connected to US-SPAN and European-SPAN (E-SPAN) are indexed. Also provided is information on the SPAN tail circuits, i.e., those remote nodes connected directly to a SPAN routing center, which is the local point of contact for resolving SPAN-related problems. Reference material is included for those who wish to know more about SPAN. Because of the rapid growth of SPAN, the SPAN Yellow Pages is reissued periodically.

Nitrogen deposition outweighs climatic variability in driving annual growth rate of canopy beech trees: Evidence from long-term growth reconstruction across a geographic gradient.

PubMed

Gentilesca, Tiziana; Rita, Angelo; Brunetti, Michele; Giammarchi, Francesco; Leonardi, Stefano; Magnani, Federico; van Noije, Twan; Tonon, Giustino; Borghetti, Marco

2018-07-01

In this study, we investigated the role of climatic variability and atmospheric nitrogen deposition in driving long-term tree growth in canopy beech trees along a geographic gradient in the montane belt of the Italian peninsula, from the Alps to the southern Apennines. We sampled dominant trees at different developmental stages (from young to mature tree cohorts, with tree ages spanning from 35 to 160 years) and used stem analysis to infer historic reconstruction of tree volume and dominant height. Annual growth volume (G V ) and height (G H ) variability were related to annual variability in model simulated atmospheric nitrogen deposition and site-specific climatic variables, (i.e. mean annual temperature, total annual precipitation, mean growing period temperature, total growing period precipitation, and standard precipitation evapotranspiration index) and atmospheric CO 2 concentration, including tree cambial age among growth predictors. Generalized additive models (GAM), linear mixed-effects models (LMM), and Bayesian regression models (BRM) were independently employed to assess explanatory variables. The main results from our study were as follows: (i) tree age was the main explanatory variable for long-term growth variability; (ii) GAM, LMM, and BRM results consistently indicated climatic variables and CO 2 effects on G V and G H were weak, therefore evidence of recent climatic variability influence on beech annual growth rates was limited in the montane belt of the Italian peninsula; (iii) instead, significant positive nitrogen deposition (N dep ) effects were repeatedly observed in G V and G H ; the positive effects of N dep on canopy height growth rates, which tended to level off at N dep values greater than approximately 1.0 g m -2  y -1 , were interpreted as positive impacts on forest stand above-ground net productivity at the selected study sites. © 2018 John Wiley & Sons Ltd.

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.

Food Allergy 101 | NIH MedlinePlus the Magazine

MedlinePlus

... reactions in adults include fish, shellfish, peanuts, and tree nuts, such as walnuts. Problem foods for children can include eggs, milk, peanuts, tree nuts, soy, and wheat. What are symptoms? The ...

Tradeoffs in basal area growth and reproduction shift over the lifetime of a long-lived tropical species.

PubMed

Staudhammer, Christina L; Wadt, Lúcia H O; Kainer, Karen A

2013-09-01

Understanding of the extent to which reproductive costs drive growth largely derives from reproductively mature temperate trees in masting and non-masting years. We modeled basal area increment (BAI) and explored current growth-reproduction tradeoffs and changes in such allocation over the life span of a long-lived, non-masting tropical tree. We integrated rainfall and soil variables with data from 190 Bertholletia excelsa trees of different diameter at breast height (DBH) sizes, crown characteristics, and liana loads, quantifying BAI and reproductive output over 4 and 6 years, respectively. While rainfall explains BAI in all models, regardless of DBH class or ontogenic stage, light (based on canopy position and crown form) is most critical in the juvenile (5 cm ≤ DBH < 50 cm) phase. Suppressed trees are only present as juveniles and grow ten times slower (1.45 ± 2.73 m(2) year(-1)) than trees in dominant and co-dominant positions (13.25 ± 0.82 and 12.90 ± 1.35 m(2) year(-1), respectively). Additionally, few juvenile trees are reproductive, and those that are, demonstrate reduced growth, as do reproductive trees in the next 50 to 100 cm DBH class, suggesting growth-reproduction tradeoffs. Upon reaching the canopy, however, and attaining a sizeable girth, this pattern gradually shifts to one where BAI and reproduction are influenced independently by variables such as liana load, crown size and soil properties. At this stage, BAI is largely unaffected by fruit production levels. Thus, while growth-reproduction tradeoffs clearly exist during early life stages, effects of reproductive allocation diminish as B. excelsa increases in size and maturity.

A Semi-Automated Machine Learning Algorithm for Tree Cover Delineation from 1-m Naip Imagery Using a High Performance Computing Architecture

NASA Astrophysics Data System (ADS)

Basu, S.; Ganguly, S.; Nemani, R. R.; Mukhopadhyay, S.; Milesi, C.; Votava, P.; Michaelis, A.; Zhang, G.; Cook, B. D.; Saatchi, S. S.; Boyda, E.

2014-12-01

Accurate tree cover delineation is a useful instrument in the derivation of Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) satellite imagery data. Numerous algorithms have been designed to perform tree cover delineation in high to coarse resolution satellite imagery, but most of them do not scale to terabytes of data, typical in these VHR datasets. In this paper, we present an automated probabilistic framework for the segmentation and classification of 1-m VHR data as obtained from the National Agriculture Imagery Program (NAIP) for deriving tree cover estimates for the whole of Continental United States, using a High Performance Computing Architecture. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field (CRF), which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by incorporating expert knowledge through the relabeling of misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the state of California, which covers a total of 11,095 NAIP tiles and spans a total geographical area of 163,696 sq. miles. Our framework produced correct detection rates of around 85% for fragmented forests and 70% for urban tree cover areas, with false positive rates lower than 3% for both regions. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR high-resolution canopy height model shows the effectiveness of our algorithm in generating accurate high-resolution tree cover maps.

Tree range expansion in eastern North America fails to keep pace with climate warming at northern range limits.

PubMed

Sittaro, Fabian; Paquette, Alain; Messier, Christian; Nock, Charles A

2017-08-01

Rising global temperatures are suggested to be drivers of shifts in tree species ranges. The resulting changes in community composition may negatively impact forest ecosystem function. However, long-term shifts in tree species ranges remain poorly documented. We test for shifts in the northern range limits of 16 temperate tree species in Quebec, Canada, using forest inventory data spanning three decades, 15° of longitude and 7° of latitude. Range shifts were correlated with climate warming and dispersal traits to understand potential mechanisms underlying changes. Shifts were calculated as the change in the 95th percentile of latitudinal occurrence between two inventory periods (1970-1978, 2000-2012) and for two life stages: saplings and adults. We also examined sapling and adult range offsets within each inventory, and changes in the offset through time. Tree species ranges shifted predominantly northward, although species responses varied. As expected shifts were greater for tree saplings, 0.34 km yr -1 , than for adults, 0.13 km yr -1 . Range limits were generally further north for adults compared to saplings, but the difference diminished through time, consistent with patterns observed for range shifts within each life stage. This suggests caution should be exercised when interpreting geographic range offsets between life stages as evidence of range shifts in the absence of temporal data. Species latitudinal velocities were on average <50% of the velocity required to equal the spatial velocity of climate change and were mostly unrelated to dispersal traits. Finally, our results add to the body of evidence suggesting tree species are mostly limited in their capacity to track climate warming, supporting concerns that warming will negatively impact the functioning of forest ecosystems. © 2017 John Wiley & Sons Ltd.

Reconciliation of Decision-Making Heuristics Based on Decision Trees Topologies and Incomplete Fuzzy Probabilities Sets

PubMed Central

Doubravsky, Karel; Dohnal, Mirko

2015-01-01

Complex decision making tasks of different natures, e.g. economics, safety engineering, ecology and biology, are based on vague, sparse, partially inconsistent and subjective knowledge. Moreover, decision making economists / engineers are usually not willing to invest too much time into study of complex formal theories. They require such decisions which can be (re)checked by human like common sense reasoning. One important problem related to realistic decision making tasks are incomplete data sets required by the chosen decision making algorithm. This paper presents a relatively simple algorithm how some missing III (input information items) can be generated using mainly decision tree topologies and integrated into incomplete data sets. The algorithm is based on an easy to understand heuristics, e.g. a longer decision tree sub-path is less probable. This heuristic can solve decision problems under total ignorance, i.e. the decision tree topology is the only information available. But in a practice, isolated information items e.g. some vaguely known probabilities (e.g. fuzzy probabilities) are usually available. It means that a realistic problem is analysed under partial ignorance. The proposed algorithm reconciles topology related heuristics and additional fuzzy sets using fuzzy linear programming. The case study, represented by a tree with six lotteries and one fuzzy probability, is presented in details. PMID:26158662

Reconciliation of Decision-Making Heuristics Based on Decision Trees Topologies and Incomplete Fuzzy Probabilities Sets.

PubMed

Doubravsky, Karel; Dohnal, Mirko

2015-01-01

Complex decision making tasks of different natures, e.g. economics, safety engineering, ecology and biology, are based on vague, sparse, partially inconsistent and subjective knowledge. Moreover, decision making economists / engineers are usually not willing to invest too much time into study of complex formal theories. They require such decisions which can be (re)checked by human like common sense reasoning. One important problem related to realistic decision making tasks are incomplete data sets required by the chosen decision making algorithm. This paper presents a relatively simple algorithm how some missing III (input information items) can be generated using mainly decision tree topologies and integrated into incomplete data sets. The algorithm is based on an easy to understand heuristics, e.g. a longer decision tree sub-path is less probable. This heuristic can solve decision problems under total ignorance, i.e. the decision tree topology is the only information available. But in a practice, isolated information items e.g. some vaguely known probabilities (e.g. fuzzy probabilities) are usually available. It means that a realistic problem is analysed under partial ignorance. The proposed algorithm reconciles topology related heuristics and additional fuzzy sets using fuzzy linear programming. The case study, represented by a tree with six lotteries and one fuzzy probability, is presented in details.

Many-to-Many Multicast Routing Schemes under a Fixed Topology

PubMed Central

Ding, Wei; Wang, Hongfa; Wei, Xuerui

2013-01-01

Many-to-many multicast routing can be extensively applied in computer or communication networks supporting various continuous multimedia applications. The paper focuses on the case where all users share a common communication channel while each user is both a sender and a receiver of messages in multicasting as well as an end user. In this case, the multicast tree appears as a terminal Steiner tree (TeST). The problem of finding a TeST with a quality-of-service (QoS) optimization is frequently NP-hard. However, we discover that it is a good idea to find a many-to-many multicast tree with QoS optimization under a fixed topology. In this paper, we are concerned with three kinds of QoS optimization objectives of multicast tree, that is, the minimum cost, minimum diameter, and maximum reliability. All of three optimization problems are distributed into two types, the centralized and decentralized version. This paper uses the dynamic programming method to devise an exact algorithm, respectively, for the centralized and decentralized versions of each optimization problem. PMID:23589706

Grading sugar pine saw logs in trees.

Treesearch

John W. Henley

1972-01-01

Small limbs and small overgrown limbs cause problems when grading saw logs in sugar pine trees. Surface characteristics and lumber recovery information for 426 logs from 64 sugar pine trees were examined. Resulting modifications in the grading specification that allow a grader to ignore small limbs and small limb indicators do not appear to decrease the performance of...

Goal Programming: A New Tool for the Christmas Tree Industry

Treesearch

Bruce G. Hansen

1977-01-01

Goal programing (GP) can be useful for decision making in the natural Christmas tree industry. Its usefulness is demonstrated through an analysis of a hypothetical problem in which two potential growers decide how to use 10 acres in growing Christmas trees. Though the physical settings are identical, distinct differences between their goals significantly influence the...

Tree improvement opportunities in the North-Central States related to economic trends, a problem analysis.

Treesearch

David H. Dawson; John A. Pitcher

1970-01-01

Economic trends are interpreted and related to planning applied forest tree-improvement programs for the North-Central Region. Projected demands for forest products are considered in light of the forest resource and alternatives for its use. Suggestions are given for tree-improvement programs for seven conifer and three hardwood species.

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

PubMed

Ramu, Avinash; Kahveci, Tamer; Burleigh, J Gordon

2012-10-03

We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees

PubMed Central

2012-01-01

Background We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. Results We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Conclusions Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses. PMID:23033843

Satellite image analysis for surveillance, vegetation and climate change

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

Cai, D Michael

2011-01-18

Recently, many studies have provided abundant evidence to show the trend of tree mortality is increasing in many regions, and the cause of tree mortality is associated with drought, insect outbreak, or fire. Unfortunately, there is no current capability available to monitor vegetation changes, and correlate and predict tree mortality with CO{sub 2} change, and climate change on the global scale. Different survey platforms (methods) have been used for forest management. Typical ground-based forest surveys measure tree stem diameter, species, and alive or dead. The measurements are low-tech and time consuming, but the sample sizes are large, running into millionsmore » of trees, covering large areas, and spanning many years. These field surveys provide powerful ground validation for other survey methods such as photo survey, helicopter GPS survey, and aerial overview survey. The satellite imagery has much larger coverage. It is easier to tile the different images together, and more important, the spatial resolution has been improved such that close to or even higher than aerial survey platforms. Today, the remote sensing satellite data have reached sub-meter spatial resolution for panchromatic channels (IKONOS 2: 1 m; Quickbird-2: 0.61 m; Worldview-2: 0.5 m) and meter spatial resolution for multi-spectral channels (IKONOS 2: 4 meter; Quickbird-2: 2.44 m; Worldview-2: 2 m). Therefore, high resolution satellite imagery can allow foresters to discern individual trees. This vital information should allow us to quantify physiological states of trees, e.g. healthy or dead, shape and size of tree crowns, as well as species and functional compositions of trees. This is a powerful data resource, however, due to the vast amount of the data collected daily, it is impossible for human analysts to review the imagery in detail to identify the vital biodiversity information. Thus, in this talk, we will discuss the opportunities and challenges to use high resolution satellite imagery and machine learning theory to monitor tree mortality at the level of individual trees.« less

Monitoring stress-related mass variations in Amazon trees using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, T. H. M.; Steele-Dunne, S. C.; Gentine, P.; Hut, R.; Guerin, M. F.; Leus, G.; Oliveira, R. S.; Van De Giesen, N.

2016-12-01

Containing half of the world's rainforests, the Amazon plays a key role in the global water and carbon budget. However, the Amazon remains poorly understood, but appears to be vulnerable to increasing moisture stress, and future droughts have the potential to considerably change the global water and carbon budget. Field measurements will allow further investigations of the effects of moisture stress and droughts on tree dynamics, and its impact on the water and carbon budget. This study focuses on studying the diurnal mass variations of seven Amazonian tree species. The mass of trees is influenced by physiological processes within the tree (e.g. transpiration and root water uptake), as well as external loads (e.g. intercepted precipitation). Depending on the physiological traits of an individual tree, moisture stress and drought affect processes such as photosynthesis, assimilation, transpiration, and root water uptake. In turn, these have their influence on diurnal mass variations of a tree. Our study uses measured three-dimensional displacement and acceleration of trees, to detect and quantify their diurnal (bio)mass variations. Nineteen accelerometers and dendrometers were installed on seven different tree species in the Amazon rainforest, covering an area of 250 x 250 m. The selected species span a wide range in wood density (0.5 - 1.1), diameter (15 - 40 cm) and height (25 - 60 m). Acceleration was measured with a frequency of 10 Hz, from August 2015 to June 2016, covering both the wet and dry season. On-site additional measurements of net radiation, wind speed at three heights, temperature, and precipitation as available every 15 minutes. Dendrometers measured variation in xylem and bark thickness every 5 minutes. The MUltiple SIgnal Classification (MUSIC) algorithm was applied to the acceleration time series to estimate the frequency spectrum of each tree. A correction was necessary to account for the dominant effect of wind. The resulting spectra reveal clear diurnal variations, as well as changes during precipitation events. Comparison with ancillary data suggests that we can extract information on diurnal mass variations from the accelerometer data. This may provide valuable insight into the effects of water stress on mass variations in different Amazon tree species.

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.

Tree regeneration following drought- and insect-induced mortality in piñon-juniper woodlands.

PubMed

Redmond, Miranda D; Barger, Nichole N

2013-10-01

Widespread piñon (Pinus edulis) mortality occurred across the southwestern USA during 2002-2003 in response to drought and bark beetle infestations. Given the recent mortality and changes in regional climate over the past several decades, there is a keen interest in post-mortality regeneration dynamics in piñon-juniper woodlands. Here, we examined piñon and Utah juniper (Juniperus osteosperma) recruitment at 30 sites across southwestern Colorado, USA that spanned a gradient of adult piñon mortality levels (10-100%) to understand current regeneration dynamics. Piñon and juniper recruitment was greater at sites with more tree and shrub cover. Piñon recruitment was more strongly facilitated than juniper recruitment by trees and shrubs. New (post-mortality) piñon recruitment was negatively affected by recent mortality. However, mortality had no effect on piñon advanced regeneration (juveniles established pre-mortality) and did not shift juvenile piñon dominance. Our results highlight the importance of shrubs and juniper trees for the facilitation of piñon establishment and survival. Regardless of adult piñon mortality levels, areas with low tree and shrub cover may become increasingly juniper dominated as a result of the few suitable microsites for piñon establishment and survival. In areas with high piñon mortality and high tree and shrub cover, our results suggest that piñon is regenerating via advanced regeneration. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

The spanwise distribution of lift for minimum induced drag of wings having a given lift and a given bending moment

NASA Technical Reports Server (NTRS)

Jones, R. T.

1950-01-01

The problem of the minimum induced drag of wings having a given lift and a given span is extended to include cases in which the bending moment to be supported by the wing is also given. The theory is limited to lifting surfaces traveling at subsonic speeds. It is found that the required shape of the downwash distribution can be obtained in an elementary way which is applicable to a variety of such problems. Expressions for the minimum drag and the corresponding spanwise load distributions are also given for the case in which the lift and the bending moment about the wing root are fixed while the span is allowed to vary. The results show a 15-percent reduction of the induced drag with a 15-percent increase in span as compared with results for an elliptically loaded wing having the same total lift and bending moment.

Challenging process to make the Lateglacial tree-ring chronologies from Europe absolute - an inventory

NASA Astrophysics Data System (ADS)

Kaiser, Klaus Felix; Friedrich, Michael; Miramont, Cécile; Kromer, Bernd; Sgier, Mario; Schaub, Matthias; Boeren, Ilse; Remmele, Sabine; Talamo, Sahra; Guibal, Frédéric; Sivan, Olivier

2012-03-01

Here we present the entire range of Lateglacial tree-ring chronologies from Switzerland, Germany, France, covering the Lateglacial north and west of the Alps without interruption as well as finds from northern Italy, complemented by a 14C data set of the Swiss chronologies. Geographical expansion of cross-matched European Lateglacial chronologies, limits and prospects of teleconnection between remote sites and extension of the absolute tree-ring chronology are discussed. High frequency signals and long-term fluctuations are revealed by the ring-width data sets of the newly constructed Swiss Late-glacial Master Chronology (SWILM) as well as the Central European Lateglacial Master Chronology (CELM) spanning 1606 years. They agree well with the characteristics of Boelling/Alleroed (GI-1) and the transition into Younger Dryas (GS-1). The regional chronologies of Central Europe may provide improved interconnection to other terrestrial or marine high-resolution archives. Nevertheless the breakthrough to a continuous absolute chronology back to Boelling (GI-1e) has not yet been achieved. A gap remains, even though it is covered by several floating chronologies from France and Switzerland.

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

The probability of monophyly of a sample of gene lineages on a species tree

PubMed Central

Mehta, Rohan S.; Bryant, David; Rosenberg, Noah A.

2016-01-01

Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte. PMID:27432988

Ranking of tree-ring based temperature reconstructions of the past millennium

NASA Astrophysics Data System (ADS)

Esper, Jan; Krusic, Paul J.; Ljungqvist, Fredrik C.; Luterbacher, Jürg; Carrer, Marco; Cook, Ed; Davi, Nicole K.; Hartl-Meier, Claudia; Kirdyanov, Alexander; Konter, Oliver; Myglan, Vladimir; Timonen, Mauri; Treydte, Kerstin; Trouet, Valerie; Villalba, Ricardo; Yang, Bao; Büntgen, Ulf

2016-08-01

Tree-ring chronologies are widely used to reconstruct high-to low-frequency variations in growing season temperatures over centuries to millennia. The relevance of these timeseries in large-scale climate reconstructions is often determined by the strength of their correlation against instrumental temperature data. However, this single criterion ignores several important quantitative and qualitative characteristics of tree-ring chronologies. Those characteristics are (i) data homogeneity, (ii) sample replication, (iii) growth coherence, (iv) chronology development, and (v) climate signal including the correlation with instrumental data. Based on these 5 characteristics, a reconstruction-scoring scheme is proposed and applied to 39 published, millennial-length temperature reconstructions from Asia, Europe, North America, and the Southern Hemisphere. Results reveal no reconstruction scores highest in every category and each has their own strengths and weaknesses. Reconstructions that perform better overall include N-Scan and Finland from Europe, E-Canada from North America, Yamal and Dzhelo from Asia. Reconstructions performing less well include W-Himalaya and Karakorum from Asia, Tatra and S-Finland from Europe, and Great Basin from North America. By providing a comprehensive set of criteria to evaluate tree-ring chronologies we hope to improve the development of large-scale temperature reconstructions spanning the past millennium. All reconstructions and their corresponding scores are provided at http://www.blogs.uni-mainz.de/fb09climatology.

The Creation and Statistical Evaluation of a Deterministic Model of the Human Bronchial Tree from HRCT Images.

PubMed

Montesantos, Spyridon; Katz, Ira; Pichelin, Marine; Caillibotte, Georges

2016-01-01

A quantitative description of the morphology of lung structure is essential prior to any form of predictive modeling of ventilation or aerosol deposition implemented within the lung. The human lung is a very complex organ, with airway structures that span two orders of magnitude and having a multitude of interfaces between air, tissue and blood. As such, current medical imaging protocols cannot provide medical practitioners and researchers with in-vivo knowledge of deeper lung structures. In this work a detailed algorithm for the generation of an individualized 3D deterministic model of the conducting part of the human tracheo-bronchial tree is described. Distinct initial conditions were obtained from the high-resolution computed tomography (HRCT) images of seven healthy volunteers. The algorithm developed is fractal in nature and is implemented as a self-similar space sub-division procedure. The expansion process utilizes physiologically realistic relationships and thresholds to produce an anatomically consistent human airway tree. The model was validated through extensive statistical analysis of the results and comparison of the most common morphological features with previously published morphometric studies and other equivalent models. The resulting trees were shown to be in good agreement with published human lung geometric characteristics and can be used to study, among other things, structure-function relationships in simulation studies.

Cognitive strategy interventions improve word problem solving and working memory in children with math disabilities.

PubMed

Swanson, H Lee

2015-01-01

This study investigated the role of strategy instruction and working memory capacity (WMC) on problem solving solution accuracy in children with and without math disabilities (MD). Children in grade 3 (N = 204) with and without MD subdivided into high and low WMC were randomly assigned to 1 of 4 conditions: verbal strategies (e.g., underlining question sentence), visual strategies (e.g., correctly placing numbers in diagrams), verbal + visual strategies, and an untreated control. The dependent measures for training were problem solving accuracy and two working memory transfer measures (operation span and visual-spatial span). Three major findings emerged: (1) strategy instruction facilitated solution accuracy but the effects of strategy instruction were moderated by WMC, (2) some strategies yielded higher post-test scores than others, but these findings were qualified as to whether children were at risk for MD, and (3) strategy training on problem solving measures facilitated transfer to working memory measures. The main findings were that children with MD, but high WM spans, were more likely to benefit from strategy conditions on target and transfer measures than children with lower WMC. The results suggest that WMC moderates the influence of cognitive strategies on both the targeted and non-targeted measures.

Cognitive strategy interventions improve word problem solving and working memory in children with math disabilities

PubMed Central

Swanson, H. Lee

2015-01-01

This study investigated the role of strategy instruction and working memory capacity (WMC) on problem solving solution accuracy in children with and without math disabilities (MD). Children in grade 3 (N = 204) with and without MD subdivided into high and low WMC were randomly assigned to 1 of 4 conditions: verbal strategies (e.g., underlining question sentence), visual strategies (e.g., correctly placing numbers in diagrams), verbal + visual strategies, and an untreated control. The dependent measures for training were problem solving accuracy and two working memory transfer measures (operation span and visual-spatial span). Three major findings emerged: (1) strategy instruction facilitated solution accuracy but the effects of strategy instruction were moderated by WMC, (2) some strategies yielded higher post-test scores than others, but these findings were qualified as to whether children were at risk for MD, and (3) strategy training on problem solving measures facilitated transfer to working memory measures. The main findings were that children with MD, but high WM spans, were more likely to benefit from strategy conditions on target and transfer measures than children with lower WMC. The results suggest that WMC moderates the influence of cognitive strategies on both the targeted and non-targeted measures. PMID:26300803

Maximum parsimony, substitution model, and probability phylogenetic trees.

PubMed

Weng, J F; Thomas, D A; Mareels, I

2011-01-01

The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

A new tool for post-AGB SED classification

NASA Astrophysics Data System (ADS)

Bendjoya, P.; Suarez, O.; Galluccio, L.; Michel, O.

We present the results of an unsupervised classification method applied on a set of 344 spectral energy distributions (SED) of post-AGB stars extracted from the Torun catalogue of Galactic post-AGB stars. This method aims to find a new unbiased method for post-AGB star classification based on the information contained in the IR region of the SED (fluxes, IR excess, colours). We used the data from IRAS and MSX satellites, and from the 2MASS survey. We applied a classification method based on the construction of the dataset of a minimal spanning tree (MST) with the Prim's algorithm. In order to build this tree, different metrics have been tested on both flux and color indices. Our method is able to classify the set of 344 post-AGB stars in 9 distinct groups according to their SEDs.

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.

Topology of the South African stock market network across the 2008 financial crisis

NASA Astrophysics Data System (ADS)

Majapa, Mohamed; Gossel, Sean Joss

2016-03-01

This study uses the cross-correlations in the daily closing prices of the South African Top 100 companies listed on the JSE All share index (ALSI) from June 2003 to June 2013 to compute minimum spanning tree maps. In addition to the full sample, the analysis also uses three sub-periods to investigate the topological evolution before, during, and after the 2008 financial crisis. The findings show that although there is substantial clustering and homogeneity on the JSE, the most connected nodes are in the financial and resources sectors. The sub-sample results further reveal that the JSE network tree shrank in the run-up to, and during the financial crisis, and slowly expanded afterwards. In addition, the different clusters in the network are connected by various nodes that are significantly affected by diversification and credit market dynamics.

Functional roles of the cingulo-frontal network in performance on working memory.

PubMed

Kondo, Hirohito; Morishita, Masanao; Osaka, Naoyuki; Osaka, Mariko; Fukuyama, Hidenao; Shibasaki, Hiroshi

2004-01-01

We examined the relationship between brain activities and task performance on working memory. A large-scale study was initially administered to identify good and poor performers using the operation span and reading span tasks. On the basis of those span scores, we divided 20 consenting participants into high- and low-span groups. In an fMRI study, the participants performed verification of arithmetic problems and retention of target words either concurrently or separately. The behavioral results showed that performance was better in the high-span group than in the low-span group under a dual-task condition, but not under two single-task conditions. The anterior cingulate cortex (ACC), left prefrontal cortex (PFC), left inferior frontal cortex, and bilateral parietal cortex were primarily activated for both span groups. We found that signal changes in the ACC were greater in the high-span group than in the low-span group under the dual-task condition, but not under the single-task conditions. Structural equation modeling indicated that an estimate of effective connectivity from the ACC to the left PFC was positive for the high-span group and negative for the-low span group, suggesting that closer cooperation between the two brain regions was strongly related to working memory performance. We conclude that central executive functioning for attention shifting is modulated by the cingulo-frontal network.

Non-unique key B-Tree implementation

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

Ries, D.R.

1980-12-23

The B-Trees are an indexed method to allow fast retrieval and order preserving updates to a FRAMIS relation based on a designated set of keys in the relation. A B-Tree access method is being implemented to provide indexed and sequential (in index order) access to FRAMIS relations. The implementation modifies the basic B-Tree structure to correctly allow multiple key values and still maintain the balanced page fill property of B-Trees. The data structures of the B-Tree are presented first, including the FRAMIS solution to the duplicate key value problem. Then the access level routines and utilities are presented. These routinesmore » include the original B-Tree creation; searching the B-Tree; and inserting, deleting, and replacing tuples on the B-Tree. In conclusion, the uses of the B-Tree access structures at the semantic level to enhance the FRAMIS performance are discussed. 10 figures.« less

Everyday problem solving across the adult life span: solution diversity and efficacy.

PubMed

Mienaltowski, Andrew

2011-10-01

Everyday problem solving involves examining the solutions that individuals generate when faced with problems that take place in their everyday experiences. Problems can range from medication adherence and meal preparation to disagreeing with a physician over a recommended medical procedure or compromising with extended family members over where to host Thanksgiving dinner. Across the life span, research has demonstrated divergent patterns of change in performance based on the type of everyday problems used as well as based on the way that problem-solving efficacy is operationally defined. Advancing age is associated with worsening performance when tasks involve single-solution or fluency-based definitions of effectiveness. However, when efficacy is defined in terms of the diversity of strategies used, as well as by the social and emotional impact of solution choice on the individual, performance is remarkably stable and sometimes even improves in the latter half of life. This article discusses how both of these approaches to everyday problem solving inform research on the influence that aging has on everyday functioning. © 2011 New York Academy of Sciences.

Everyday problem solving across the adult life span: solution diversity and efficacy

PubMed Central

Mienaltowski, Andrew

2013-01-01

Everyday problem solving involves examining the solutions that individuals generate when faced with problems that take place in their everyday experiences. Problems can range from medication adherence and meal preparation to disagreeing with a physician over a recommended medical procedure or compromising with extended family members over where to host Thanksgiving dinner. Across the life span, research has demonstrated divergent patterns of change in performance based on the type of everyday problems used as well as based on the way that problem-solving efficacy is operationally defined. Advancing age is associated with worsening performance when tasks involve single-solution or fluency-based definitions of effectiveness. However, when efficacy is defined in terms of the diversity of strategies used, as well as by the social and emotional impact of solution choice on the individual, performance is remarkably stable and sometimes even improves in the latter half of life. This article discusses how both of these approaches to everyday problem solving inform research on the influence that aging has on everyday functioning. PMID:22023569

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

PubMed Central

Cui, Yun; Jansson, Jesper

2012-01-01

Abstract A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host–parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists. PMID:22963134

Polynomial-time algorithms for building a consensus MUL-tree.

PubMed

Cui, Yun; Jansson, Jesper; Sung, Wing-Kin

2012-09-01

A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host-parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists.

A highly efficient machine planting system for forestry research plantations—the Wright-MSU method

Treesearch

James R. McKenna; Oriana Rueda-Krauss; Brian Beheler

2011-01-01

For forestry research purposes, grid planting with uniform tree spacing is superior to planting with nonuniform spacing because it controls density across the plantation and facilitates accurate repeat measurements. The ability to cross-check tree positions in a grid-type plantation avoids problems associated with dead or missing trees and increases the efficiency and...

Stocking levels and underlying assumptions for uneven-aged Ponderosa Pine stands.

Treesearch

P.H. Cochran

1992-01-01

Potential Problems With Q-Values Many ponderosa pine stands have a limited number of size classes, and it may be desirable to carry very large trees through several cutting cycles. Large numbers of trees below commercial size are not needed to provide adequate numbers of future replacement trees. Under these conditions, application of stand density index (SDI) can have...

Agent-based approach for generation of a money-centered star network

NASA Astrophysics Data System (ADS)

Yang, Jae-Suk; Kwon, Okyu; Jung, Woo-Sung; Kim, In-mook

2008-09-01

The history of trade is a progression from a pure barter system. A medium of exchange emerges autonomously in the market, a position currently occupied by money. We investigate an agent-based computational economics model consisting of interacting agents considering distinguishable properties of commodities which represent salability. We also analyze the properties of the commodity network using a spanning tree. We find that the “storage fee” is more crucial than “demand” in determining which commodity is used as a medium of exchange.

Longevity of guard cell chloroplasts in falling leaves: implication for stomatal function and cellular aging.

PubMed

Zeiger, E; Schwartz, A

1982-11-12

Guard cell chloroplasts in senescing leaves from 12 species of perennial trees and three species of annual plants survived considerably longer than their mesophyll counterparts. In Ginkgo biloba, stomata from yellow leaves opened during the day and closed at night; guard cell chloroplasts from these leaves showed fluorescence transients associated with electron transport and photophosphorylation. These findings indicate that guard cell chloroplasts are highly conserved throughout the life-span of the leaf and that leaves retain stomatal control during senescence.

Weighted network analysis of high-frequency cross-correlation measures

NASA Astrophysics Data System (ADS)

Iori, Giulia; Precup, Ovidiu V.

2007-03-01

In this paper we implement a Fourier method to estimate high-frequency correlation matrices from small data sets. The Fourier estimates are shown to be considerably less noisy than the standard Pearson correlation measures and thus capable of detecting subtle changes in correlation matrices with just a month of data. The evolution of correlation at different time scales is analyzed from the full correlation matrix and its minimum spanning tree representation. The analysis is performed by implementing measures from the theory of random weighted networks.

Longevity of guard cell chloroplasts in falling leaves: implication for stomatal function and cellular aging

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

Zeiger, E.; Schwartz, A.

1982-11-12

Guard cell chloroplasts in senescing leaves from 12 species of perennial trees and three species of annual plants survived considerably longer than their mesophyll counterparts. In Ginkgo biloba, stomata from yellow leaves opened during the day and closed at night; guard cell chloroplasts from these leaves showed fluorescence transients associated with electron transport and photophosphorylation. These findings indicate that guard cell chloroplasts are highly conserved throughout the life-span of the leaf and that leaves retain stomatal control during senescence.

Corona graphs as a model of small-world networks

NASA Astrophysics Data System (ADS)

Lv, Qian; Yi, Yuhao; Zhang, Zhongzhi

2015-11-01

We introduce recursive corona graphs as a model of small-world networks. We investigate analytically the critical characteristics of the model, including order and size, degree distribution, average path length, clustering coefficient, and the number of spanning trees, as well as Kirchhoff index. Furthermore, we study the spectra for the adjacency matrix and the Laplacian matrix for the model. We obtain explicit results for all the quantities of the recursive corona graphs, which are similar to those observed in real-life networks.

Using Tutte polynomials to analyze the structure of the benzodiazepines

NASA Astrophysics Data System (ADS)

Cadavid Muñoz, Juan José

2014-05-01

Graph theory in general and Tutte polynomials in particular, are implemented for analyzing the chemical structure of the benzodiazepines. Similarity analysis are used with the Tutte polynomials for finding other molecules that are similar to the benzodiazepines and therefore that might show similar psycho-active actions for medical purpose, in order to evade the drawbacks associated to the benzodiazepines based medicine. For each type of benzodiazepines, Tutte polynomials are computed and some numeric characteristics are obtained, such as the number of spanning trees and the number of spanning forests. Computations are done using the computer algebra Maple's GraphTheory package. The obtained analytical results are of great importance in pharmaceutical engineering. As a future research line, the usage of the chemistry computational program named Spartan, will be used to extent and compare it with the obtained results from the Tutte polynomials of benzodiazepines.

MDTS: automatic complex materials design using Monte Carlo tree search.

PubMed

M Dieb, Thaer; Ju, Shenghong; Yoshizoe, Kazuki; Hou, Zhufeng; Shiomi, Junichiro; Tsuda, Koji

2017-01-01

Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability. We succeeded in designing large Silicon-Germanium (Si-Ge) alloy structures that Bayesian optimization could not deal with due to excessive computational cost. MDTS is available at https://github.com/tsudalab/MDTS.

MDTS: automatic complex materials design using Monte Carlo tree search

NASA Astrophysics Data System (ADS)

Dieb, Thaer M.; Ju, Shenghong; Yoshizoe, Kazuki; Hou, Zhufeng; Shiomi, Junichiro; Tsuda, Koji

2017-12-01

Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability. We succeeded in designing large Silicon-Germanium (Si-Ge) alloy structures that Bayesian optimization could not deal with due to excessive computational cost. MDTS is available at https://github.com/tsudalab/MDTS.

Initialization Method for Grammar-Guided Genetic Programming

NASA Astrophysics Data System (ADS)

García-Arnau, M.; Manrique, D.; Ríos, J.; Rodríguez-Patón, A.

This paper proposes a new tree-generation algorithm for grammarguided genetic programming that includes a parameter to control the maximum size of the trees to be generated. An important feature of this algorithm is that the initial populations generated are adequately distributed in terms of tree size and distribution within the search space. Consequently, genetic programming systems starting from the initial populations generated by the proposed method have a higher convergence speed. Two different problems have been chosen to carry out the experiments: a laboratory test involving searching for arithmetical equalities and the real-world task of breast cancer prognosis. In both problems, comparisons have been made to another five important initialization methods.

A study of hierarchical structure on South China industrial electricity-consumption correlation

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Ji-Nan; Liu, Xiao-Feng

2016-02-01

Based on industrial electricity-consumption data of five southern provinces of China from 2005 to 2013, we study the industrial correlation mechanism with MST (minimal spanning tree) and HT (hierarchical tree) models. First, we comparatively analyze the industrial electricity-consumption correlation structure in pre-crisis and after-crisis period using MST model and Bootstrap technique of statistical reliability test of links. Results exhibit that all industrial electricity-consumption trees of five southern provinces of China in pre-crisis and after-crisis time are in formation of chain, and the "center-periphery structure" of those chain-like trees is consistent with industrial specialization in classical industrial chain theory. Additionally, the industrial structure of some provinces is reorganized and transferred in pre-crisis and after-crisis time. Further, the comparative analysis with hierarchical tree and Bootstrap technique demonstrates that as for both observations of GD and overall NF, the industrial electricity-consumption correlation is non-significant clustered in pre-crisis period, whereas it turns significant clustered in after-crisis time. Therefore we propose that in perspective of electricity-consumption, their industrial structures are directed to optimized organization and global correlation. Finally, the analysis of distance of HTs verifies that industrial reorganization and development may strengthen market integration, coordination and correlation of industrial production. Except GZ, other four provinces have a shorter distance of industrial electricity-consumption correlation in after-crisis period, revealing a better performance of regional specialization and integration.

A family of small-world network models built by complete graph and iteration-function

NASA Astrophysics Data System (ADS)

Ma, Fei; Yao, Bing

2018-02-01

Small-world networks are popular in real-life complex systems. In the past few decades, researchers presented amounts of small-world models, in which some are stochastic and the rest are deterministic. In comparison with random models, it is not only convenient but also interesting to study the topological properties of deterministic models in some fields, such as graph theory, theorem computer sciences and so on. As another concerned darling in current researches, community structure (modular topology) is referred to as an useful statistical parameter to uncover the operating functions of network. So, building and studying such models with community structure and small-world character will be a demanded task. Hence, in this article, we build a family of sparse network space N(t) which is different from those previous deterministic models. Even though, our models are established in the same way as them, iterative generation. By randomly connecting manner in each time step, every resulting member in N(t) has no absolutely self-similar feature widely shared in a large number of previous models. This makes our insight not into discussing a class certain model, but into investigating a group various ones spanning a network space. Somewhat surprisingly, our results prove all members of N(t) to possess some similar characters: (a) sparsity, (b) exponential-scale feature P(k) ∼α-k, and (c) small-world property. Here, we must stress a very screming, but intriguing, phenomenon that the difference of average path length (APL) between any two members in N(t) is quite small, which indicates this random connecting way among members has no great effect on APL. At the end of this article, as a new topological parameter correlated to reliability, synchronization capability and diffusion properties of networks, the number of spanning trees on a representative member NB(t) of N(t) is studied in detail, then an exact analytical solution for its spanning trees entropy is also obtained.

Evolution and selection of river networks: Statics, dynamics, and complexity

PubMed Central

Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

2014-01-01

Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

Assessing the Dynamic Effects of Climate on Individual Tree Growth Across Time and Space

NASA Astrophysics Data System (ADS)

Itter, M.; Finley, A. O.; D'Amato, A. W.; Foster, J. R.; Bradford, J. B.

2015-12-01

The relationship between climate variability and an ecosystem process, such as forest growth, is frequently not fixed over time, but changes due to complex interactions between unobserved ecological factors and the process of interest. Climate data and forecasts are frequently spatially and temporally misaligned with ecological observations making inference regarding the effects of climate on ecosystem processes particularly challenging. Here we develop a Bayesian dynamic hierarchical model for annual tree growth increment that allows the effects of climate to evolve over time, applies climate data at a spatial-temporal scale consistent with observations, and controls for individual-level variability commonly encountered in ecological datasets. The model is applied to individual tree data from northern Minnesota using a modified Thornthwaite-type water balance model to transform PRISM temperature and precipitation estimates to physiologically relevant values of actual and potential evapotranspiration (AET, PET), and climatic water deficit. Model results indicate that mean tree growth is most sensitive to AET during the growing season and PET and minimum temperature in the spring prior to growth. The effects of these variables on tree growth, however, are not stationary with significant effects observed in only a subset of years during the 111-year study period. Importantly, significant effects of climate do not result from anomalous climate observations, but follow from large growth deviations unexplained by tree age and size, and time since forest disturbance. Results differ markedly from alternative models that assume the effects of climate are stationary over time or apply climate estimates at the individual scale. Forecasts of future tree growth as a function of climate follow directly from the dynamic hierarchical model allowing for assessment of forest change. Current work is focused on extending the model framework to include regional climate and ecosystem effects for application to a larger tree growth dataset spanning a latitudinal gradient within the US from Maine to Florida.

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

PubMed Central

2010-01-01

Background Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. Results We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. Conclusions GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events. PMID:20534164

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

PubMed

Thomas, Paul D

2010-06-09

Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.

Condition trees as a mechanism for communicating the meaning of uncertainties

NASA Astrophysics Data System (ADS)

Beven, Keith

2015-04-01

Uncertainty communication for environmental problems is fraught with difficulty for good epistemic reasons. The fact that most sources of uncertainty are subject to, and often dominated by, epistemic uncertainties means that the unthinking use of probability theory might actually be misleading and lead to false inference (even in some cases where the assumptions of a probabilistic error model might seem to be reasonably valid). This therefore creates problems in communicating the meaning of probabilistic uncertainties of model predictions to potential users (there are many examples in hydrology, hydraulics, climate change and other domains). It is suggested that one way of being more explicit about the meaning of uncertainties is to associate each type of application with a condition tree of assumptions that need to be made in producing an estimate of uncertainty. The condition tree then provides a basis for discussion and communication of assumptions about uncertainties with users. Agreement of assumptions (albeit generally at some institutional level) will provide some buy-in on the part of users, and a basis for commissioning of future studies. Even in some relatively well-defined problems, such as mapping flood risk, such a condition tree can be rather extensive, but by making each step in the tree explicit then an audit trail is established for future reference. This can act to provide focus in the exercise of agreeing more realistic assumptions.

Automatic translation of digraph to fault-tree models

NASA Technical Reports Server (NTRS)

Iverson, David L.

1992-01-01

The author presents a technique for converting digraph models, including those models containing cycles, to a fault-tree format. A computer program which automatically performs this translation using an object-oriented representation of the models has been developed. The fault-trees resulting from translations can be used for fault-tree analysis and diagnosis. Programs to calculate fault-tree and digraph cut sets and perform diagnosis with fault-tree models have also been developed. The digraph to fault-tree translation system has been successfully tested on several digraphs of varying size and complexity. Details of some representative translation problems are presented. Most of the computation performed by the program is dedicated to finding minimal cut sets for digraph nodes in order to break cycles in the digraph. Fault-trees produced by the translator have been successfully used with NASA's Fault-Tree Diagnosis System (FTDS) to produce automated diagnostic systems.

Efficient Decoding of Compressed Data.

ERIC Educational Resources Information Center

Bassiouni, Mostafa A.; Mukherjee, Amar

1995-01-01

Discusses the problem of enhancing the speed of Huffman decoding of compressed data. Topics addressed include the Huffman decoding tree; multibit decoding; binary string mapping problems; and algorithms for solving mapping problems. (22 references) (LRW)

An Inquiry-Oriented Approach to Span and Linear Independence: The Case of the Magic Carpet Ride Sequence

ERIC Educational Resources Information Center

Wawro, Megan; Rasmussen, Chris; Zandieh, Michelle; Sweeney, George Franklin; Larson, Christine

2012-01-01

In this paper we present an innovative instructional sequence for an introductory linear algebra course that supports students' reinvention of the concepts of span, linear dependence, and linear independence. Referred to as the Magic Carpet Ride sequence, the problems begin with an imaginary scenario that allows students to build rich imagery and…

Seed dispersal limitations shift over time in tropical forest restoration.

PubMed

Reid, J Leighton; Holl, Karen D; Zahawi, Rakan A

2015-06-01

Past studies have shown that tropical forest regeneration on degraded farmlands is initially limited by lack of seed dispersal, but few studies have tracked changes in abundance and composition of seed rain past the first few years after land abandonment. We measured seed rain for 12 months in 10 6-9-year-old restoration sites and five mature, reference forests in southern Costa Rica in order to learn (1) if seed rain limitation persists past the first few years of regeneration; (2) how restoration treatments influence seed community structure and composition; and (3) whether seed rain limitation is contingent on landscape context. Each restoration site contained three 0.25-ha treatment plots: (1) a naturally regenerating control, (2) tree islands, and (3) a mixed-species tree plantation. Sites spanned a deforestation gradient with 9-89% forest area within 500 m around the treatment plots. Contrary to previous studies, we found that tree seeds were abundant and ubiquitous across all treatment plots (585.1 ± 142.0 seeds · m(-2) · yr(-1) [mean ± SE]), indicating that lack of seed rain ceased to limit forest regeneration within the first decade of recovery. Pioneer trees and shrubs comprised the vast majority of seeds, but compositional differences between restoration sites and reference forests were driven by rarer, large-seeded species. Large, animal-dispersed tree seeds were more abundant in tree islands (4.6 ± 2.9 seeds · m(-2) · yr(-1)) and plantations (5.8 ± 3.0 seeds · m(-2) · yr(-1)) than control plots (0.2 ± 0.1 seeds · m(-2) · yr(-1)), contributing to greater tree species richness in actively restored plots. Planted tree species accounted for < 1% of seeds. We found little evidence for landscape forest cover effects on seed rain, consistent with previous studies. We conclude that seed rain limitation shifted from an initial, complete lack of tree seeds to a specific limitation on large-seeded, mature forest species over the first decade. Although total seed abundance was equal among restoration treatments, tree plantations and tree islands continued to diversify seed rain communities compared to naturally regenerating controls. Compositional differences between regenerating plots and mature forests suggest that large-seeded tree species are appropriate candidates for enrichment planting.

Ecosystem services from converted land: the importance of tree cover in Amazonian pastures

USGS Publications Warehouse

Barrett, Kirsten; Valentim, Judson; Turner, B. L.

2013-01-01

Deforestation is responsible for a substantial fraction of global carbon emissions and changes in surface energy budgets that affect climate. Deforestation losses include wildlife and human habitat, and myriad forest products on which rural and urban societies depend for food, fiber, fuel, fresh water, medicine, and recreation. Ecosystem services gained in the transition from forests to pasture and croplands, however, are often ignored in assessments of the impact of land cover change. The role of converted lands in tropical areas in terms of carbon uptake and storage is largely unknown. Pastures represent the fastest-growing form of converted land use in the tropics, even in some areas of rapid urban expansion. Tree biomass stored in these areas spans a broad range, depending on tree cover. Trees in pasture increase carbon storage, provide shade for cattle, and increase productivity of forage material. As a result, increasing fractional tree cover can provide benefits land managers as well as important ecosystem services such as reducing conversion pressure on forests adjacent to pastures. This study presents an estimation of fractional tree cover in pasture in a dynamic region on the verge of large-scale land use change. An appropriate sampling interval is established for similar studies, one that balances the need for independent samples of sufficient number to characterize a pasture in terms of fractional tree cover. This information represents a useful policy tool for government organizations and NGOs interested in encouraging ecosystem services on converted lands. Using high spatial resolution remotely sensed imagery, fractional tree cover in pasture is quantified for the municipality of Rio Branco, Brazil. A semivariogram and devolving spatial resolution are employed to determine the coarsest sampling interval that may be used, minimizing effects of spatial autocorrelation. The coarsest sampling interval that minimizes spatial dependence was about 22 m. The area-weighted fractional tree cover for the study area was 1.85 %, corrected for a slight bias associated with the coarser sampling resolution. The pastures sampled for fractional tree cover were divided between ‘high’ and ‘low’ tree cover, which may be the result of intentional incorporation of arboreal species in pasture. Further research involving those ranchers that have a higher fractional tree cover may indicate ways to promote the practice on a broader scale in the region.

Bacterial Leaf Scorch of Amenity Trees a Wide-Spread Problem of Economic Significance to the Urban Forest

Treesearch

James Lashomb; Alan Iskra; Ann Brooks Gould; George Hamilton

2003-01-01

Bacterial leaf scorch (BLS) of amenity trees is caused by the bacterium Xylella fastidiosa, a xylem-limited pathogen that causes water stress resulting in leaf scorch, decline, and eventual death of affected trees. Recent surveys indicate that BLS is widespread throughout the eastern half of the United States. In New Jersey, BLS primarily affects red and pin oaks...

Jane: a new tool for the cophylogeny reconstruction problem.

PubMed

Conow, Chris; Fielder, Daniel; Ovadia, Yaniv; Libeskind-Hadas, Ran

2010-02-03

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.

A short note on the use of the red-black tree in Cartesian adaptive mesh refinement algorithms

NASA Astrophysics Data System (ADS)

Hasbestan, Jaber J.; Senocak, Inanc

2017-12-01

Mesh adaptivity is an indispensable capability to tackle multiphysics problems with large disparity in time and length scales. With the availability of powerful supercomputers, there is a pressing need to extend time-proven computational techniques to extreme-scale problems. Cartesian adaptive mesh refinement (AMR) is one such method that enables simulation of multiscale, multiphysics problems. AMR is based on construction of octrees. Originally, an explicit tree data structure was used to generate and manipulate an adaptive Cartesian mesh. At least eight pointers are required in an explicit approach to construct an octree. Parent-child relationships are then used to traverse the tree. An explicit octree, however, is expensive in terms of memory usage and the time it takes to traverse the tree to access a specific node. For these reasons, implicit pointerless methods have been pioneered within the computer graphics community, motivated by applications requiring interactivity and realistic three dimensional visualization. Lewiner et al. [1] provides a concise review of pointerless approaches to generate an octree. Use of a hash table and Z-order curve are two key concepts in pointerless methods that we briefly discuss next.

Investigation of the Stability of a Two-Span Bridge with the use of a High-Precision Laser Displacement Sensors

NASA Astrophysics Data System (ADS)

Poddaeva, O.; Churin, P.; Fedosova, A.; Truhanov, S.

2018-03-01

Studies of aerodynamics of bridge structures are an actual problem. Such attention is paid to the study of wind influence on bridge structures not at all by chance; a large number of cases of loss of stability of such structures are known under the influence of wind up to their complete destruction. The development of non-contact systems of measuring equipment allows solving this problem with a high level of accuracy and reliability. This article presents the results of experimental studies of wind impact on a two-span bridge using specialized measuring system based on high-precision laser displacement sensors.

Reconstructing Unrooted Phylogenetic Trees from Symbolic Ternary Metrics.

PubMed

Grünewald, Stefan; Long, Yangjing; Wu, Yaokun

2018-03-09

Böcker and Dress (Adv Math 138:105-125, 1998) presented a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree T with leaf set X and a proper vertex coloring of its interior vertices, we can map every triple of three different leaves to the color of its median vertex. We characterize all ternary maps that can be obtained in this way in terms of 4- and 5-point conditions, and we show that the corresponding tree and its coloring can be reconstructed from a ternary map that satisfies those conditions. Further, we give an additional condition that characterizes whether the tree is binary, and we describe an algorithm that reconstructs general trees in a bottom-up fashion.

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2016-11-11

Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.

Computing Role Assignments of Proper Interval Graphs in Polynomial Time

NASA Astrophysics Data System (ADS)

Heggernes, Pinar; van't Hof, Pim; Paulusma, Daniël

A homomorphism from a graph G to a graph R is locally surjective if its restriction to the neighborhood of each vertex of G is surjective. Such a homomorphism is also called an R-role assignment of G. Role assignments have applications in distributed computing, social network theory, and topological graph theory. The Role Assignment problem has as input a pair of graphs (G,R) and asks whether G has an R-role assignment. This problem is NP-complete already on input pairs (G,R) where R is a path on three vertices. So far, the only known non-trivial tractable case consists of input pairs (G,R) where G is a tree. We present a polynomial time algorithm that solves Role Assignment on all input pairs (G,R) where G is a proper interval graph. Thus we identify the first graph class other than trees on which the problem is tractable. As a complementary result, we show that the problem is Graph Isomorphism-hard on chordal graphs, a superclass of proper interval graphs and trees.

A Sharp methodology for VLSI layout

NASA Astrophysics Data System (ADS)

Bapat, Shekhar

1993-01-01

The layout problem for VLSI circuits is recognized as a very difficult problem and has been traditionally decomposed into the several seemingly independent sub-problems of placement, global routing, and detailed routing. Although this structure achieves a reduction in programming complexity, it is also typically accompanied by a reduction in solution quality. Most current placement research recognizes that the separation is artificial, and that the placement and routing problems should be solved ideally in tandem. We propose a new interconnection model, Sharp and an associated partitioning algorithm. The Sharp interconnection model uses a partitioning shape that roughly resembles the musical sharp 'number sign' and makes extensive use of pre-computed rectilinear Steiner trees. The model is designed to generate strategic routing information along with the partitioning results. Additionally, the Sharp model also generates estimates of the routing congestion. We also propose the Sharp layout heuristic that solves the layout problem in its entirety. The Sharp layout heuristic makes extensive use of the Sharp partitioning model. The use of precomputed Steiner tree forms enables the method to model accurately net characteristics. For example, the Steiner tree forms can model both the length of the net and more importantly its route. In fact, the tree forms are also appropriate for modeling the timing delays of nets. The Sharp heuristic works to minimize both the total layout area by minimizing total net length (thus reducing the total wiring area), and the congestion imbalances in the various channels (thus reducing the unused or wasted channel area). Our heuristic uses circuit element movements amongst the different partitioning blocks and selection of alternate minimal Steiner tree forms to achieve this goal. The objective function for the algorithm can be modified readily to include other important circuit constraints like propagation delays. The layout technique first computes a very high-level approximation of the layout solution (i.e., the positions of the circuit elements and the associated net routes). The approximate solution is alternately refined, objective function. The technique creates well defined sub-problems and offers intermediary steps that can be solved in parallel, as well as a parallel mechanism to merge the sub-problem solutions.

Biogeochemical and Ecomorphological Niche Segregation of Mediterranean Woody Species along a Local Gradient.

PubMed

de la Riva, Enrique G; Marañón, Teodoro; Violle, Cyrille; Villar, Rafael; Pérez-Ramos, Ignacio M

2017-01-01

According with niche theory the species are specialized in different ecological niches, being able to coexist as result of a differential use of resources. In this context, the biogeochemical niche hypothesis proposes that species have an optimal elemental composition which results from the link between the chemical and morphological traits for the optimum plant functioning. Thus, and attending to the limiting similarity concept, different elemental composition and plant structure among co-occurring species may reduce competition, promoting different functional niches. Different functional habits associated with leaf life-span or growth forms are associated with different strategies for resource uptake, which could promote niche partitioning. In the present study, based on the biogeochemical niche concept and the use of resources in different proportions, we have focused on leaf traits (morphological and chemical) associated with resource uptake, and explored the niche partitioning among functional habits: leaf life-span (deciduous, evergreen, and semideciduous) and growth (tree, shrub, and arborescent-shrub). To this end, we have quantified the hypervolume of the leaf functional trait space (both structure and chemical composition) in a sample of 45 Mediterranean woody species from Sierra Morena Mountains (Spain) growing along a local soil resource gradient. Our results show consistent variation in functional space for woody communities distributed along the environmental gradient. Thus, communities dominated by deciduous trees with faster growth and a predominant acquisitive strategy were characteristic of bottom forests and showed highest leaf biogeochemical space. While semideciduous shrubs and evergreen (arborescent, trees) species, characterized by a conservative strategy, dominated ridge forests and showed smaller functional space. In addition, within each topographical zone or environment type, the foliar biogeochemical niche partitioning would underlie the species ability to coexist by diverging on leaf nutrient composition and resource uptake. Lower niche overlap among functional habits were found, which support that different growth forms and leaf life-habits may facilitate the coexistence of the woody species and niche partitioning along and within the gradient.

Large-scale disturbance legacies and the climate sensitivity of primary Picea abies forests.

PubMed

Schurman, Jonathan S; Trotsiuk, Volodymyr; Bače, Radek; Čada, Vojtěch; Fraver, Shawn; Janda, Pavel; Kulakowski, Dominik; Labusova, Jana; Mikoláš, Martin; Nagel, Thomas A; Seidl, Rupert; Synek, Michal; Svobodová, Kristýna; Chaskovskyy, Oleh; Teodosiu, Marius; Svoboda, Miroslav

2018-05-01

Determining the drivers of shifting forest disturbance rates remains a pressing global change issue. Large-scale forest dynamics are commonly assumed to be climate driven, but appropriately scaled disturbance histories are rarely available to assess how disturbance legacies alter subsequent disturbance rates and the climate sensitivity of disturbance. We compiled multiple tree ring-based disturbance histories from primary Picea abies forest fragments distributed throughout five European landscapes spanning the Bohemian Forest and the Carpathian Mountains. The regional chronology includes 11,595 tree cores, with ring dates spanning the years 1750-2000, collected from 560 inventory plots in 37 stands distributed across a 1,000 km geographic gradient, amounting to the largest disturbance chronology yet constructed in Europe. Decadal disturbance rates varied significantly through time and declined after 1920, resulting in widespread increases in canopy tree age. Approximately 75% of current canopy area recruited prior to 1900. Long-term disturbance patterns were compared to an historical drought reconstruction, and further linked to spatial variation in stand structure and contemporary disturbance patterns derived from LANDSAT imagery. Historically, decadal Palmer drought severity index minima corresponded to higher rates of canopy removal. The severity of contemporary disturbances increased with each stand's estimated time since last major disturbance, increased with mean diameter, and declined with increasing within-stand structural variability. Reconstructed spatial patterns suggest that high small-scale structural variability has historically acted to reduce large-scale susceptibility and climate sensitivity of disturbance. Reduced disturbance rates since 1920, a potential legacy of high 19th century disturbance rates, have contributed to a recent region-wide increase in disturbance susceptibility. Increasingly common high-severity disturbances throughout primary Picea forests of Central Europe should be reinterpreted in light of both legacy effects (resulting in increased susceptibility) and climate change (resulting in increased exposure to extreme events). © 2018 John Wiley & Sons Ltd.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Insights into intraspecific wood density variation and its relationship to growth, height and elevation in a treeline species.

PubMed

Fajardo, A

2018-05-01

The wood economics spectrum provides a general framework for interspecific trait-trait coordination across wide environmental gradients. Whether global patterns are mirrored within species constitutes a poorly explored subject. In this study, I first determined whether wood density co-varies together with elevation, tree growth and height at the within-species level. Second, I determined the variation of wood density in different stem parts (trunk, branch and twigs). In situ trunk sapwood, trunk heartwood, branch and twig densities, in addition to stem growth rates and tree height were determined in adult trees of Nothofagus pumilio at four elevations in five locations spanning 18° of latitude. Mixed effects models were fitted to test relationships among variables. The variation in wood density reported in this study was narrow (ca. 0.4-0.6 g cm -3 ) relative to global density variation (ca. 0.3-1.0 g cm -3 ). There was no significant relationship between stem growth rates and wood density. Furthermore, the elevation gradient did not alter the wood density of any stem part. Trunk sapwood density was negatively related to tree height. Twig density was higher than branch and trunk densities. Trunk heartwood density was always significantly higher than sapwood density. Negative across-species trends found in the growth-wood density relationship may not emerge as the aggregate of parallel intraspecific patterns. Actually, trees with contrasting growth rates show similar wood density values. Tree height, which is tightly related to elevation, showed a negative relationship with sapwood density. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland.

PubMed

Xia, Wenjing; Nielly-Thibault, Lou; Charron, Guillaume; Landry, Christian R; Kasimer, Dahlia; Anderson, James B; Kohn, Linda M

2017-02-01

Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km 2 in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies. © 2016 John Wiley & Sons Ltd.

There is no temperature dependence of net biochemical fractionation of hydrogen and oxygen isotopes in tree-ring cellulose.

PubMed

Roden, J S; Ehleringer, J R

2000-01-01

The isotopic composition of tree-ring cellulose was obtained over a two-year period from small diameter, riparian zone trees along an elevational transect in Big Cottonwood Canyon, Utah, USA to test for a possible temperature dependence of net biological fractionation during cellulose synthesis. The isotope ratios of stream water varied by only 3.6% and 0.2% in deltaD and delta18O, respectively, over an elevation change of 810m. The similarity in stream water and macroenvironment over the short (13km) transect produced nearly constant stem and leaf water deltaD and delta18O values. In addition, what few seasonal variations observed in the isotopic composition of source water and atmospheric water vapor or in leaf water evaporative enrichment were experienced equally by all sites along the elevational transect. The temperature at each site along the transect spanned a range of > or = 5 degrees C as calculated using the adiabatic lapse rate. Since the deltaD and delta18O values of stem and leaf water varied little for these trees over this elevation/temperature transect, any differences in tree-ring cellulose deltaD and delta18O values should have been associated with temperature effects on net biological fractionation. However, the slopes of the regressions of elevation versus the deltaD and delta18O values of tree-ring cellulose were not significantly different from zero indicating little or no temperature dependence of net biological fractionation. Therefore, cross-site climatic reconstruction studies using the isotope ratios of cellulose need not be concerned that temperatures during the growing season have influenced results.

Minimal spanning tree algorithm for γ-ray source detection in sparse photon images: cluster parameters and selection strategies

DOE PAGES

Campana, R.; Bernieri, E.; Massaro, E.; ...

2013-05-22

We present that the minimal spanning tree (MST) algorithm is a graph-theoretical cluster-finding method. We previously applied it to γ-ray bidimensional images, showing that it is quite sensitive in finding faint sources. Possible sources are associated with the regions where the photon arrival directions clusterize. MST selects clusters starting from a particular “tree” connecting all the point of the image and performing a cut based on the angular distance between photons, with a number of events higher than a given threshold. In this paper, we show how a further filtering, based on some parameters linked to the cluster properties, canmore » be applied to reduce spurious detections. We find that the most efficient parameter for this secondary selection is the magnitudeM of a cluster, defined as the product of its number of events by its clustering degree. We test the sensitivity of the method by means of simulated and real Fermi-Large Area Telescope (LAT) fields. Our results show that √M is strongly correlated with other statistical significance parameters, derived from a wavelet based algorithm and maximum likelihood (ML) analysis, and that it can be used as a good estimator of statistical significance of MST detections. Finally, we apply the method to a 2-year LAT image at energies higher than 3 GeV, and we show the presence of new clusters, likely associated with BL Lac objects.« less

MISTICA: Minimum Spanning Tree-based Coarse Image Alignment for Microscopy Image Sequences

PubMed Central

Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T.

2016-01-01

Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to re-order the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries. PMID:26415193

MISTICA: Minimum Spanning Tree-Based Coarse Image Alignment for Microscopy Image Sequences.

PubMed

Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T

2016-11-01

Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to reorder the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by the way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries.

Tree-Ring-Based Reconstruction of Precipitation in the Bighorn Basin, Wyoming, since 1260 a.d.

NASA Astrophysics Data System (ADS)

Gray, Stephen T.; Fastie, Christopher L.; Jackson, Stephen T.; Betancourt, Julio L.

2004-10-01

Cores and cross sections from 79 Douglas fir () and limber pine (Pinus flexilis) trees at four sites in the Bighorn Basin of north-central Wyoming and south-central Montana were used to develop a proxy for annual (June June) precipitation spanning 1260 1998 A.D. The reconstruction exhibits considerable nonstationarity, and the instrumental era (post-1900) in particular fails to capture the full range of precipitation variability experienced in the past 750 years. Both single-year and decadal-scale dry events were more severe before 1900. Dry spells in the late thirteenth and sixteenth centuries surpass both magnitude and duration of any droughts in the Bighorn Basin after 1900. Precipitation variability appears to shift to a higher-frequency mode after 1750, with 15 20-yr droughts becoming rare. Comparisons between instrumental and reconstructed values of precipitation and indices of Pacific basin variability reveal that precipitation in the Bighorn Basin generally responds to Pacific forcing in a manner similar to that of the southwestern United States (drier during La Niña events), but high country precipitation in areas surrounding the basin displays the opposite response (drier during El Niño events).

Efficient structure from motion for oblique UAV images based on maximal spanning tree expansion

NASA Astrophysics Data System (ADS)

Jiang, San; Jiang, Wanshou

2017-10-01

The primary contribution of this paper is an efficient Structure from Motion (SfM) solution for oblique unmanned aerial vehicle (UAV) images. First, an algorithm, considering spatial relationship constraints between image footprints, is designed for match pair selection with the assistance of UAV flight control data and oblique camera mounting angles. Second, a topological connection network (TCN), represented by an undirected weighted graph, is constructed from initial match pairs, which encodes the overlap areas and intersection angles into edge weights. Then, an algorithm, termed MST-Expansion, is proposed to extract the match graph from the TCN, where the TCN is first simplified by a maximum spanning tree (MST). By further analysis of the local structure in the MST, expansion operations are performed on the vertices of the MST for match graph enhancement, which is achieved by introducing critical connections in the expansion directions. Finally, guided by the match graph, an efficient SfM is proposed. Under extensive analysis and comparison, its performance is verified by using three oblique UAV datasets captured with different multi-camera systems. Experimental results demonstrate that the efficiency of image matching is improved, with speedup ratios ranging from 19 to 35, and competitive orientation accuracy is achieved from both relative bundle adjustment (BA) without GCPs (Ground Control Points) and absolute BA with GCPs. At the same time, images in the three datasets are successfully oriented. For the orientation of oblique UAV images, the proposed method can be a more efficient solution.

The relations between network-operation and topological-property in a scale-free and small-world network with community structure

NASA Astrophysics Data System (ADS)

Ma, Fei; Yao, Bing

2017-10-01

It is always an open, demanding and difficult task for generating available model to simulate dynamical functions and reveal inner principles from complex systems and networks. In this article, due to lots of real-life and artificial networks are built from series of simple and small groups (components), we discuss some interesting and helpful network-operation to generate more realistic network models. In view of community structure (modular topology), we present a class of sparse network models N(t , m) . At the moment, we capture the fact the N(t , 4) has not only scale-free feature, which means that the probability that a randomly selected vertex with degree k decays as a power-law, following P(k) ∼k-γ, where γ is the degree exponent, but also small-world property, which indicates that the typical distance between two uniform randomly chosen vertices grows proportionally to logarithm of the order of N(t , 4) , namely, relatively shorter diameter and lower average path length, simultaneously displays higher clustering coefficient. Next, as a new topological parameter correlating to reliability, synchronization capability and diffusion properties of networks, the number of spanning trees over a network is studied in more detail, an exact analytical solution for the number of spanning trees of the N(t , 4) is obtained. Based on the network-operation, part hub-vertex linking with each other will be helpful for structuring various network models and investigating the rules related with real-life networks.

Minimum spanning tree analysis of the human connectome

PubMed Central

Sommer, Iris E.; Bohlken, Marc M.; Tewarie, Prejaas; Draaisma, Laurijn; Zalesky, Andrew; Di Biase, Maria; Brown, Jesse A.; Douw, Linda; Otte, Willem M.; Mandl, René C.W.; Stam, Cornelis J.

2018-01-01

Abstract One of the challenges of brain network analysis is to directly compare network organization between subjects, irrespective of the number or strength of connections. In this study, we used minimum spanning tree (MST; a unique, acyclic subnetwork with a fixed number of connections) analysis to characterize the human brain network to create an empirical reference network. Such a reference network could be used as a null model of connections that form the backbone structure of the human brain. We analyzed the MST in three diffusion‐weighted imaging datasets of healthy adults. The MST of the group mean connectivity matrix was used as the empirical null‐model. The MST of individual subjects matched this reference MST for a mean 58%–88% of connections, depending on the analysis pipeline. Hub nodes in the MST matched with previously reported locations of hub regions, including the so‐called rich club nodes (a subset of high‐degree, highly interconnected nodes). Although most brain network studies have focused primarily on cortical connections, cortical–subcortical connections were consistently present in the MST across subjects. Brain network efficiency was higher when these connections were included in the analysis, suggesting that these tracts may be utilized as the major neural communication routes. Finally, we confirmed that MST characteristics index the effects of brain aging. We conclude that the MST provides an elegant and straightforward approach to analyze structural brain networks, and to test network topological features of individual subjects in comparison to empirical null models. PMID:29468769

Major Mesoamerican droughts of the past millennium

NASA Astrophysics Data System (ADS)

Stahle, D. W.; Diaz, J. Villanueva; Burnette, D. J.; Paredes, J. Cerano; Heim, R. R., Jr.; Fye, F. K.; Acuna Soto, R.; Therrell, M. D.; Cleaveland, M. K.; Stahle, D. K.

2011-03-01

Ancient Montezuma baldcypress (Taxodium mucronatum) trees found in Barranca de Amealco, Queretaro, have been used to develop a 1,238-year tree-ring chronology that is correlated with precipitation, temperature, drought indices, and crop yields in central Mexico. This chronology has been used to reconstruct the spring-early summer soil moisture balance over the heartland of the Mesoamerican cultural province, and is the first exactly dated, annually resolved paleoclimatic record for Mesoamerica spanning the Late Classic, Post Classic, Colonial, and modern eras. The reconstruction indicates that the Terminal Classic drought extended into central Mexico, supporting other sedimentary and speleothem evidence for this early 10th century drought in Mesoamerica. The reconstruction also documents severe and sustained drought during the decline of the Toltec state (1149-1167) and during the Spanish conquest of the Aztec state (1514-1539), providing a new precisely dated climate framework for Mesoamerican cultural change.

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.

Analysis of linkage effects among industry sectors in China's stock market before and after the financial crisis

NASA Astrophysics Data System (ADS)

Yang, Rui; Li, Xiangyang; Zhang, Tong

2014-10-01

This paper uses two physics-derived techniques, the minimum spanning tree and the hierarchical tree, to investigate the networks formed by CITIC (China International Trust and Investment Corporation) industry indices in three periods from 2006 to 2013. The study demonstrates that obvious industry clustering effects exist in the networks, and Durable Consumer Goods, Industrial Products, Information Technology, Frequently Consumption and Financial Industry are the core nodes in the networks. We also use the rolling window technique to investigate the dynamic evolution of the networks' stability, by calculating the mean correlations and mean distances, as well as the variance of correlations and the distances of these indices. China's stock market is still immature and subject to administrative interventions. Therefore, through this analysis, regulators can focus on monitoring the core nodes to ensure the overall stability of the entire market, while investors can enhance their portfolio allocations or investment decision-making.

Debt and growth: A non-parametric approach

NASA Astrophysics Data System (ADS)

Brida, Juan Gabriel; Gómez, David Matesanz; Seijas, Maria Nela

2017-11-01

In this study, we explore the dynamic relationship between public debt and economic growth by using a non-parametric approach based on data symbolization and clustering methods. The study uses annual data of general government consolidated gross debt-to-GDP ratio and gross domestic product for sixteen countries between 1977 and 2015. Using symbolic sequences, we introduce a notion of distance between the dynamical paths of different countries. Then, a Minimal Spanning Tree and a Hierarchical Tree are constructed from time series to help detecting the existence of groups of countries sharing similar economic performance. The main finding of the study appears for the period 2008-2016 when several countries surpassed the 90% debt-to-GDP threshold. During this period, three groups (clubs) of countries are obtained: high, mid and low indebted countries, suggesting that the employed debt-to-GDP threshold drives economic dynamics for the selected countries.

Global Interactions Analysis of Epileptic ECoG Data

NASA Astrophysics Data System (ADS)

Ortega, Guillermo J.; Sola, Rafael G.; Pastor, Jesús

2007-05-01

Localization of the epileptogenic zone is an important issue in epileptology, even though there is not a unique definition of the epileptic focus. The objective of the present study is to test ultrametric analysis to uncover cortical interactions in human epileptic data. Correlation analysis has been carried out over intraoperative Electro-Corticography (ECoG) data in 2 patients suffering from temporal lobe epilepsy (TLE). Recordings were obtained using a grid of 20 electrodes (5×4) covering the lateral temporal lobe and a strip of either 4 or 8 electrodes at the mesial temporal lobe. Ultrametric analysis was performed in the averaged final correlation matrices. By using the matrix of linear correlation coefficients and the appropriate metric distance between pairs of electrodes time series, we were able to construct Minimum Spanning Trees (MST). The topological connectivity displayed by these trees gives useful and valuable information regarding physiological and pathological information in the temporal lobe of epileptic patients.

A Survey on Robotic Coconut Tree Climbers - Existing Methods and Techniques

NASA Astrophysics Data System (ADS)

Kannan Megalingam, Rajesh; Sakthiprasad, K. M.; Sreekanth, M. M.; Vamsy Vivek, Gedela

2017-08-01

As the coconut palm growers are struggling with the acute shortage of human coconut tree climbers to climb and harvest the coconuts, many are working towards possible alternatives to help them handle this situation. In this study paper we analyse the problems associated with the shortage of human coconut tree climbers in -depth. We also present details of various existing mechanical models available in the market and have not yet solved this issue. Along with this we discuss how robotics and automation could be a possible solution for this entire problem. In this context we discuss about the features of such robotic system and also give suggestions on various unmanned robotic models that can be designed and implemented.

The risk factors of laryngeal pathology in Korean adults using a decision tree model.

PubMed

Byeon, Haewon

2015-01-01

The purpose of this study was to identify risk factors affecting laryngeal pathology in the Korean population and to evaluate the derived prediction model. Cross-sectional study. Data were drawn from the 2008 Korea National Health and Nutritional Examination Survey. The subjects were 3135 persons (1508 male and 2114 female) aged 19 years and older living in the community. The independent variables were age, sex, occupation, smoking, alcohol drinking, and self-reported voice problems. A decision tree analysis was done to identify risk factors for predicting a model of laryngeal pathology. The significant risk factors of laryngeal pathology were age, gender, occupation, smoking, and self-reported voice problem in decision tree model. Four significant paths were identified in the decision tree model for the prediction of laryngeal pathology. Those identified as high risk groups for laryngeal pathology included those who self-reported a voice problem, those who were males in their 50s who did not recognize a voice problem, those who were not economically active males in their 40s, and male workers aged 19 and over and under 50 or 60 and over who currently smoked. The results of this study suggest that individual risk factors, such as age, sex, occupation, health behavior, and self-reported voice problem, affect the onset of laryngeal pathology in a complex manner. Based on the results of this study, early management of the high-risk groups is needed for the prevention of laryngeal pathology. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Effects of photochemical smog on lemons and navel oranges

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

Thompson, C.R.; Taylor, O.C.; Richards, B.L.

1970-05-01

Experiments were carried out on lemon and Navel orange trees to determine the kind and extent of damage caused by air pollution in the Los Angeles Basin. Trees were enclosed in filter-equipped greenhouses and compared with control trees which were exposed to ambient air. Yield of lemons was about one third more in filtered trees, and with oranges, the yield was about doubled. Fruit drop in oranges was a major problem associated with the exposure to ambient air pollution. Trees in ambient air were reduced in photosynthesis to 66% of filtered-air treatments. Fluoride, while present in the atmosphere was ofmore » minor importance to the health and performance of the trees. 2 tables.« less

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Recursive algorithms for phylogenetic tree counting.

PubMed

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Economic analysis of the gypsy moth problem in the northeast: II. applied to residential property

Treesearch

Brian R. Payne; William B. White; Roger E. McCay; Robert R. McNichols

1973-01-01

Guidelines are presented for determining dollar losses in residential property values from tree mortality caused by the gypsy moth. The method is based on an earlier study in Amherst, Massachusetts, of the contribution of trees to property values. For each target area, the method requires data on property value, lot size, and number of trees 6 inches dbh and larger for...

Floodplain forest loss and changes in forest community composition and structure in the upper Mississippi River: a wildlife habitat at risk

USGS Publications Warehouse

Knutson, M.G.; Klaas, E.E.

1998-01-01

Large floodplain forests represent a threatened and endangered type of ecosystem in the United States. Estimates of cumulative losses of floodplain forest range from 57% to 95% at different locations within the continental United Stales. Floodplain forests of the Upper Mississippi River (UMR) have significantly declined in extent due to agriculture, lock and dam construction, and urban development since European settlement. We collected data on shrubs, herbs, and trees from 56 floodplain forest plots in 1992 and compared our results with a previous analysis of historical tree data from the same area recorded by the General Land Office Survey in the 1840s. Acer saccharinum strongly dominates among mature trees and its relative dominance has increased over time. Salix spp. And Betula nigra have declined in relative dominance. Tree sizes are similar to those of presettlement forests, but present forests have fewer trees. The lack of early successional tree species and a trend toward an increasing monoculture of A. Saccharinum in the mature stages indicate problems with regeneration. Because floodplain forests represent a rare habitat type, losses and changes in habitat quality could pose serious problems for wildlife that depend upon these habitats, especially birds.

Evaluation of different iron compounds in chlorotic Italian lemon trees (Citrus lemon).

PubMed

Ortiz, Patricio Rivera; Castro Meza, Blanca I; de la Garza Requena, Francisco R; Flores, Guillermo Mendoza; Etchevers Barra, Jorge D

2007-05-01

The severe deficiency of iron or ferric chlorosis is a serious problem of most citrus trees established in calcareous soils, as a result of the low availability of iron in these soils and the poor uptake and limited transport of this nutrient in trees. The objective of this study was to evaluate the response of chlorotic Italian lemon trees (Citrus lemon) to the application of iron compounds to roots and stems. On comparing the effects of aqueous solutions of ferric citrate, ferrous sulphate and FeEDDHA chelate, applied to 20% of the roots grown in soil and sand, of trees that were planted in pots containing calcareous soil, it was observed that the chelate fully corrected ferric chlorosis, while citrate and sulphate did not solve the problem. EDDHA induced the root uptake of iron as well as the movement of the nutrient up to the leaves. With the use of injections of ferric solutions into the secondary stem of adult trees, ferric citrate corrected chlorosis but ferrous sulphate did not. The citrate ion expanded the mobility of iron within the plant, from the injection points up to the leaves, whereas the sulphate ion did not sufficiently improve the movement of iron towards the leaf mesophyll.

A linear programming approach to max-sum problem: a review.

PubMed

Werner, Tomás

2007-07-01

The max-sum labeling problem, defined as maximizing a sum of binary (i.e., pairwise) functions of discrete variables, is a general NP-hard optimization problem with many applications, such as computing the MAP configuration of a Markov random field. We review a not widely known approach to the problem, developed by Ukrainian researchers Schlesinger et al. in 1976, and show how it contributes to recent results, most importantly, those on the convex combination of trees and tree-reweighted max-product. In particular, we review Schlesinger et al.'s upper bound on the max-sum criterion, its minimization by equivalent transformations, its relation to the constraint satisfaction problem, the fact that this minimization is dual to a linear programming relaxation of the original problem, and the three kinds of consistency necessary for optimality of the upper bound. We revisit problems with Boolean variables and supermodular problems. We describe two algorithms for decreasing the upper bound. We present an example application for structural image analysis.

Elevated CO2 and O3 effects on fine-root survivorship in ponderosa pine mesocosms.

PubMed

Phillips, Donald L; Johnson, Mark G; Tingey, David T; Storm, Marjorie J

2009-07-01

Atmospheric carbon dioxide (CO(2)) and ozone (O(3)) concentrations are rising, which may have opposing effects on tree C balance and allocation to fine roots. More information is needed on interactive CO(2) and O(3) effects on roots, particularly fine-root life span, a critical demographic parameter and determinant of soil C and N pools and cycling rates. We conducted a study in which ponderosa pine (Pinus ponderosa) seedlings were exposed to two levels of CO(2) and O(3) in sun-lit controlled-environment mesocosms for 3 years. Minirhizotrons were used to monitor individual fine roots in three soil horizons every 28 days. Proportional hazards regression was used to analyze effects of CO(2), O(3), diameter, depth, and season of root initiation on fine-root survivorship. More fine roots were produced in the elevated CO(2) treatment than in ambient CO(2). Elevated CO(2), increasing root diameter, and increasing root depth all significantly increased fine-root survivorship and median life span. Life span was slightly, but not significantly, lower in elevated O(3), and increased O(3) did not reduce the effect of elevated CO(2). Median life spans varied from 140 to 448 days depending on the season of root initiation. These results indicate the potential for elevated CO(2) to increase the number of fine roots and their residence time in the soil, which is also affected by root diameter, root depth, and phenology.

Dissimilar responses of larch stands in northern Siberia to increasing temperatures-a field and simulation based study.

PubMed

Wieczorek, Mareike; Kruse, Stefan; Epp, Laura S; Kolmogorov, Alexei; Nikolaev, Anatoly N; Heinrich, Ingo; Jeltsch, Florian; Pestryakova, Lyudmila A; Zibulski, Romy; Herzschuh, Ulrike

2017-09-01

Arctic and alpine treelines worldwide differ in their reactions to climate change. A northward advance of or densification within the treeline ecotone will likely influence climate-vegetation feedback mechanisms. In our study, which was conducted in the Taimyr Depression in the North Siberian Lowlands, w present a combined field- and model-based approach helping us to better understand the population processes involved in the responses of the whole treeline ecotone, spanning from closed forest to single-tree tundra, to climate warming. Using information on stand structure, tree age, and seed quality and quantity from seven sites, we investigate effects of intra-specific competition and seed availability on the specific impact of recent climate warming on larch stands. Field data show that tree density is highest in the forest-tundra, and average tree size decreases from closed forest to single-tree tundra. Age-structure analyses indicate that the trees in the closed forest and forest-tundra have been present for at least ~240 yr. At all sites except the most southerly ones, past establishment is positively correlated with regional temperature increase. In the single-tree tundra, however, a change in growth form from krummholz to erect trees, beginning ~130 yr ago, rather than establishment date has been recorded. Seed mass decreases from south to north, while seed quantity increases. Simulations with LAVESI (Larix Vegetation Simulator) further suggest that relative density changes strongly in response to a warming signal in the forest-tundra while intra-specific competition limits densification in the closed forest and seed limitation hinders densification in the single-tree tundra. We find striking differences in strength and timing of responses to recent climate warming. While forest-tundra stands recently densified, recruitment is almost non-existent at the southern and northern end of the ecotone due to autecological processes. Palaeo-treelines may therefore be inappropriate to infer past temperature changes at a fine scale. Moreover, a lagged treeline response to past warming will, via feedback mechanisms, influence climate change in the future. © 2017 by the Ecological Society of America.

Tree Diversity Enhances Stand Carbon Storage but Not Leaf Area in a Subtropical Forest.

PubMed

Castro-Izaguirre, Nadia; Chi, Xiulian; Baruffol, Martin; Tang, Zhiyao; Ma, Keping; Schmid, Bernhard; Niklaus, Pascal A

2016-01-01

Research about biodiversity-productivity relationships has focused on herbaceous ecosystems, with results from tree field studies only recently beginning to emerge. Also, the latter are concentrated largely in the temperate zone. Tree species diversity generally is much higher in subtropical and tropical than in temperate or boreal forests, with reasons not fully understood. Niche overlap and thus complementarity in the use of resources that support productivity may be lower in forests than in herbaceous ecosystems, suggesting weaker productivity responses to diversity change in forests. We studied stand basal area, vertical structure, leaf area, and their relationship with tree species richness in a subtropical forest in south-east China. Permanent forest plots of 30 x 30 m were selected to span largely independent gradients in tree species richness and secondary successional age. Plots with higher tree species richness had a higher stand basal area. Also, stand basal area increases over a 4-year census interval were larger at high than at low diversity. These effects translated into increased carbon stocks in aboveground phytomass (estimated using allometric equations). A higher variability in tree height in more diverse plots suggested that these effects were facilitated by denser canopy packing due to architectural complementarity between species. In contrast, leaf area was not or even negatively affected by tree diversity, indicating a decoupling of carbon accumulation from leaf area. Alternatively, the same community leaf area might have assimilated more C per time interval in more than in less diverse plots because of differences in leaf turnover and productivity or because of differences in the display of leaves in vertical and horizontal space. Overall, our study suggests that in species-rich forests niche-based processes support a positive diversity-productivity relationship and that this translates into increased carbon storage in long-lived woody structures. Given the high growth rates of these forests during secondary succession, our results further indicate that a forest management promoting tree diversity after disturbance may accelerate CO2 sequestration from the atmosphere and thus be relevant in a climate-change context.

Trees tell of past climates: but are they speaking less clearly today?

PubMed Central

Briffa, K. R.

1998-01-01

The annual growth of trees, as represented by a variety of ring-width, densitometric, or chemical parameters, represents a combined record of different environmental forcings, one of which is climate. Along with climate, relatively large-scale positive growth influences such as hypothesized 'fertilization' due to increased levels of atmospheric carbon dioxide or various nitrogenous compounds, or possibly deleterious effects of 'acid rain' or increased ultra-violet radiation, might all be expected to exert some influence on recent tree growth rates. Inferring the details of past climate variability from tree-ring data remains a largely empirical exercise, but one that goes hand-in-hand with the development of techniques that seek to identify and isolate the confounding influence of local and larger-scale non-climatic factors. By judicious sampling, and the use of rigorous statistical procedures, dendroclimatology has provided unique insight into the nature of past climate variability, but most significantly at interannual, decadal, and centennial timescales. Here, examples are shown that illustrate the reconstruction of annually resolved patterns of past summer temperature around the Northern Hemisphere, as well as some more localized reconstructions, but ones which span 1000 years or more. These data provide the means of exploring the possible role of different climate forcings; for example, they provide evidence of the large-scale effects of explosive volcanic eruptions on regional and hemispheric temperatures during the last 400 years. However, a dramatic change in the sensitivity of hemispheric tree-growth to temperature forcing has become apparent during recent decades, and there is additional evidence of major tree-growth (and hence, probably, ecosystem biomass) increases in the northern boreal forests, most clearly over the last century. These possibly anthropogenically related changes in the ecology of tree growth have important implications for modelling future atmospheric CO2 concentrations. Also, where dendroclimatology is concerned to reconstruct longer (increasingly above centennial) temperature histories, such alterations of 'normal' (pre-industrial) tree-growth rates and climate-growth relationships must be accounted for in our attempts to translate the evidence of past tree growth changes.

Variation in wood nutrients along a tropical soil fertility gradient.

PubMed

Heineman, Katherine D; Turner, Benjamin L; Dalling, James W

2016-07-01

Wood contains the majority of the nutrients in tropical trees, yet controls over wood nutrient concentrations and their function are poorly understood. We measured wood nutrient concentrations in 106 tree species in 10 forest plots spanning a regional fertility gradient in Panama. For a subset of species, we quantified foliar nutrients and wood density to test whether wood nutrients scale with foliar nutrients at the species level, or wood nutrient storage increases with wood density as predicted by the wood economics spectrum. Wood nutrient concentrations varied enormously among species from fourfold in nitrogen (N) to > 30-fold in calcium (Ca), potassium (K), magnesium (Mg) and phosphorus (P). Community-weighted mean wood nutrient concentrations correlated positively with soil Ca, K, Mg and P concentrations. Wood nutrients scaled positively with leaf nutrients, supporting the hypothesis that nutrient allocation is conserved across plant organs. Wood P was most sensitive to variation in soil nutrient availability, and significant radial declines in wood P indicated that tropical trees retranslocate P as sapwood transitions to heartwood. Wood P decreased with increasing wood density, suggesting that low wood P and dense wood are traits associated with tree species persistence on low fertility soils. Substantial variation among species and communities in wood nutrient concentrations suggests that allocation of nutrients to wood, especially P, influences species distributions and nutrient dynamics in tropical forests. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change.

PubMed

Rico, L; Ogaya, R; Barbeta, A; Peñuelas, J

2014-03-01

Rapid genetic changes in plants have been reported in response to current climate change. We assessed the capacity of trees in a natural forest to produce rapid acclimation responses based on epigenetic modifications. We analysed natural populations of Quercus ilex, the dominant tree species of Mediterranean forests, using the methylation-sensitive amplified polymorphism (MSAP) technique to assess patterns and levels of methylation in individuals from unstressed forest plots and from plots experimentally exposed to drought for 12 years at levels projected for the coming decades. The percentage of hypermethylated loci increased, and the percentage of fully methylated loci clearly decreased in plants exposed to drought. Multivariate analyses exploring the status of methylation at MSAP loci also showed clear differentiation depending on stress. The PCA scores for the MSAP profiles clearly separated the genetic from the epigenetic structure, and also significantly separated the samples within each group in response to drought. Changes in DNA methylation highlight the large capacity of plants to rapidly acclimate to changing environmental conditions, including trees with long life spans, and our results demonstrate those changes. These changes, although unable to prevent the decreased growth and higher mortality associated with this experimental drought, occurred together with a dampening in such decreases as the long-term treatment progressed. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

A new approach to enhance the performance of decision tree for classifying gene expression data.

PubMed

Hassan, Md; Kotagiri, Ramamohanarao

2013-12-20

Gene expression data classification is a challenging task due to the large dimensionality and very small number of samples. Decision tree is one of the popular machine learning approaches to address such classification problems. However, the existing decision tree algorithms use a single gene feature at each node to split the data into its child nodes and hence might suffer from poor performance specially when classifying gene expression dataset. By using a new decision tree algorithm where, each node of the tree consists of more than one gene, we enhance the classification performance of traditional decision tree classifiers. Our method selects suitable genes that are combined using a linear function to form a derived composite feature. To determine the structure of the tree we use the area under the Receiver Operating Characteristics curve (AUC). Experimental analysis demonstrates higher classification accuracy using the new decision tree compared to the other existing decision trees in literature. We experimentally compare the effect of our scheme against other well known decision tree techniques. Experiments show that our algorithm can substantially boost the classification performance of the decision tree.

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.

Diagnosing plant problems

Treesearch

Cheryl A. Smith

2008-01-01

Diagnosing Christmas tree problems can be a challenge, requiring a basic knowledge of plant culture and physiology, the effect of environmental influences on plant health, and the ability to identify the possible causes of plant problems. Developing a solution or remedy to the problem depends on a proper diagnosis, a process that requires recognition of a problem and...

Visualizing phylogenetic tree landscapes.

PubMed

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.

Morphological comparison of Fusarium species associated with Euwallacea ambrosia beetles

USDA-ARS?s Scientific Manuscript database

Tree damage caused by Euwallacea ambrosia beetles, including those of fruit trees, has become a severe problem worldwide. Euwallacea species cultivate Fusarium in their galleries as a source of nutrition. Concerning the ambrosia species of Fusarium, 12 phylogenetic species have been discovered based...

Top tips from tree tops

NASA Astrophysics Data System (ADS)

Ornes, Stephen

2018-04-01

The ability of trees to cool by transporting water from their roots to the leaves has been known for centuries. But as Stephen Ornes discovers, the principles of transpiration are also inspiring innovative techniques to cool vehicles travelling at hypersonic speeds, where unwanted heat is a problem too

Risk Analysis of Return Support Material on Gas Compressor Platform Project

NASA Astrophysics Data System (ADS)

Silvianita; Aulia, B. U.; Khakim, M. L. N.; Rosyid, Daniel M.

2017-07-01

On a fixed platforms project are not only carried out by a contractor, but two or more contractors. Cooperation in the construction of fixed platforms is often not according to plan, it is caused by several factors. It takes a good synergy between the contractor to avoid miss communication may cause problems on the project. For the example is about support material (sea fastening, skid shoe and shipping support) used in the process of sending a jacket structure to operation place often does not return to the contractor. It needs a systematic method to overcome the problem of support material. This paper analyses the causes and effects of GAS Compressor Platform that support material is not return, using Fault Tree Analysis (FTA) and Event Tree Analysis (ETA). From fault tree analysis, the probability of top event is 0.7783. From event tree analysis diagram, the contractors lose Rp.350.000.000, - to Rp.10.000.000.000, -.

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

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

Yoginath, Srikanth B.; Perumalla, Kalyan S.

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Liquid Therapy Delivery Models Using Microfluidic Airways

NASA Astrophysics Data System (ADS)

Mulligan, Molly K.; Grotberg, James B.; Waisman, Dan; Filoche, Marcel; Sznitman, Josué

2013-11-01

The propagation and break-up of viscous and surfactant-laden liquid plugs in the lungs is an active area of research in view of liquid plug installation in the lungs to treat a host of different pulmonary conditions. This includes Infant Respiratory Distress Syndrome (IRDS) the primary cause of neonatal death and disability. Until present, experimental studies of liquid plugs have generally been restricted to low-viscosity Newtonian fluids along a single bifurcation. However, these fluids reflect poorly the actual liquid medication therapies used to treat pulmonary conditions. The present work attempts to uncover the propagation, rupture and break-up of liquid plugs in the airway tree using microfluidic models spanning three or more generations of the bronchiole tree. Our approach allows the dynamics of plug propagation and break-up to be studied in real-time, in a one-to-one scale in vitro model, as a function of fluid rheology, trailing film dynamics and bronchial tree geometry. Understanding these dynamics are a first and necessary step to deliver more effectively boluses of liquid medication to the lungs while minimizing the injury caused to epithelial cells lining the lungs from the rupture of such liquid plugs.

Open tundra persist, but arctic features decline-Vegetation changes in the warming Fennoscandian tundra.

PubMed

Vuorinen, Katariina E M; Oksanen, Lauri; Oksanen, Tarja; Pyykönen, Anni; Olofsson, Johan; Virtanen, Risto

2017-09-01

In the forest-tundra ecotone of the North Fennoscandian inland, summer and winter temperatures have increased by two to three centigrades since 1965, which is expected to result in major vegetation changes. To document the expected expansion of woodlands and scrublands and its impact on the arctic vegetation, we repeated a vegetation transect study conducted in 1976 in the Darju, spanning from woodland to a summit, 200 m above the tree line. Contrary to our expectations, tree line movement was not detected, and there was no increase in willows or shrubby mountain birches, either. Nevertheless, the stability of tundra was apparent. Small-sized, poorly competing arctic species had declined, lichen cover had decreased, and vascular plants, especially evergreen ericoid dwarf shrubs, had gained ground. The novel climate seems to favour competitive clonal species and species thriving in closed vegetation, creating a community hostile for seedling establishment, but equally hostile for many arctic species, too. Preventing trees and shrubs from invading the tundra is thus not sufficient for conserving arctic biota in the changing climate. The only dependable cure is to stop the global warming. © 2017 John Wiley & Sons Ltd.

The relationships between electricity consumption and GDP in Asian countries, using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Kantar, Ersin; Keskin, Mustafa

2013-11-01

This study uses hierarchical structure methods (minimal spanning tree (MST) and hierarchical tree (HT)) to examine the relationship between energy consumption and economic growth in a sample of 30 Asian countries covering the period 1971-2008. These countries are categorized into four panels based on the World Bank income classification, namely high, upper middle, lower middle, and low income. In particular, we use the data of electricity consumption and real gross domestic product (GDP) per capita to detect the topological properties of the countries. We show a relationship between electricity consumption and economic growth by using the MST and HT. We also use the bootstrap technique to investigate a value of the statistical reliability to the links of the MST. Finally, we use a clustering linkage procedure in order to observe the cluster structure. The results of the structural topologies of these trees are as follows: (i) we identified different clusters of countries according to their geographical location and economic growth, (ii) we found a strong relationship between energy consumption and economic growth for all income groups considered in this study and (iii) the results are in good agreement with the causal relationship between electricity consumption and economic growth.

Divergence of species responses to climate change

PubMed Central

Fei, Songlin; Desprez, Johanna M.; Potter, Kevin M.; Jo, Insu; Knott, Jonathan A.; Oswalt, Christopher M.

2017-01-01

Climate change can have profound impacts on biodiversity and the sustainability of many ecosystems. Various studies have investigated the impacts of climate change, but large-scale, trait-specific impacts are less understood. We analyze abundance data over time for 86 tree species/groups across the eastern United States spanning the last three decades. We show that more tree species have experienced a westward shift (73%) than a poleward shift (62%) in their abundance, a trend that is stronger for saplings than adult trees. The observed shifts are primarily due to the changes of subpopulation abundances in the leading edges and are significantly associated with changes in moisture availability and successional processes. These spatial shifts are associated with species that have similar traits (drought tolerance, wood density, and seed weight) and evolutionary histories (most angiosperms shifted westward and most gymnosperms shifted poleward). Our results indicate that changes in moisture availability have stronger near-term impacts on vegetation dynamics than changes in temperature. The divergent responses to climate change by trait- and phylogenetic-specific groups could lead to changes in composition of forest ecosystems, putting the resilience and sustainability of various forest ecosystems in question. PMID:28560343