Category of trees in representation theory of quantum algebras

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

Moskaliuk, N. M.; Moskaliuk, S. S., E-mail: mss@bitp.kiev.ua

2013-10-15

New applications of categorical methods are connected with new additional structures on categories. One of such structures in representation theory of quantum algebras, the category of Kuznetsov-Smorodinsky-Vilenkin-Smirnov (KSVS) trees, is constructed, whose objects are finite rooted KSVS trees and morphisms generated by the transition from a KSVS tree to another one.

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)].

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

ERIC Educational Resources Information Center

Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

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.

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.

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

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.

Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.

C-semiring Frameworks for Minimum Spanning Tree Problems

NASA Astrophysics Data System (ADS)

Bistarelli, Stefano; Santini, Francesco

In this paper we define general algebraic frameworks for the Minimum Spanning Tree problem based on the structure of c-semirings. We propose general algorithms that can compute such trees by following different cost criteria, which must be all specific instantiation of c-semirings. Our algorithms are extensions of well-known procedures, as Prim or Kruskal, and show the expressivity of these algebraic structures. They can deal also with partially-ordered costs on the edges.

Positivity, Grassmannian geometry and simplex-like structures of scattering amplitudes

NASA Astrophysics Data System (ADS)

Rao, Junjie

2017-12-01

This article revisits and elaborates the significant role of positive geometry of momentum twistor Grassmannian for planar N=4 SYM scattering amplitudes. First we establish the fundamentals of positive Grassmannian geometry for tree amplitudes, including the ubiquitous Plücker coordinates and the representation of reduced Grassmannian geometry. Then we formulate this subject, without making reference to on-shell diagrams and decorated permutations, around these four major facets: 1. Deriving the tree and 1-loop BCFW recursion relations solely from positivity, after introducing the simple building blocks called positive components for a positive matrix. 2. Applying Grassmannian geometry and Plücker coordinates to determine the signs of N2MHV homological identities, which interconnect various Yangian invariants. It reveals that most of the signs are in fact the secret incarnation of the simple 6-term NMHV identity. 3. Deriving the stacking positivity relation, which is powerful for parameterizing matrix representatives in terms of positive variables in the d log form. It will be used with the reduced Grassmannian geometry representation to produce the positive matrix of a given geometric configuration, which is an independent approach besides the combinatoric way involving a sequence of BCFW bridges. 4. Introducing an elegant and highly refined formalism of BCFW recursion relation for tree amplitudes, which reveals its two-fold simplex-like structures. First, the BCFW contour in terms of (reduced) Grassmannian geometry representatives is delicately dissected into a triangle-shape sum, as only a small fraction of the sum needs to be explicitly identified. Second, this fraction can be further dissected, according to different growing modes with corresponding growing parameters. The growing modes possess the shapes of solid simplices of various dimensions, with which infinite number of BCFW cells can be entirely captured by the characteristic objects called fully-spanning cells. We find that for a given k, beyond n =4 k+1 there is no more new fully-spanning cell, which signifies the essential termination of the recursive growth of BCFW cells. As n increases beyond the termination point, the BCFW contour simply replicates itself according to the simplex-like patterns, which enables us to master all BCFW cells once for all without actually identifying most of them.

Building of fuzzy decision trees using ID3 algorithm

NASA Astrophysics Data System (ADS)

Begenova, S. B.; Avdeenko, T. V.

2018-05-01

Decision trees are widely used in the field of machine learning and artificial intelligence. Such popularity is due to the fact that with the help of decision trees graphic models, text rules can be built and they are easily understood by the final user. Because of the inaccuracy of observations, uncertainties, the data, collected in the environment, often take an unclear form. Therefore, fuzzy decision trees becoming popular in the field of machine learning. This article presents a method that includes the features of the two above-mentioned approaches: a graphical representation of the rules system in the form of a tree and a fuzzy representation of the data. The approach uses such advantages as high comprehensibility of decision trees and the ability to cope with inaccurate and uncertain information in fuzzy representation. The received learning method is suitable for classifying problems with both numerical and symbolic features. In the article, solution illustrations and numerical results are given.

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.

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

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.

Greedy algorithms in disordered systems

NASA Astrophysics Data System (ADS)

Duxbury, P. M.; Dobrin, R.

1999-08-01

We discuss search, minimal path and minimal spanning tree algorithms and their applications to disordered systems. Greedy algorithms solve these problems exactly, and are related to extremal dynamics in physics. Minimal cost path (Dijkstra) and minimal cost spanning tree (Prim) algorithms provide extremal dynamics for a polymer in a random medium (the KPZ universality class) and invasion percolation (without trapping) respectively.

MToS: A Tree of Shapes for Multivariate Images.

PubMed

Carlinet, Edwin; Géraud, Thierry

2015-12-01

The topographic map of a gray-level image, also called tree of shapes, provides a high-level hierarchical representation of the image contents. This representation, invariant to contrast changes and to contrast inversion, has been proved very useful to achieve many image processing and pattern recognition tasks. Its definition relies on the total ordering of pixel values, so this representation does not exist for color images, or more generally, multivariate images. Common workarounds, such as marginal processing, or imposing a total order on data, are not satisfactory and yield many problems. This paper presents a method to build a tree-based representation of multivariate images, which features marginally the same properties of the gray-level tree of shapes. Briefly put, we do not impose an arbitrary ordering on values, but we only rely on the inclusion relationship between shapes in the image definition domain. The interest of having a contrast invariant and self-dual representation of multivariate image is illustrated through several applications (filtering, segmentation, and object recognition) on different types of data: color natural images, document images, satellite hyperspectral imaging, multimodal medical imaging, and videos.

Application of 2D graphic representation of protein sequence based on Huffman tree method.

PubMed

Qi, Zhao-Hui; Feng, Jun; Qi, Xiao-Qin; Li, Ling

2012-05-01

Based on Huffman tree method, we propose a new 2D graphic representation of protein sequence. This representation can completely avoid loss of information in the transfer of data from a protein sequence to its graphic representation. The method consists of two parts. One is about the 0-1 codes of 20 amino acids by Huffman tree with amino acid frequency. The amino acid frequency is defined as the statistical number of an amino acid in the analyzed protein sequences. The other is about the 2D graphic representation of protein sequence based on the 0-1 codes. Then the applications of the method on ten ND5 genes and seven Escherichia coli strains are presented in detail. The results show that the proposed model may provide us with some new sights to understand the evolution patterns determined from protein sequences and complete genomes. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Hebb repetition effect in simple and complex memory span.

PubMed

Oberauer, Klaus; Jones, Timothy; Lewandowsky, Stephan

2015-08-01

The Hebb repetition effect refers to the finding that immediate serial recall is improved over trials for memory lists that are surreptitiously repeated across trials, relative to new lists. We show in four experiments that the Hebb repetition effect is also observed with a complex-span task, in which encoding or retrieval of list items alternates with an unrelated processing task. The interruption of encoding or retrieval by the processing task did not reduce the size of the Hebb effect, demonstrating that incidental long-term learning forms integrated representations of lists, excluding the interleaved processing events. Contrary to the assumption that complex-span performance relies more on long-term memory than standard immediate serial recall (simple span), the Hebb effect was not larger in complex-span than in simple-span performance. The Hebb effect in complex span was also not modulated by the opportunity for refreshing list items, questioning a role of refreshing for the acquisition of the long-term memory representations underlying the effect.

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

PubMed Central

2011-01-01

Background The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices. Results Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store. Conclusions CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore. PMID:21496247

CDAO-store: ontology-driven data integration for phylogenetic analysis.

PubMed

Chisham, Brandon; Wright, Ben; Le, Trung; Son, Tran Cao; Pontelli, Enrico

2011-04-15

The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices. Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store. CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore.

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.

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.

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.

PubMed

Li, Jinghui; Nagamochi, Hiroshi; Akutsu, Tatsuya

2018-01-01

Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph with no other cycles than benzene rings is called tree-like, and becomes a tree possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation are called the substituted benzene isomers of . When we replace each virtual atom in with a benzene ring to obtain a substituted benzene isomer, distinct isomers of are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation . Our algorithm first counts the number of all the isomers of the tree representation by a dynamic programming method. To enumerate all the isomers, for each , our algorithm then generates the th isomer by backtracking the counting phase of the dynamic programming. We also implemented our algorithm for computational experiments.

Correspondence between spanning trees and the Ising model on a square lattice

NASA Astrophysics Data System (ADS)

Viswanathan, G. M.

2017-06-01

An important problem in statistical physics concerns the fascinating connections between partition functions of lattice models studied in equilibrium statistical mechanics on the one hand and graph theoretical enumeration problems on the other hand. We investigate the nature of the relationship between the number of spanning trees and the partition function of the Ising model on the square lattice. The spanning tree generating function T (z ) gives the spanning tree constant when evaluated at z =1 , while giving the lattice green function when differentiated. It is known that for the infinite square lattice the partition function Z (K ) of the Ising model evaluated at the critical temperature K =Kc is related to T (1 ) . Here we show that this idea in fact generalizes to all real temperatures. We prove that [Z(K ) s e c h 2 K ] 2=k exp[T (k )] , where k =2 tanh(2 K )s e c h (2 K ) . The identical Mahler measure connects the two seemingly disparate quantities T (z ) and Z (K ) . In turn, the Mahler measure is determined by the random walk structure function. Finally, we show that the the above correspondence does not generalize in a straightforward manner to nonplanar lattices.

Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

2017-02-01

Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

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.

Can Children Read Evolutionary Trees?

ERIC Educational Resources Information Center

Ainsworth, Shaaron; Saffer, Jessica

2013-01-01

Representations of the "tree of life" such as cladograms show the history of lineages and their relationships. They are increasingly found in formal and informal learning settings. Unfortunately, there is evidence that these representations can be challenging to interpret correctly. This study explored the question of whether children…

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.

Exploiting Non-sequence Data in Dynamic Model Learning

DTIC Science & Technology

2013-10-01

For our experiments here and in Section 3.5, we implement the proposed algorithms in MATLAB and use the maximum directed spanning tree solver...embarrassingly parallelizable, whereas PM’s maximum directed spanning tree procedure is harder to parallelize. In this experiment, our MATLAB ...some estimation problems, this approach is able to give unique and consistent estimates while the maximum- likelihood method gets entangled in

Hyper-heuristic Evolution of Dispatching Rules: A Comparison of Rule Representations.

PubMed

Branke, Jürgen; Hildebrandt, Torsten; Scholz-Reiter, Bernd

2015-01-01

Dispatching rules are frequently used for real-time, online scheduling in complex manufacturing systems. Design of such rules is usually done by experts in a time consuming trial-and-error process. Recently, evolutionary algorithms have been proposed to automate the design process. There are several possibilities to represent rules for this hyper-heuristic search. Because the representation determines the search neighborhood and the complexity of the rules that can be evolved, a suitable choice of representation is key for a successful evolutionary algorithm. In this paper we empirically compare three different representations, both numeric and symbolic, for automated rule design: A linear combination of attributes, a representation based on artificial neural networks, and a tree representation. Using appropriate evolutionary algorithms (CMA-ES for the neural network and linear representations, genetic programming for the tree representation), we empirically investigate the suitability of each representation in a dynamic stochastic job shop scenario. We also examine the robustness of the evolved dispatching rules against variations in the underlying job shop scenario, and visualize what the rules do, in order to get an intuitive understanding of their inner workings. Results indicate that the tree representation using an improved version of genetic programming gives the best results if many candidate rules can be evaluated, closely followed by the neural network representation that already leads to good results for small to moderate computational budgets. The linear representation is found to be competitive only for extremely small computational budgets.

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.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

PubMed

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.

PubMed

Teixeira, Andreia Sofia; Monteiro, Pedro T; Carriço, João A; Ramirez, Mário; Francisco, Alexandre P

2015-01-01

Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by introducing a new edge betweenness metric for undirected and weighted graphs. This spanning edge betweenness metric is defined as the fraction of equivalent MSTs where a given edge is present. The metric provides a per edge statistic that is similar to that of the bootstrap approach frequently used in phylogenetics to support the grouping of taxa. We provide methods for the exact computation of this metric based on the well known Kirchhoff's matrix tree theorem. Moreover, we implement and make available a module for the PHYLOViZ software and evaluate the proposed metric concerning both effectiveness and computational performance. Analysis of trees generated using multilocus sequence typing data (MLST) and the goeBURST algorithm revealed that the space of possible MSTs in real data sets is extremely large. Selection of the edge to be represented using bootstrap could lead to unreliable results since alternative edges are present in the same fraction of equivalent MSTs. The choice of the MST to be presented, results from criteria implemented in the algorithm that must be based in biologically plausible models.

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.

The gravity apple tree

NASA Astrophysics Data System (ADS)

Espinosa Aldama, Mariana

2015-04-01

The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion.

Exploring the Complexity of Tree Thinking Expertise in an Undergraduate Systematics Course

ERIC Educational Resources Information Center

Halverson, Kristy L.; Pires, Chris J.; Abell, Sandra K.

2011-01-01

Student understanding of biological representations has not been well studied. Yet, we know that to be efficient problem solvers in evolutionary biology and systematics, college students must develop expertise in thinking with a particular type of representation, phylogenetic trees. The purpose of this study was to understand how undergraduates…

Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics

PubMed Central

Goldberg, David H.; Grafstein, Bernice; Robert, Adrian; Gardner, Esther P.

2009-01-01

The Neuroscience Information Framework (NIF), developed for the NIH Blueprint for Neuroscience Research and available at http://nif.nih.gov and http://neurogateway.org, is built upon a set of coordinated terminology components enabling data and web-resource description and selection. Core NIF terminologies use a straightforward syntax designed for ease of use and for navigation by familiar web interfaces, and readily exportable to aid development of relational-model databases for neuroscience data sharing. Datasets, data analysis tools, web resources, and other entities are characterized by multiple descriptors, each addressing core concepts, including data type, acquisition technique, neuroanatomy, and cell class. Terms for each concept are organized in a tree structure, providing is-a and has-a relations. Broad general terms near each root span the category or concept and spawn more detailed entries for specificity. Related but distinct concepts (e.g., brain area and depth) are specified by separate trees, for easier navigation than would be required by graph representation. Semantics enabling NIF data discovery were selected at one or more workshops by investigators expert in particular systems (vision, olfaction, behavioral neuroscience, neurodevelopment), brain areas (cerebellum, thalamus, hippocampus), preparations (molluscs, fly), diseases (neurodegenerative disease), or techniques (microscopy, computation and modeling, neurogenetics). Workshop-derived integrated term lists are available Open Source at http://brainml.org; a complete list of participants is at http://brainml.org/workshops. PMID:18958630

Investigating how students communicate tree-thinking

NASA Astrophysics Data System (ADS)

Boyce, Carrie Jo

Learning is often an active endeavor that requires students work at building conceptual understandings of complex topics. Personal experiences, ideas, and communication all play large roles in developing knowledge of and understanding complex topics. Sometimes these experiences can promote formation of scientifically inaccurate or incomplete ideas. Representations are tools used to help individuals understand complex topics. In biology, one way that educators help people understand evolutionary histories of organisms is by using representations called phylogenetic trees. In order to understand phylogenetics trees, individuals need to understand the conventions associated with phylogenies. My dissertation, supported by the Tree-Thinking Representational Competence and Word Association frameworks, is a mixed-methods study investigating the changes in students' tree-reading, representational competence and mental association of phylogenetic terminology after participation in varied instruction. Participants included 128 introductory biology majors from a mid-sized southern research university. Participants were enrolled in either Introductory Biology I, where they were not taught phylogenetics, or Introductory Biology II, where they were explicitly taught phylogenetics. I collected data using a pre- and post-assessment consisting of a word association task and tree-thinking diagnostic (n=128). Additionally, I recruited a subset of students from both courses (n=37) to complete a computer simulation designed to teach students about phylogenetic trees. I then conducted semi-structured interviews consisting of a word association exercise with card sort task, a retrospective pre-assessment discussion, a post-assessment discussion, and interview questions. I found that students who received explicit lecture instruction had a significantly higher increase in scores on a tree-thinking diagnostic than students who did not receive lecture instruction. Students who received both explicit lecture instruction and the computer simulation had a higher level of representational competence and were better able to understand abstract-style phylogenetic trees than students who only completed the simulation. Students who received explicit lecture instruction had a slightly more scientific association of phylogenetic terms than students who received did not receive lecture instruction. My findings suggest that technological instruction alone is not as beneficial as lecture instruction.

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.

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...

Categorizing Ideas about Trees: A Tree of Trees

PubMed Central

Fisler, Marie; Lecointre, Guillaume

2013-01-01

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization. PMID:23950877

Obtaining correct compile results by absorbing mismatches between data types representations

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

Horie, Michihiro; Horii, Hiroshi H.; Kawachiya, Kiyokuni

Methods and a system are provided. A method includes implementing a function, which a compiler for a first language does not have, using a compiler for a second language. The implementing step includes generating, by the compiler for the first language, a first abstract syntax tree. The implementing step further includes converting, by a converter, the first abstract syntax tree to a second abstract syntax tree of the compiler for the second language using a conversion table from data representation types in the first language to data representation types in the second language. When a compilation error occurs, the implementingmore » step also includes generating a special node for error processing in the second abstract syntax tree and storing an error token in the special node. When unparsing, the implementing step additionally includes outputting the error token, in the form of source code written in the first language.« less

Obtaining correct compile results by absorbing mismatches between data types representations

DOEpatents

Horie, Michihiro; Horii, Hiroshi H.; Kawachiya, Kiyokuni; Takeuchi, Mikio

2017-03-21

Methods and a system are provided. A method includes implementing a function, which a compiler for a first language does not have, using a compiler for a second language. The implementing step includes generating, by the compiler for the first language, a first abstract syntax tree. The implementing step further includes converting, by a converter, the first abstract syntax tree to a second abstract syntax tree of the compiler for the second language using a conversion table from data representation types in the first language to data representation types in the second language. When a compilation error occurs, the implementing step also includes generating a special node for error processing in the second abstract syntax tree and storing an error token in the special node. When unparsing, the implementing step additionally includes outputting the error token, in the form of source code written in the first language.

Obtaining correct compile results by absorbing mismatches between data types representations

DOEpatents

Horie, Michihiro; Horii, Hiroshi H.; Kawachiya, Kiyokuni; Takeuchi, Mikio

2017-11-21

Methods and a system are provided. A method includes implementing a function, which a compiler for a first language does not have, using a compiler for a second language. The implementing step includes generating, by the compiler for the first language, a first abstract syntax tree. The implementing step further includes converting, by a converter, the first abstract syntax tree to a second abstract syntax tree of the compiler for the second language using a conversion table from data representation types in the first language to data representation types in the second language. When a compilation error occurs, the implementing step also includes generating a special node for error processing in the second abstract syntax tree and storing an error token in the special node. When unparsing, the implementing step additionally includes outputting the error token, in the form of source code written in the first language.

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.

Isomorphism of dimer configurations and spanning trees on finite square lattices

NASA Astrophysics Data System (ADS)

Brankov, J. G.

1995-09-01

One-to-one mappings of the close-packed dimer configurations on a finite square lattice with free boundaries L onto the spanning trees of a related graph (or two-graph) G are found. The graph (two-graph) G can be constructed from L by: (1) deleting all the vertices of L with arbitrarily fixed parity of the row and column numbers; (2) suppressing all the vertices of degree 2 except those of degree 2 in L; (3) merging all the vertices of degree 1 into a single vertex g. The matrix Kirchhoff theorem reduces the enumeration problem for the spanning trees on G to the eigenvalue problem for the discrete Laplacian on the square lattice L'=G g with mixed Dirichlet-Neumann boundary conditions in at least one direction. That fact explains some of the unusual finite-size properties of the dimer model.

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.

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.

Integrated Approach To Design And Analysis Of Systems

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Iverson, David L.

1993-01-01

Object-oriented fault-tree representation unifies evaluation of reliability and diagnosis of faults. Programming/fault tree described more fully in "Object-Oriented Algorithm For Evaluation Of Fault Trees" (ARC-12731). Augmented fault tree object contains more information than fault tree object used in quantitative analysis of reliability. Additional information needed to diagnose faults in system represented by fault tree.

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

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.

Using Computer-Assisted Multiple Representations in Learning Geometry Proofs

ERIC Educational Resources Information Center

Wong, Wing-Kwong; Yin, Sheng-Kai; Yang, Hsi-Hsun; Cheng, Ying-Hao

2011-01-01

Geometry theorem proving involves skills that are difficult to learn. Instead of working with abstract and complicated representations, students might start with concrete, graphical representations. A proof tree is a graphical representation of a formal proof, with each node representing a proposition or given conditions. A computer-assisted…

Study on Cloud Security Based on Trust Spanning Tree Protocol

NASA Astrophysics Data System (ADS)

Lai, Yingxu; Liu, Zenghui; Pan, Qiuyue; Liu, Jing

2015-09-01

Attacks executed on Spanning Tree Protocol (STP) expose the weakness of link layer protocols and put the higher layers in jeopardy. Although the problems have been studied for many years and various solutions have been proposed, many security issues remain. To enhance the security and credibility of layer-2 network, we propose a trust-based spanning tree protocol aiming at achieving a higher credibility of LAN switch with a simple and lightweight authentication mechanism. If correctly implemented in each trusted switch, the authentication of trust-based STP can guarantee the credibility of topology information that is announced to other switch in the LAN. To verify the enforcement of the trusted protocol, we present a new trust evaluation method of the STP using a specification-based state model. We implement a prototype of trust-based STP to investigate its practicality. Experiment shows that the trusted protocol can achieve security goals and effectively avoid STP attacks with a lower computation overhead and good convergence performance.

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.

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.

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

Ground States of Random Spanning Trees on a D-Wave 2X

NASA Astrophysics Data System (ADS)

Hall, J. S.; Hobl, L.; Novotny, M. A.; Michielsen, Kristel

The performances of two D-Wave 2 machines (476 and 496 qubits) and of a 1097-qubit D-Wave 2X were investigated. Each chip has a Chimera interaction graph calG . Problem input consists of values for the fields hj and for the two-qubit interactions Ji , j of an Ising spin-glass problem formulated on calG . Output is returned in terms of a spin configuration {sj } , with sj = +/- 1 . We generated random spanning trees (RSTs) uniformly distributed over all spanning trees of calG . On the 476-qubit D-Wave 2, RSTs were generated on the full chip with Ji , j = - 1 and hj = 0 and solved one thousand times. The distribution of solution energies and the average magnetization of each qubit were determined. On both the 476- and 1097-qubit machines, four identical spanning trees were generated on each quadrant of the chip. The statistical independence of these regions was investigated. In another study, on the D-Wave 2X, one hundred RSTs with random Ji , j ∈ { - 1 , 1 } and hj = 0 were generated on the full chip. Each RST problem was solved one hundred times and the number of times the ground state energy was found was recorded. This procedure was repeated for square subgraphs, with dimensions ranging from 7 ×7 to 11 ×11. Supported in part by NSF Grants DGE-0947419 and DMR-1206233. D-Wave time provided by D-Wave Systems and by the USRA Quantum Artificial Intelligence Laboratory Research Opportunity.

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...

Assessment of student learning associated with tree thinking in an undergraduate introductory organismal biology course.

PubMed

Smith, James J; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is "better"; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor-descendant relationships. A pre-post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor-descendant relationships.

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

PubMed Central

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor–descendant relationships, a core concept of evolutionary theory. We introduced “tree thinking” into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is “better”; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor–descendant relationships. A pre–post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor–descendant relationships. PMID:24006401

Phylogenetic tree construction based on 2D graphical representation

NASA Astrophysics Data System (ADS)

Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

2006-04-01

A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

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.

In the right place at the right time: habitat representation in protected areas of South American Nothofagus-dominated plants after a dispersal constrained climate change scenario.

PubMed

Alarcón, Diego; Cavieres, Lohengrin A

2015-01-01

In order to assess the effects of climate change in temperate rainforest plants in southern South America in terms of habitat size, representation in protected areas, considering also if the expected impacts are similar for dominant trees and understory plant species, we used niche modeling constrained by species migration on 118 plant species, considering two groups of dominant trees and two groups of understory ferns. Representation in protected areas included Chilean national protected areas, private protected areas, and priority areas planned for future reserves, with two thresholds for minimum representation at the country level: 10% and 17%. With a 10% representation threshold, national protected areas currently represent only 50% of the assessed species. Private reserves are important since they increase up to 66% the species representation level. Besides, 97% of the evaluated species may achieve the minimum representation target only if the proposed priority areas were included. With the climate change scenario representation levels slightly increase to 53%, 69%, and 99%, respectively, to the categories previously mentioned. Thus, the current location of all the representation categories is useful for overcoming climate change by 2050. Climate change impacts on habitat size and representation of dominant trees in protected areas are not applicable to understory plants, highlighting the importance of assessing these effects with a larger number of species. Although climate change will modify the habitat size of plant species in South American temperate rainforests, it will have no significant impact in terms of the number of species adequately represented in Chile, where the implementation of the proposed reserves is vital to accomplish the present and future minimum representation. Our results also show the importance of using migration dispersal constraints to develop more realistic future habitat maps from climate change predictions.

In the Right Place at the Right Time: Habitat Representation in Protected Areas of South American Nothofagus-Dominated Plants after a Dispersal Constrained Climate Change Scenario

PubMed Central

Alarcón, Diego; Cavieres, Lohengrin A.

2015-01-01

In order to assess the effects of climate change in temperate rainforest plants in southern South America in terms of habitat size, representation in protected areas, considering also if the expected impacts are similar for dominant trees and understory plant species, we used niche modeling constrained by species migration on 118 plant species, considering two groups of dominant trees and two groups of understory ferns. Representation in protected areas included Chilean national protected areas, private protected areas, and priority areas planned for future reserves, with two thresholds for minimum representation at the country level: 10% and 17%. With a 10% representation threshold, national protected areas currently represent only 50% of the assessed species. Private reserves are important since they increase up to 66% the species representation level. Besides, 97% of the evaluated species may achieve the minimum representation target only if the proposed priority areas were included. With the climate change scenario representation levels slightly increase to 53%, 69%, and 99%, respectively, to the categories previously mentioned. Thus, the current location of all the representation categories is useful for overcoming climate change by 2050. Climate change impacts on habitat size and representation of dominant trees in protected areas are not applicable to understory plants, highlighting the importance of assessing these effects with a larger number of species. Although climate change will modify the habitat size of plant species in South American temperate rainforests, it will have no significant impact in terms of the number of species adequately represented in Chile, where the implementation of the proposed reserves is vital to accomplish the present and future minimum representation. Our results also show the importance of using migration dispersal constraints to develop more realistic future habitat maps from climate change predictions. PMID:25786226

Conversion from Tree to Graph Representation of Requirements

NASA Technical Reports Server (NTRS)

Mayank, Vimal; Everett, David Frank; Shmunis, Natalya; Austin, Mark

2009-01-01

A procedure and software to implement the procedure have been devised to enable conversion from a tree representation to a graph representation of the requirements governing the development and design of an engineering system. The need for this procedure and software and for other requirements-management tools arises as follows: In systems-engineering circles, it is well known that requirements- management capability improves the likelihood of success in the team-based development of complex systems involving multiple technological disciplines. It is especially desirable to be able to visualize (in order to identify and manage) requirements early in the system- design process, when errors can be corrected most easily and inexpensively.

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

Functional grouping of similar genes using eigenanalysis on minimum spanning tree based neighborhood graph.

PubMed

Jothi, R; Mohanty, Sraban Kumar; Ojha, Aparajita

2016-04-01

Gene expression data clustering is an important biological process in DNA microarray analysis. Although there have been many clustering algorithms for gene expression analysis, finding a suitable and effective clustering algorithm is always a challenging problem due to the heterogeneous nature of gene profiles. Minimum Spanning Tree (MST) based clustering algorithms have been successfully employed to detect clusters of varying shapes and sizes. This paper proposes a novel clustering algorithm using Eigenanalysis on Minimum Spanning Tree based neighborhood graph (E-MST). As MST of a set of points reflects the similarity of the points with their neighborhood, the proposed algorithm employs a similarity graph obtained from k(') rounds of MST (k(')-MST neighborhood graph). By studying the spectral properties of the similarity matrix obtained from k(')-MST graph, the proposed algorithm achieves improved clustering results. We demonstrate the efficacy of the proposed algorithm on 12 gene expression datasets. Experimental results show that the proposed algorithm performs better than the standard clustering algorithms. Copyright © 2016 Elsevier Ltd. All rights reserved.

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...

Tree-structured information file and its subprogram subtree

NASA Technical Reports Server (NTRS)

Mesztenyi, C. K.

1970-01-01

Development documentation programs are considered. A document tree is defined as the syntactic representation of a document when it is divided into subdivisions such as chapters and sections; a developmental tree is also defined as a tree of information obtained during the course of the development of the computer program. A developmental subtree is emphasized and described. A printed subprogram is also included.

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

PubMed Central

Dees, Jonathan; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. PMID:25452489

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

ERIC Educational Resources Information Center

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted…

Mof-Tree: A Spatial Access Method To Manipulate Multiple Overlapping Features.

ERIC Educational Resources Information Center

Manolopoulos, Yannis; Nardelli, Enrico; Papadopoulos, Apostolos; Proietti, Guido

1997-01-01

Investigates the manipulation of large sets of two-dimensional data representing multiple overlapping features, and presents a new access method, the MOF-tree. Analyzes storage requirements and time with respect to window query operations involving multiple features. Examines both the pointer-based and pointerless MOF-tree representations.…

Neuromodulation of Behavioral and Cognitive Development across the Life Span

ERIC Educational Resources Information Center

Li, Shu-Chen

2012-01-01

Among other mechanisms, behavioral and cognitive development entail, on the one hand, contextual scaffolding and, on the other hand, neuromodulation of adaptive neurocognitive representations across the life span. Key brain networks underlying cognition, emotion, and motivation are innervated by major transmitter systems (e.g., the catecholamines…

Bayesian inference on multiscale models for poisson intensity estimation: applications to photon-limited image denoising.

PubMed

Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George

2009-08-01

We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.

Representations of the language recognition problem for a theorem prover

NASA Technical Reports Server (NTRS)

Minker, J.; Vanderbrug, G. J.

1972-01-01

Two representations of the language recognition problem for a theorem prover in first order logic are presented and contrasted. One of the representations is based on the familiar method of generating sentential forms of the language, and the other is based on the Cocke parsing algorithm. An augmented theorem prover is described which permits recognition of recursive languages. The state-transformation method developed by Cordell Green to construct problem solutions in resolution-based systems can be used to obtain the parse tree. In particular, the end-order traversal of the parse tree is derived in one of the representations. An inference system, termed the cycle inference system, is defined which makes it possible for the theorem prover to model the method on which the representation is based. The general applicability of the cycle inference system to state space problems is discussed. Given an unsatisfiable set S, where each clause has at most one positive literal, it is shown that there exists an input proof. The clauses for the two representations satisfy these conditions, as do many state space problems.

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.

Path Network Recovery Using Remote Sensing Data and Geospatial-Temporal Semantic Graphs

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

William C. McLendon III; Brost, Randy C.

Remote sensing systems produce large volumes of high-resolution images that are difficult to search. The GeoGraphy (pronounced Geo-Graph-y) framework [2, 20] encodes remote sensing imagery into a geospatial-temporal semantic graph representation to enable high level semantic searches to be performed. Typically scene objects such as buildings and trees tend to be shaped like blocks with few holes, but other shapes generated from path networks tend to have a large number of holes and can span a large geographic region due to their connectedness. For example, we have a dataset covering the city of Philadelphia in which there is a singlemore » road network node spanning a 6 mile x 8 mile region. Even a simple question such as "find two houses near the same street" might give unexpected results. More generally, nodes arising from networks of paths (roads, sidewalks, trails, etc.) require additional processing to make them useful for searches in GeoGraphy. We have assigned the term Path Network Recovery to this process. Path Network Recovery is a three-step process involving (1) partitioning the network node into segments, (2) repairing broken path segments interrupted by occlusions or sensor noise, and (3) adding path-aware search semantics into GeoQuestions. This report covers the path network recovery process, how it is used, and some example use cases of the current capabilities.« less

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.

Lifemap: Exploring the Entire Tree of Life.

PubMed

de Vienne, Damien M

2016-12-01

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent

PubMed Central

Zhu, Sha; Degnan, James H.

2017-01-01

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

A novel knowledge-based system for interpreting complex engineering drawings: theory, representation, and implementation.

PubMed

Lu, Tong; Tai, Chiew-Lan; Yang, Huafei; Cai, Shijie

2009-08-01

We present a novel knowledge-based system to automatically convert real-life engineering drawings to content-oriented high-level descriptions. The proposed method essentially turns the complex interpretation process into two parts: knowledge representation and knowledge-based interpretation. We propose a new hierarchical descriptor-based knowledge representation method to organize the various types of engineering objects and their complex high-level relations. The descriptors are defined using an Extended Backus Naur Form (EBNF), facilitating modification and maintenance. When interpreting a set of related engineering drawings, the knowledge-based interpretation system first constructs an EBNF-tree from the knowledge representation file, then searches for potential engineering objects guided by a depth-first order of the nodes in the EBNF-tree. Experimental results and comparisons with other interpretation systems demonstrate that our knowledge-based system is accurate and robust for high-level interpretation of complex real-life engineering projects.

Optimality problem of network topology in stocks market analysis

NASA Astrophysics Data System (ADS)

Djauhari, Maman Abdurachman; Gan, Siew Lee

2015-02-01

Since its introduction fifteen years ago, minimal spanning tree has become an indispensible tool in econophysics. It is to filter the important economic information contained in a complex system of financial markets' commodities. Here we show that, in general, that tool is not optimal in terms of topological properties. Consequently, the economic interpretation of the filtered information might be misleading. To overcome that non-optimality problem, a set of criteria and a selection procedure of an optimal minimal spanning tree will be developed. By using New York Stock Exchange data, the advantages of the proposed method will be illustrated in terms of the power-law of degree distribution.

Long-term semantic representations moderate the effect of attentional refreshing on episodic memory.

PubMed

Loaiza, Vanessa M; Duperreault, Kayla A; Rhodes, Matthew G; McCabe, David P

2015-02-01

The McCabe effect (McCabe, Journal of Memory and Language 58:480-494, 2008) refers to an advantage in episodic memory (EM) retrieval for memoranda studied in complex span versus simple span tasks, particularly for memoranda presented in earlier serial positions. This finding has been attributed to the necessity to refresh memoranda during complex span tasks that, in turn, promotes content-context binding in working memory (WM). Several frameworks have conceptualized WM as being embedded in long-term memory. Thus, refreshing may be less efficient when memoranda are not well-established in long-term semantic memory (SM). To investigate this, we presented words and nonwords in simple and complex span trials in order to manipulate the long-term semantic representations of the memoranda with the requirement to refresh the memoranda during WM. A recognition test was administered that required participants to make a remember-know decision for each memorandum recognized as old. The results replicated the McCabe effect, but only for words, and the beneficial effect of refreshing opportunities was exclusive to recollection. These results extend previous research by indicating that the predictive relationship between WM refreshing and long-term EM is specific to recollection and, furthermore, moderated by representations in long-term SM. This supports the predictions of WM frameworks that espouse the importance of refreshing in content-context binding, but also those that view WM as being an activated subset of and, therefore, constrained by the contents of long-term memory.

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Complementing forest inventory data with information from unmanned aerial vehicle imagery and photogrammetry

Treesearch

Nikolay S. Strigul; Demetrios Gatziolis; Jean F. Liénard; Andre Vogs

2015-01-01

Although a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity, measurements conducive to three-dimensional (3D) representations of individual trees are seldom part of forest inventory operations. This is in part because until recently our ability to measure the dimensionality, spatial arrangement, and shape of trees and...

K-SPAN: A lexical database of Korean surface phonetic forms and phonological neighborhood density statistics.

PubMed

Holliday, Jeffrey J; Turnbull, Rory; Eychenne, Julien

2017-10-01

This article presents K-SPAN (Korean Surface Phonetics and Neighborhoods), a database of surface phonetic forms and several measures of phonological neighborhood density for 63,836 Korean words. Currently publicly available Korean corpora are limited by the fact that they only provide orthographic representations in Hangeul, which is problematic since phonetic forms in Korean cannot be reliably predicted from orthographic forms. We describe the method used to derive the surface phonetic forms from a publicly available orthographic corpus of Korean, and report on several statistics calculated using this database; namely, segment unigram frequencies, which are compared to previously reported results, along with segment-based and syllable-based neighborhood density statistics for three types of representation: an "orthographic" form, which is a quasi-phonological representation, a "conservative" form, which maintains all known contrasts, and a "modern" form, which represents the pronunciation of contemporary Seoul Korean. These representations are rendered in an ASCII-encoded scheme, which allows users to query the corpus without having to read Korean orthography, and permits the calculation of a wide range of phonological measures.

A link representation for gravity amplitudes

NASA Astrophysics Data System (ADS)

He, Song

2013-10-01

We derive a link representation for all tree amplitudes in supergravity, from a recent conjecture by Cachazo and Skinner. The new formula explicitly writes amplitudes as contour integrals over constrained link variables, with an integrand naturally expressed in terms of determinants, or equivalently tree diagrams. Important symmetries of the amplitude, such as supersymmetry, parity and (partial) permutation invariance, are kept manifest in the formulation. We also comment on rewriting the formula in a GL( k)-invariant manner, which may serve as a starting point for the generalization to possible Grassmannian contour integrals.

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

Probability and possibility-based representations of uncertainty in fault tree analysis.

PubMed

Flage, Roger; Baraldi, Piero; Zio, Enrico; Aven, Terje

2013-01-01

Expert knowledge is an important source of input to risk analysis. In practice, experts might be reluctant to characterize their knowledge and the related (epistemic) uncertainty using precise probabilities. The theory of possibility allows for imprecision in probability assignments. The associated possibilistic representation of epistemic uncertainty can be combined with, and transformed into, a probabilistic representation; in this article, we show this with reference to a simple fault tree analysis. We apply an integrated (hybrid) probabilistic-possibilistic computational framework for the joint propagation of the epistemic uncertainty on the values of the (limiting relative frequency) probabilities of the basic events of the fault tree, and we use possibility-probability (probability-possibility) transformations for propagating the epistemic uncertainty within purely probabilistic and possibilistic settings. The results of the different approaches (hybrid, probabilistic, and possibilistic) are compared with respect to the representation of uncertainty about the top event (limiting relative frequency) probability. Both the rationale underpinning the approaches and the computational efforts they require are critically examined. We conclude that the approaches relevant in a given setting depend on the purpose of the risk analysis, and that further research is required to make the possibilistic approaches operational in a risk analysis context. © 2012 Society for Risk Analysis.

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...

Comparing alternative tree canopy cover estimates derived from digital aerial photography and field-based assessments

Treesearch

Tracey S. Frescino; Gretchen G. Moisen

2012-01-01

A spatially-explicit representation of live tree canopy cover, such as the National Land Cover Dataset (NLCD) percent tree canopy cover layer, is a valuable tool for many applications, such as defining forest land, delineating wildlife habitat, estimating carbon, and modeling fire risk and behavior. These layers are generated by predictive models wherein their accuracy...

Integrating LIDAR and forest inventories to fill the trees outside forests data gap

Treesearch

Kristofer D. Johnson; Richard Birdsey; Jason Cole; Anu Swatantran; Jarlath O' Neil-Dunne; Ralph Dubayah; Andrew Lister

2015-01-01

Forest inventories are commonly used to estimate total tree biomass of forest land even though they are not traditionally designed to measure biomass of trees outside forests (TOF). The consequence may be an inaccurate representation of all of the aboveground biomass, which propagates error to the outputs of spatial and process models that rely on the inventory data....

Object-oriented fault tree models applied to system diagnosis

NASA Technical Reports Server (NTRS)

Iverson, David L.; Patterson-Hine, F. A.

1990-01-01

When a diagnosis system is used in a dynamic environment, such as the distributed computer system planned for use on Space Station Freedom, it must execute quickly and its knowledge base must be easily updated. Representing system knowledge as object-oriented augmented fault trees provides both features. The diagnosis system described here is based on the failure cause identification process of the diagnostic system described by Narayanan and Viswanadham. Their system has been enhanced in this implementation by replacing the knowledge base of if-then rules with an object-oriented fault tree representation. This allows the system to perform its task much faster and facilitates dynamic updating of the knowledge base in a changing diagnosis environment. Accessing the information contained in the objects is more efficient than performing a lookup operation on an indexed rule base. Additionally, the object-oriented fault trees can be easily updated to represent current system status. This paper describes the fault tree representation, the diagnosis algorithm extensions, and an example application of this system. Comparisons are made between the object-oriented fault tree knowledge structure solution and one implementation of a rule-based solution. Plans for future work on this system are also discussed.

Beyond capacity limitations II: Effects of lexical processes on word recall in verbal working memory tasks in children with and without specific language impairment

PubMed Central

Mainela-Arnold, Elina; Evans, Julia L.; Coady, Jeffry

2010-01-01

Purpose This study investigated the impact of lexical processes on target word recall in sentence span tasks in children with and without specific language impairment (SLI). Method Participants were 42 children (ages 8;2–12;3), 21 with SLI and 21 typically developing peers matched on age and nonverbal IQ. Children completed a sentence span task where target words to be recalled varied in word frequency and neighborhood density. Two measures of lexical processes were examined, the number of non-target competitor words activated during a gating task (lexical cohort competition) and word definitions. Results Neighborhood density had no effect on word recall for either group. However, both groups recalled significantly more high than low frequency words. Lexical cohort competition and specificity of semantic representations accounted for unique variance in the number of target word recalled in the SLI and CA groups combined. Conclusions Performance on verbal working memory span tasks for both SLI and CA children is influenced by word frequency, lexical cohorts, and semantic representations. Future studies need to examine the extent to which verbal working memory capacity is a cognitive construct independent of extant language knowledge representations. PMID:20705747

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.

Organizing Books and Authors by Multilayer SOM.

PubMed

Zhang, Haijun; Chow, Tommy W S; Wu, Q M Jonathan

2016-12-01

This paper introduces a new framework for the organization of electronic books (e-books) and their corresponding authors using a multilayer self-organizing map (MLSOM). An author is modeled by a rich tree-structured representation, and an MLSOM-based system is used as an efficient solution to the organizational problem of structured data. The tree-structured representation formulates author features in a hierarchy of author biography, books, pages, and paragraphs. To efficiently tackle the tree-structured representation, we used an MLSOM algorithm that serves as a clustering technique to handle e-books and their corresponding authors. A book and author recommender system is then implemented using the proposed framework. The effectiveness of our approach was examined in a large-scale data set containing 3868 authors along with the 10500 e-books that they wrote. We also provided visualization results of MLSOM for revealing the relevance patterns hidden from presented author clusters. The experimental results corroborate that the proposed method outperforms other content-based models (e.g., rate adapting poisson, latent Dirichlet allocation, probabilistic latent semantic indexing, and so on) and offers a promising solution to book recommendation, author recommendation, and visualization.

Towards a more molecular taxonomy of disease.

PubMed

Park, Jisoo; Hescott, Benjamin J; Slonim, Donna K

2017-07-27

Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data. We compare this technique with both an established ontology inference method (CliXO) and a minimum weight spanning tree approach. Because there is no gold standard molecular disease taxonomy available, we compare our inferred hierarchies to both the Medical Subject Headings (MeSH) category C forest of diseases and to subnetworks of the Disease Ontology (DO). This comparison provides insights about the inference algorithms, choices of evaluation metrics, and the existing molecular content of various subnetworks of MeSH and the DO. Our results suggest that the Parent Promotion method performs well in most cases. Performance across MeSH trees is also correlated between inference methods. Specifically, inferred relationships are more consistent with those in smaller MeSH disease trees than larger ones, but there are some notable exceptions that may correlate with higher molecular content in MeSH. Our experiments provide insights about learning relationships between diseases from disease genes alone. Future work should explore the prospect of disease term discovery from molecular data and how best to integrate molecular data with anatomical and clinical knowledge. This study nonetheless suggests that disease gene information has the potential to form an important part of the foundation for future representations of the disease landscape.

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation.

PubMed

Wang, Zhaocai; Huang, Dongmei; Meng, Huajun; Tang, Chengpei

2013-10-01

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m+n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

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

Graphic Representations as Tools for Decision Making.

ERIC Educational Resources Information Center

Howard, Judith

2001-01-01

Focuses on the use of graphic representations to enable students to improve their decision making skills in the social studies. Explores three visual aids used in assisting students with decision making: (1) the force field; (2) the decision tree; and (3) the decision making grid. (CMK)

An assessment of geographical distribution of different plant functional types over North America simulated using the CLASS-CTEM modelling framework

NASA Astrophysics Data System (ADS)

Shrestha, Rudra K.; Arora, Vivek K.; Melton, Joe R.; Sushama, Laxmi

2017-10-01

The performance of the competition module of the CLASS-CTEM (Canadian Land Surface Scheme and Canadian Terrestrial Ecosystem Model) modelling framework is assessed at 1° spatial resolution over North America by comparing the simulated geographical distribution of its plant functional types (PFTs) with two observation-based estimates. The model successfully reproduces the broad geographical distribution of trees, grasses and bare ground although limitations remain. In particular, compared to the two observation-based estimates, the simulated fractional vegetation coverage is lower in the arid southwest North American region and higher in the Arctic region. The lower-than-observed simulated vegetation coverage in the southwest region is attributed to lack of representation of shrubs in the model and plausible errors in the observation-based data sets. The observation-based data indicate vegetation fractional coverage of more than 60 % in this arid region, despite only 200-300 mm of precipitation that the region receives annually, and observation-based leaf area index (LAI) values in the region are lower than one. The higher-than-observed vegetation fractional coverage in the Arctic is likely due to the lack of representation of moss and lichen PFTs and also likely because of inadequate representation of permafrost in the model as a result of which the C3 grass PFT performs overly well in the region. The model generally reproduces the broad spatial distribution and the total area covered by the two primary tree PFTs (needleleaf evergreen trees, NDL-EVG; and broadleaf cold deciduous trees, BDL-DCD-CLD) reasonably well. The simulated fractional coverage of tree PFTs increases after the 1960s in response to the CO2 fertilization effect and climate warming. Differences between observed and simulated PFT coverages highlight model limitations and suggest that the inclusion of shrubs, and moss and lichen PFTs, and an adequate representation of permafrost will help improve model performance.

Representations and processes of human spatial competence.

PubMed

Gunzelmann, Glenn; Lyon, Don R

2011-10-01

This article presents an approach to understanding human spatial competence that focuses on the representations and processes of spatial cognition and how they are integrated with cognition more generally. The foundational theoretical argument for this research is that spatial information processing is central to cognition more generally, in the sense that it is brought to bear ubiquitously to improve the adaptivity and effectiveness of perception, cognitive processing, and motor action. We describe research spanning multiple levels of complexity to understand both the detailed mechanisms of spatial cognition, and how they are utilized in complex, naturalistic tasks. In the process, we discuss the critical role of cognitive architectures in developing a consistent account that spans this breadth, and we note some areas in which the current version of a popular architecture, ACT-R, may need to be augmented. Finally, we suggest a framework for understanding the representations and processes of spatial competence and their role in human cognition generally. Copyright © 2011 Cognitive Science Society, Inc.

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.

Coherent multiscale image processing using dual-tree quaternion wavelets.

PubMed

Chan, Wai Lam; Choi, Hyeokho; Baraniuk, Richard G

2008-07-01

The dual-tree quaternion wavelet transform (QWT) is a new multiscale analysis tool for geometric image features. The QWT is a near shift-invariant tight frame representation whose coefficients sport a magnitude and three phases: two phases encode local image shifts while the third contains image texture information. The QWT is based on an alternative theory for the 2-D Hilbert transform and can be computed using a dual-tree filter bank with linear computational complexity. To demonstrate the properties of the QWT's coherent magnitude/phase representation, we develop an efficient and accurate procedure for estimating the local geometrical structure of an image. We also develop a new multiscale algorithm for estimating the disparity between a pair of images that is promising for image registration and flow estimation applications. The algorithm features multiscale phase unwrapping, linear complexity, and sub-pixel estimation accuracy.

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.

Multi-model comparison on the effects of climate change on tree species in the eastern U.S.: results from an enhanced niche model and process-based ecosystem and landscape models

Treesearch

Louis R. Iverson; Frank R. Thompson; Stephen Matthews; Matthew Peters; Anantha Prasad; William D. Dijak; Jacob Fraser; Wen J. Wang; Brice Hanberry; Hong He; Maria Janowiak; Patricia Butler; Leslie Brandt; Chris Swanston

2016-01-01

Context. Species distribution models (SDM) establish statistical relationships between the current distribution of species and key attributes whereas process-based models simulate ecosystem and tree species dynamics based on representations of physical and biological processes. TreeAtlas, which uses DISTRIB SDM, and Linkages and LANDIS PRO, process...

EDNA: Expert fault digraph analysis using CLIPS

NASA Technical Reports Server (NTRS)

Dixit, Vishweshwar V.

1990-01-01

Traditionally fault models are represented by trees. Recently, digraph models have been proposed (Sack). Digraph models closely imitate the real system dependencies and hence are easy to develop, validate and maintain. However, they can also contain directed cycles and analysis algorithms are hard to find. Available algorithms tend to be complicated and slow. On the other hand, the tree analysis (VGRH, Tayl) is well understood and rooted in vast research effort and analytical techniques. The tree analysis algorithms are sophisticated and orders of magnitude faster. Transformation of a digraph (cyclic) into trees (CLP, LP) is a viable approach to blend the advantages of the representations. Neither the digraphs nor the trees provide the ability to handle heuristic knowledge. An expert system, to capture the engineering knowledge, is essential. We propose an approach here, namely, expert network analysis. We combine the digraph representation and tree algorithms. The models are augmented by probabilistic and heuristic knowledge. CLIPS, an expert system shell from NASA-JSC will be used to develop a tool. The technique provides the ability to handle probabilities and heuristic knowledge. Mixed analysis, some nodes with probabilities, is possible. The tool provides graphics interface for input, query, and update. With the combined approach it is expected to be a valuable tool in the design process as well in the capture of final design knowledge.

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.

Comparison between BIDE, PrefixSpan, and TRuleGrowth for Mining of Indonesian Text

NASA Astrophysics Data System (ADS)

Sa'adillah Maylawati, Dian; Irfan, Mohamad; Budiawan Zulfikar, Wildan

2017-01-01

Mining proscess for Indonesian language still be an interesting research. Multiple of words representation was claimed can keep the meaning of text better than bag of words. In this paper, we compare several sequential pattern algortihm, among others BIDE (BIDirectional Extention), PrefixSpan, and TRuleGrowth. All of those algorithm produce frequent word sequence to keep the meaning of text. However, the experiment result, with 14.006 of Indonesian tweet from Twitter, shows that BIDE can produce more efficient frequent word sequence than PrefixSpan and TRuleGrowth without missing the meaning of text. Then, the average of time process of PrefixSpan is faster than BIDE and TRuleGrowth. In the other hand, PrefixSpan and TRuleGrowth is more efficient in using memory than BIDE.

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."

Stress Conflation: Evidence from Sooke.

ERIC Educational Resources Information Center

Davis, Stuart

A comparison of the application of two current theories of stress to a particular stress pattern found in the Salish language Sooke is presented. Hammond's (1986) grid-like tree structure representation of stress is compared with Halle and Vergnaud's (1986) tree-like grid structure. Examples in the Australian language Maranungku show that, in…

Tree versus Geometric Representation of Tests and Items.

ERIC Educational Resources Information Center

Beller, Michael

1990-01-01

Geometric approaches to representing interrelations among tests and items are compared with an additive tree model (ATM), using 2,644 examinees and 2 other data sets. The ATM's close fit to the data and its coherence of presentation indicate that it is the best means of representing tests and items. (TJH)

Surface pollen and its relationship to vegetation in the Zoige Basin, eastern Tibetan Plateau

NASA Astrophysics Data System (ADS)

Li, Furong; Zhao, Yan; Sun, Jinghui; Zhao, Wenwei; Guo, Xiaoli; Zhang, Ke

2011-09-01

We use a data set of 23 surface pollen samples from moss polsters in the Zoige Basin to explore the relationship between modern pollen assemblages and contemporary vegetation patterns. The surface pollen samples spanned four types of plant communities: Carex muliensis marsh, Stipa and Kobresia meadow, Carex-dominated forb meadow and Sibiraea angustata scrub. Principal-components analysis (PCA) was used to determine the relationships between modern pollen and vegetation and environmental variables. The results show that the pollen assemblages of surface moss samples generally reflect the features of the modern vegetation, basically similar in the vegetation types and the dominant genera; however, they don't show a very clear distinction between different communities. Our results also demonstrate that pollen representation of different families or genus varied. Some tree taxa, such as Pinus and Betula, and herb types, such as Artemisia are over-represented, while Asteraceae, Ranunculaceae and Cyperaceae are moderately represented, and Poaceae and Rosaceae are usually under-represented in our study region. PCA results indicate that the distribution of vegetation in the Zoige Basin is mainly controlled by precipitation and altitude.

SGR 1822-1606: Constant Spin Period

NASA Astrophysics Data System (ADS)

Serim, M.; Baykal, A.; Inam, S. C.

2011-08-01

We have analyzed light curve of the new source SGR 1822-1606 (Cummings et al. GCN 12159) using the real time data of RXTE observations. We have extracted light curve for 11 pointings with a time span of about 20 days and employed pulse timing analysis using the harmonic representation of pulses. Using the cross correlation of harmonic representation of pulses, we have obtained pulse arrival times.

Polyhedral gamut representation of natural objects based on spectral reflectance database and its application

NASA Astrophysics Data System (ADS)

Haneishi, Hideaki; Sakuda, Yasunori; Honda, Toshio

2002-06-01

Spectral reflectance of most reflective objects such as natural objects and color hardcopy is relatively smooth and can be approximated by several numbers of principal components with high accuracy. Though the subspace spanned by those principal components represents a space in which reflective objects can exist, it dos not provide the bound in which the samples distribute. In this paper we propose to represent the gamut of reflective objects in more distinct form, i.e., as a polyhedron in the subspace spanned by several principal components. Concept of the polyhedral gamut representation and its application to calculation of metamer ensemble are described. Color-mismatch volume caused by different illuminant and/or observer for a metamer ensemble is also calculated and compared with theoretical one.

[Effect of concreteness of target words on verbal working memory: an evaluation using Japanese version of reading span test].

PubMed

Kondo, H; Osaka, N

2000-04-01

Effects of concreteness and representation mode (kanji/hiragana) of target words on working memory during reading was tested using Japanese version of reading span test (RST), developed by Osaka and Osaka (1994). Concreteness and familiarity of target words and difficulty of sentences were carefully controlled. The words with high concreteness resulted in significantly higher RST scores, which suggests the high efficiency of working memory in processing these words. The results suggest that high concrete noun-words associated with visual clues consume less working memory capacity during reading. The effect of representation mode is different between subjects with high-RST and low-RST scores. Characteristic of the high concrete words that may be responsible for the effectiveness of processing are discussed.

Software For Fault-Tree Diagnosis Of A System

NASA Technical Reports Server (NTRS)

Iverson, Dave; Patterson-Hine, Ann; Liao, Jack

1993-01-01

Fault Tree Diagnosis System (FTDS) computer program is automated-diagnostic-system program identifying likely causes of specified failure on basis of information represented in system-reliability mathematical models known as fault trees. Is modified implementation of failure-cause-identification phase of Narayanan's and Viswanadham's methodology for acquisition of knowledge and reasoning in analyzing failures of systems. Knowledge base of if/then rules replaced with object-oriented fault-tree representation. Enhancement yields more-efficient identification of causes of failures and enables dynamic updating of knowledge base. Written in C language, C++, and Common LISP.

Carrier-envelope phase dynamics and noise analysis in octave-spanning Ti:sapphire lasers.

PubMed

Matos, Lia; Mücke, Oliver D; Chen, Jian; Kärtner, Franz X

2006-03-20

We investigate the carrier-envelope phase dynamics of octave-spanning Ti:sapphire lasers and perform a complete noise analysis of the carrier-envelope phase stabilization. We model the effect of the laser dynamics on the residual carrier-envelope phase noise by deriving a transfer function representation of the octave-spanning frequency comb. The modelled phase noise and the experimental results show excellent agreement. This greatly enhances our capability of predicting the dependence of the residual carrier-envelope phase noise on the feedback loop filter, the carrier-envelope frequency control mechanism and the pump laser used.

Some trees with partition dimension three

NASA Astrophysics Data System (ADS)

Fredlina, Ketut Queena; Baskoro, Edy Tri

2016-02-01

The concept of partition dimension of a graph was introduced by Chartrand, E. Salehi and P. Zhang (1998) [2]. Let G(V, E) be a connected graph. For S ⊆ V (G) and v ∈ V (G), define the distance d(v, S) from v to S is min{d(v, x)|x ∈ S}. Let Π be an ordered partition of V (G) and Π = {S1, S2, ..., Sk }. The representation r(v|Π) of vertex v with respect to Π is (d(v, S1), d(v, S2), ..., d(v, Sk)). If the representations of all vertices are distinct, then the partition Π is called a resolving partition of G. The partition dimension of G is the minimum k such that G has a resolving partition with k partition classes. In this paper, we characterize some classes of trees with partition dimension three, namely olive trees, weeds, and centipedes.

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...

Phonological similarity effect in complex span task.

PubMed

Camos, Valérie; Mora, Gérôme; Barrouillet, Pierre

2013-01-01

The aim of our study was to test the hypothesis that two systems are involved in verbal working memory; one is specifically dedicated to the maintenance of phonological representations through verbal rehearsal while the other would maintain multimodal representations through attentional refreshing. This theoretical framework predicts that phonologically related phenomena such as the phonological similarity effect (PSE) should occur when the domain-specific system is involved in maintenance, but should disappear when concurrent articulation hinders its use. Impeding maintenance in the domain-general system by a concurrent attentional demand should impair recall performance without affecting PSE. In three experiments, we manipulated the concurrent articulation and the attentional demand induced by the processing component of complex span tasks in which participants had to maintain lists of either similar or dissimilar words. Confirming our predictions, PSE affected recall performance in complex span tasks. Although both the attentional demand and the articulatory requirement of the concurrent task impaired recall, only the induction of an articulatory suppression during maintenance made the PSE disappear. These results suggest a duality in the systems devoted to verbal maintenance in the short term, constraining models of working memory.

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)

Relative Suffix Trees.

PubMed

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-05-01

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.

Relative Suffix Trees

PubMed Central

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-01-01

Abstract Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees. PMID:29795706

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.

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.

Student interpretations of phylogenetic trees in an introductory biology course.

PubMed

Dees, Jonathan; Momsen, Jennifer L; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. © 2014 J. Dees et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

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.

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.

Drought-associated tree mortality: Global patterns and insights from tree-ring studies in the southwestern U.S.A

NASA Astrophysics Data System (ADS)

Macalady, Alison Kelly

Forests play an important role in the earth system, regulating climate, maintaining biodiversity, and provisioning human communities with water, food and fuel. Interactions between climate and forest dynamics are not well constrained, and high uncertainty characterizes projections of global warming impacts on forests and associated ecosystem services. Recently observed tree mortality and forest die-off forewarn an acceleration of forest change with rising temperature and increased drought. However, the processes leading to tree death during drought are poorly understood, limiting our ability to anticipate future forest dynamics. The objective of this dissertation was to improve understanding of drought-associated tree mortality through literature synthesis and tree-ring studies on trees that survived and died during droughts in the southwestern USA. Specifically, this dissertation 1) documented global tree mortality patterns and identified emerging trends and research gaps; 2) quantified relationships between growth, climate, competition and mortality of pinon pine during droughts in New Mexico; 3) investigated tree defense anatomy as a potentially key element in pinon avoidance of death; and, 4) characterized the climate sensitivity of pinon resin ducts in order to gain insight into potential trends in tree defenses with climate variability and change. There has been an increase in studies reporting tree mortality linked to drought, heat, and the associated activity of insects and pathogens. Cases span the forested continents and occurred in water, light and temperature-limited forests. We hypothesized that increased tree mortality may be an emerging global phenomenon related to rising temperatures and drought (Appendix A). Recent radial growth was 53% higher on average in pinon that survived versus died during two episodes of drought-associated mortality, and statistical models of mortality risk based on average growth, growth variability, and abrupt growth changes correctly classified the status of ˜70% of trees. Climate responses and competitive interactions partly explained growth differences between dying and surviving trees, with muted response to wet/cool conditions and enhanced sensitivity to competition from congeners linked to growth patterns associated with death. Discrimination and validation of models of mortality risk varied widely across sites and drought events, indicating shifting growth-mortality relationships and differences in mortality processes across space and time (Appendix B). Pre-formed defense anatomy is strongly associated with pinon survivorship over a range of sites and stand conditions. Models of mortality risk that account for both growth and resin duct attributes had ≈10 19 more support than models that contained only growth. The greatest improvement in classification was among trees from the 2000s drought, suggesting an enhanced role for tree defense allocation and/or bark beetle activity during recent warm versus historic cool drought. Accounting for defense characteristics and growth-defense allocation is likely to be important for improving representation of drought-associated mortality (Appendix C). Pinon resin duct chronologies contain climate responses that are coherent and distinct from those of radial growth. Growth responds positively and strongly to previous fall and current winter precipitation, and negatively to late spring and early summer temperature. A relatively equal positive resin duct response to winter precipitation and positive response to mid-to-late summer drought suggests that changes in climate will affect tree defense anatomy in complex ways, with the outcome determined by seasonal changes in precipitation and temperature (Appendix D).

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.

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)...

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.

A Model for Flexibly Editing CSCL Scripts

ERIC Educational Resources Information Center

Sobreira, Pericles; Tchounikine, Pierre

2012-01-01

This article presents a model whose primary concern and design rationale is to offer users (teachers) with basic ICT skills an intuitive, easy, and flexible way of editing scripts. The proposal is based on relating an end-user representation as a table and a machine model as a tree. The table-tree model introduces structural expressiveness and…

An object-oriented forest landscape model and its representation of tree species

Treesearch

Hong S. He; David J. Mladenoff; Joel Boeder

1999-01-01

LANDIS is a forest landscape model that simulates the interaction of large landscape processes and forest successional dynamics at tree species level. We discuss how object-oriented design (OOD) approaches such as modularity, abstraction and encapsulation are integrated into the design of LANDIS. We show that using OOD approaches, model decisions (olden as model...

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.

The FTA Method And A Possibility Of Its Application In The Area Of Road Freight Transport

NASA Astrophysics Data System (ADS)

Poliaková, Adela

2015-06-01

The Fault Tree process utilizes logic diagrams to portray and analyse potentially hazardous events. Three basic symbols (logic gates) are adequate for diagramming any fault tree. However, additional recently developed symbols can be used to reduce the time and effort required for analysis. A fault tree is a graphical representation of the relationship between certain specific events and the ultimate undesired event (2). This paper deals to method of Fault Tree Analysis basic description and provides a practical view on possibility of application by quality improvement in road freight transport company.

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.

Process model simulations of the divergence effect

NASA Astrophysics Data System (ADS)

Anchukaitis, K. J.; Evans, M. N.; D'Arrigo, R. D.; Smerdon, J. E.; Hughes, M. K.; Kaplan, A.; Vaganov, E. A.

2007-12-01

We explore the extent to which the Vaganov-Shashkin (VS) model of conifer tree-ring formation can explain evidence for changing relationships between climate and tree growth over recent decades. The VS model is driven by daily environmental forcing (temperature, soil moisture, and solar radiation), and simulates tree-ring growth cell-by-cell as a function of the most limiting environmental control. This simplified representation of tree physiology allows us to examine using a selection of case studies whether instances of divergence may be explained in terms of changes in limiting environmental dependencies or transient climate change. Identification of model-data differences permits further exploration of the effects of tree-ring standardization, atmospheric composition, and additional non-climatic factors.

Patterns in spatial distribution and root trait syndromes for ecto and arbuscular mycorrhizal temperate trees in a mixed broadleaf forest.

PubMed

Valverde-Barrantes, Oscar J; Smemo, Kurt A; Feinstein, Larry M; Kershner, Mark W; Blackwood, Christopher B

2018-03-01

Functional differences between trees with arbuscular (AM) or ectomycorrhizal (ECM) partnerships influence important ecological processes including nutrient cycling, community assembly, and biomass allocation patterns. Although most broadleaf temperate forests show both mycorrhizal types, relatively few studies have addressed functional difference among coexisting mycorrhizal tree species. The maintenance of ECM associations usually requires higher C investment than AM, leading to (A) lower root biomass and (B) more conservative root trait syndromes in ECM tree species compared to AM species. Here we quantified the representation and trait syndromes of 14 canopy tree species associated with either AM or ECM fungi in a natural forest community. Our results showed that, whereas species root abundance was proportional to basal area, some ECM tree roots were largely under-represented (up to ~ 33%). Most of the under-representation was due to lower than expected root abundance of Quercus rubra and Fagus grandifolia. Functional root traits in tree species were similar, with the exception of higher tissue density in ECM species. Moreover, closely related AM and ECM exhibited similar traits, suggesting inherited trait syndrome from a common ancestor. Thus, we found little evidence of divergent functional root trait syndromes between mycorrhizal types. Cores dominated by ECM species influenced trait distribution at the community level, but not total biomass, suggesting that mycorrhizal affiliation may have a stronger effect on the spatial distribution of traits but not on biomass stocks. Our results present an important step toward relating belowground carbon dynamics to species traits, including mycorrhizal type, in broadleaf temperate forests.

The Diagnostic Drawing Series and the Tree Rating Scale: An Isomorphic Representation of Multiple Personality Disorder, Major Depression, and Schizophrenic Populations.

ERIC Educational Resources Information Center

Morris, Maureen Batza

1995-01-01

The tree drawings of 80 subjects, who were diagnosed with either multiple personality disorder, schizophrenia, or major depression, and a control group, were rated. Patterns were examined and graphs were used to depict results. Certain features were found to distinguish each category. The descriptive statistical findings were both consistent and…

Modular techniques for dynamic fault-tree analysis

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Dugan, Joanne B.

1992-01-01

It is noted that current approaches used to assess the dependability of complex systems such as Space Station Freedom and the Air Traffic Control System are incapable of handling the size and complexity of these highly integrated designs. A novel technique for modeling such systems which is built upon current techniques in Markov theory and combinatorial analysis is described. It enables the development of a hierarchical representation of system behavior which is more flexible than either technique alone. A solution strategy which is based on an object-oriented approach to model representation and evaluation is discussed. The technique is virtually transparent to the user since the fault tree models can be built graphically and the objects defined automatically. The tree modularization procedure allows the two model types, Markov and combinatoric, to coexist and does not require that the entire fault tree be translated to a Markov chain for evaluation. This effectively reduces the size of the Markov chain required and enables solutions with less truncation, making analysis of longer mission times possible. Using the fault-tolerant parallel processor as an example, a model is built and solved for a specific mission scenario and the solution approach is illustrated in detail.

Can Sap Flow Help Us to Better Understand Transpiration Patterns in Landscapes?

NASA Astrophysics Data System (ADS)

Hassler, S. K.; Weiler, M.; Blume, T.

2017-12-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions and for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. At the tree scale, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status, stand-specific characteristics such as basal area or stand density and site-specific characteristics such as geology, slope position or aspect control sap flow of individual trees. However, little is known about the relative importance or the dynamic interplay of these controls. We studied these influences with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km²-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we applied linear models to the daily spatial pattern of sap velocity and determined the importance of the different predictors. By upscaling sap velocities to the tree level with the help of species-dependent empirical estimates for sapwood area we also examined patterns of sap flow as a more direct representation of transpiration. Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in this landscape, namely tree species, tree diameter, geology and aspect. For sap flow, the site-specific predictors provided the largest contribution to the explained variance, however, in contrast to the sap velocity analysis, geology was more important than aspect. Spatial variability of atmospheric demand and soil moisture explained only a small fraction of the variance. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, were correlated to the temporal dynamics of potential evaporation. We conclude that spatial representation of transpiration in models could benefit from including patterns according to tree and site characteristics.

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

Cluster structure of EU-15 countries derived from the correlation matrix analysis of macroeconomic index fluctuations

NASA Astrophysics Data System (ADS)

Gligor, M.; Ausloos, M.

2007-05-01

The statistical distances between countries, calculated for various moving average time windows, are mapped into the ultrametric subdominant space as in classical Minimal Spanning Tree methods. The Moving Average Minimal Length Path (MAMLP) algorithm allows a decoupling of fluctuations with respect to the mass center of the system from the movement of the mass center itself. A Hamiltonian representation given by a factor graph is used and plays the role of cost function. The present analysis pertains to 11 macroeconomic (ME) indicators, namely the GDP (x1), Final Consumption Expenditure (x2), Gross Capital Formation (x3), Net Exports (x4), Consumer Price Index (y1), Rates of Interest of the Central Banks (y2), Labour Force (z1), Unemployment (z2), GDP/hour worked (z3), GDP/capita (w1) and Gini coefficient (w2). The target group of countries is composed of 15 EU countries, data taken between 1995 and 2004. By two different methods (the Bipartite Factor Graph Analysis and the Correlation Matrix Eigensystem Analysis) it is found that the strongly correlated countries with respect to the macroeconomic indicators fluctuations can be partitioned into stable clusters.

W-tree indexing for fast visual word generation.

PubMed

Shi, Miaojing; Xu, Ruixin; Tao, Dacheng; Xu, Chao

2013-03-01

The bag-of-visual-words representation has been widely used in image retrieval and visual recognition. The most time-consuming step in obtaining this representation is the visual word generation, i.e., assigning visual words to the corresponding local features in a high-dimensional space. Recently, structures based on multibranch trees and forests have been adopted to reduce the time cost. However, these approaches cannot perform well without a large number of backtrackings. In this paper, by considering the spatial correlation of local features, we can significantly speed up the time consuming visual word generation process while maintaining accuracy. In particular, visual words associated with certain structures frequently co-occur; hence, we can build a co-occurrence table for each visual word for a large-scale data set. By associating each visual word with a probability according to the corresponding co-occurrence table, we can assign a probabilistic weight to each node of a certain index structure (e.g., a KD-tree and a K-means tree), in order to re-direct the searching path to be close to its global optimum within a small number of backtrackings. We carefully study the proposed scheme by comparing it with the fast library for approximate nearest neighbors and the random KD-trees on the Oxford data set. Thorough experimental results suggest the efficiency and effectiveness of the new scheme.

the Role of Species, Structure, and Biochemical Traits in the Spatial Distribution of a Woodland Community

NASA Astrophysics Data System (ADS)

Adeline, K.; Ustin, S.; Roth, K. L.; Huesca Martinez, M.; Schaaf, C.; Baldocchi, D. D.; Gastellu-Etchegorry, J. P.

2015-12-01

The assessment of canopy biochemical diversity is critical for monitoring ecological and physiological functioning and for mapping vegetation change dynamics in relation to environmental resources. For example in oak woodland savannas, these dynamics are mainly driven by water constraints. Inversion using radiative transfer theory is one method for estimating canopy biochemistry. However, this approach generally only considers relatively simple scenarios to model the canopy due to the difficulty in encompassing stand heterogeneity with spatial and temporal consistency. In this research, we compared 3 modeling strategies for estimating canopy biochemistry variables (i.e. chlorophyll, carotenoids, water, dry matter) by coupling of the PROSPECT (leaf level) and DART (canopy level) models : i) a simple forest representation made of ellipsoid trees, and two representations taking into account the tree species and structural composition, and the landscape spatial pattern, using (ii) geometric tree crown shapes and iii) detailed tree crown and wood structure retrieved from terrestrial lidar acquisitions. AVIRIS 18m remote sensing data are up-scaled to simulate HyspIRI 30m images. Both spatial resolutions are validated by measurements acquired during 2013-2014 field campaigns (cover/tree inventory, LAI, leaf sampling, optical measures). The results outline the trade-off between accurate and abstract canopy modeling for inversion purposes and may provide perspectives to assess the impact of the California drought with multi-temporal monitoring of canopy biochemistry traits.

Modelling the impact of the light regime on single tree transpiration based on 3D representations of plant architecture

NASA Astrophysics Data System (ADS)

Bittner, S.; Priesack, E.

2012-04-01

We apply a functional-structural model of tree water flow to single old-growth trees in a temperate broad-leaved forest stand. Roots, stems and branches are represented by connected porous cylinder elements further divided into the inner heartwood cylinders surrounded by xylem and phloem. Xylem water flow is simulated by applying a non-linear Darcy flow in porous media driven by the water potential gradient according to the cohesion-tension theory. The flow model is based on physiological input parameters such as the hydraulic conductivity, stomatal response to leaf water potential and root water uptake capability and, thus, can reflect the different properties of tree species. The actual root water uptake is calculated using also a non-linear Darcy law based on the gradient between root xylem water potential and rhizosphere soil water potential and by the simulation of soil water flow applying Richards equation. A leaf stomatal conductance model is combined with the hydrological tree and soil water flow model and a spatially explicit three-dimensional canopy light model. The structure of the canopy and the tree architectures are derived by applying an automatic tree skeleton extraction algorithm from point clouds obtained by use of a terrestrial laser scanner allowing an explicit representation of the water flow path in the stem and branches. The high spatial resolution of the root and branch geometry and their connectivity makes the detailed modelling of the water use of single trees possible and allows for the analysis of the interaction between single trees and the influence of the canopy light regime (including different fractions of direct sunlight and diffuse skylight) on the simulated sap flow and transpiration. The model can be applied at various sites and to different tree species, enabling the up-scaling of the water usage of single trees to the total transpiration of mixed stands. Examples are given to reveal differences between diffuse- and ring-porous tree species and to simulate the diurnal dynamics of transpiration, stem sap flux, and root water uptake observed during the vegetation period in the year 2009.

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.

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2A: Accident model document, appendix

NASA Technical Reports Server (NTRS)

1972-01-01

The detailed abort sequence trees for the reference zirconium hydride (ZrH) reactor power module that have been generated for each phase of the reference Space Base program mission are presented. The trees are graphical representations of causal sequences. Each tree begins with the phase identification and the dichotomy between success and failure. The success branch shows the mission phase objective as being achieved. The failure branch is subdivided, as conditions require, into various primary initiating abort conditions.

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

Hill, David P.; D’Eustachio, Peter; Berardini, Tanya Z.

The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes inmore » the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.« less

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.

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.

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.

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.

MRL and SuperFine+MRL: new supertree methods

PubMed Central

2012-01-01

Background Supertree methods combine trees on subsets of the full taxon set together to produce a tree on the entire set of taxa. Of the many supertree methods, the most popular is MRP (Matrix Representation with Parsimony), a method that operates by first encoding the input set of source trees by a large matrix (the "MRP matrix") over {0,1, ?}, and then running maximum parsimony heuristics on the MRP matrix. Experimental studies evaluating MRP in comparison to other supertree methods have established that for large datasets, MRP generally produces trees of equal or greater accuracy than other methods, and can run on larger datasets. A recent development in supertree methods is SuperFine+MRP, a method that combines MRP with a divide-and-conquer approach, and produces more accurate trees in less time than MRP. In this paper we consider a new approach for supertree estimation, called MRL (Matrix Representation with Likelihood). MRL begins with the same MRP matrix, but then analyzes the MRP matrix using heuristics (such as RAxML) for 2-state Maximum Likelihood. Results We compared MRP and SuperFine+MRP with MRL and SuperFine+MRL on simulated and biological datasets. We examined the MRP and MRL scores of each method on a wide range of datasets, as well as the resulting topological accuracy of the trees. Our experimental results show that MRL, coupled with a very good ML heuristic such as RAxML, produced more accurate trees than MRP, and MRL scores were more strongly correlated with topological accuracy than MRP scores. Conclusions SuperFine+MRP, when based upon a good MP heuristic, such as TNT, produces among the best scores for both MRP and MRL, and is generally faster and more topologically accurate than other supertree methods we tested. PMID:22280525

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.

Seeing The "New Forest": A Visual Curricular Experiment

NASA Astrophysics Data System (ADS)

Garramone, Pariss Nicola

In contemporary Western contexts, human interaction with and interpretation of nature is a perpetually mediated process. Understandings and engagements with natural environments are informed by and often overlaid with meanings derived from representations. In other words, representations help constitute human relationships with nature. Thus learning how representations shape human understandings and experiences of nature and the resulting social, political, and ecological impact of these mediated relationships has emerged as an important field of inquiry within environmental education. This dissertation examines how a critical, self-reflexive act of looking at photographs can challenge an individual's concepts of nature/culture, real/imaginary, and self/other. The project engages in a curricular experiment where the researcher explores how photography meditates her abstract and embodied understandings of specific natural environments. A critical, self-reflexive approach to aesthetic engagement with photographs moves beyond simply deciphering or decoding representations; it incorporates the learner's own narrative and embodied responses to the photographic representations being explored. This approach also recognizes that pedagogy has a transformative effect; both the learner and the representations being explored are transformed through the process of engagement. In this dissertation, a selection of iconic photographs of Canadian tree planting from the collection of the National Gallery of Canada are looked at: Lorraine Gilbert's (1987-2004) series "Shaping the New Forest" and Sarah Anne Johnson's (2005) work "The Tree Planting Project." The aim of this project is twofold: to unravel how these photographs construct and transform knowledge of and relationships with the environment in Canada, and to demonstrate a model of environmental inquiry that can be integrated into critical environmental education curricula.

A Semantic Basis for Proof Queries and Transformations

NASA Technical Reports Server (NTRS)

Aspinall, David; Denney, Ewen W.; Luth, Christoph

2013-01-01

We extend the query language PrQL, designed for inspecting machine representations of proofs, to also allow transformation of proofs. PrQL natively supports hiproofs which express proof structure using hierarchically nested labelled trees, which we claim is a natural way of taming the complexity of huge proofs. Query-driven transformations enable manipulation of this structure, in particular, to transform proofs produced by interactive theorem provers into forms that assist their understanding, or that could be consumed by other tools. In this paper we motivate and define basic transformation operations, using an abstract denotational semantics of hiproofs and queries. This extends our previous semantics for queries based on syntactic tree representations.We define update operations that add and remove sub-proofs, and manipulate the hierarchy to group and ungroup nodes. We show that

Software tool for data mining and its applications

NASA Astrophysics Data System (ADS)

Yang, Jie; Ye, Chenzhou; Chen, Nianyi

2002-03-01

A software tool for data mining is introduced, which integrates pattern recognition (PCA, Fisher, clustering, hyperenvelop, regression), artificial intelligence (knowledge representation, decision trees), statistical learning (rough set, support vector machine), computational intelligence (neural network, genetic algorithm, fuzzy systems). It consists of nine function models: pattern recognition, decision trees, association rule, fuzzy rule, neural network, genetic algorithm, Hyper Envelop, support vector machine, visualization. The principle and knowledge representation of some function models of data mining are described. The software tool of data mining is realized by Visual C++ under Windows 2000. Nonmonotony in data mining is dealt with by concept hierarchy and layered mining. The software tool of data mining has satisfactorily applied in the prediction of regularities of the formation of ternary intermetallic compounds in alloy systems, and diagnosis of brain glioma.

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

PubMed Central

Crampton-Platt, Alex; Timmermans, Martijn J.T.N.; Gimmel, Matthew L.; Kutty, Sujatha Narayanan; Cockerill, Timothy D.; Vun Khen, Chey; Vogler, Alfried P.

2015-01-01

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity. PMID:25957318

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...

Inferring phylogenetic trees from the knowledge of rare evolutionary events.

PubMed

Hellmuth, Marc; Hernandez-Rosales, Maribel; Long, Yangjing; Stadler, Peter F

2018-06-01

Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters. In this contribution we analyze the phylogenetic information content from a combinatorial point of view by considering the binary relation on the set of taxa defined by the existence of a single event separating two taxa. We show that the graph-representation of this relation must be a tree. Moreover, we characterize completely the relationship between the tree of such relations and the underlying phylogenetic tree. With directed operations such as tandem-duplication-random-loss events in mind we demonstrate how non-symmetric information constrains the position of the root in the partially reconstructed phylogeny.

Piagetian Perspective in Draw-a-House Tree Task: A Longitudinal Study of the Drawings of Rural Children in the State of Nebraska, U.S.A.

ERIC Educational Resources Information Center

Kalyan-Masih, Violet

Children's drawings of "a house with a tree behind it" were analyzed for (1) developmental changes in graphic representation over a 3-year period; (2) relationship with Piagetian tasks (the Nebraska Wisconsin Cognitive Assessment Battery of the NC-124), Peabody IQ, and WISC-R; and (3) correspondence with the Luquet-Piaget sequence of…

Reduced Short-Term Memory Span in Aphasia and Susceptibility to Interference: Contribution of Material-Specific Maintenance Deficits

PubMed Central

Barde, Laura H.F.; Schwartz, Myrna F.; Chrysikou, Evangelia G.; Thompson-Schill, Sharon L.

2010-01-01

Semantic short-term memory (STM) deficits have been traditionally defined as an inability to maintain semantic representations over a delay (R. Martin, Shelton & Yaffee, 1994). Yet some patients with semantic STM deficits make numerous intrusions of items from previously presented lists, thus presenting an interesting paradox: Why should an inability to maintain semantic representations produce an increase in intrusions from earlier lists? In this study, we investigated the relationship between maintenance deficits and susceptibility to interference in a group of 20 aphasic patients characterized with weak semantic or weak phonological STM. Patients and matched control participants performed a modified item-recognition task designed to elicit semantic or phonological interference from list items located one, two, or three trials back (Hamilton & R. Martin, 2007). Controls demonstrated significant effects of interference in both versions of the task. Interference in patients was predicted by the type and severity of their STM deficit; that is, shorter semantic spans were associated with greater semantic interference and shorter phonological spans were associated with greater phonological interference. We interpret these results through a new perspective, the reactivation hypothesis, and we discuss their importance for accounts emphasizing the contribution of maintenance mechanisms for STM impairments in aphasia as well as susceptibility to interference. PMID:19925813

JavaGenes: Evolving Graphs with Crossover

NASA Technical Reports Server (NTRS)

Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

2000-01-01

Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction

PubMed Central

Rahman, Raziur; Haider, Saad; Ghosh, Souparno; Pal, Ranadip

2015-01-01

Random forests consisting of an ensemble of regression trees with equal weights are frequently used for design of predictive models. In this article, we consider an extension of the methodology by representing the regression trees in the form of probabilistic trees and analyzing the nature of heteroscedasticity. The probabilistic tree representation allows for analytical computation of confidence intervals (CIs), and the tree weight optimization is expected to provide stricter CIs with comparable performance in mean error. We approached the ensemble of probabilistic trees’ prediction from the perspectives of a mixture distribution and as a weighted sum of correlated random variables. We applied our methodology to the drug sensitivity prediction problem on synthetic and cancer cell line encyclopedia dataset and illustrated that tree weights can be selected to reduce the average length of the CI without increase in mean error. PMID:27081304

Simulating Various Terrestrial and Uav LIDAR Scanning Configurations for Understory Forest Structure Modelling

NASA Astrophysics Data System (ADS)

Hämmerle, M.; Lukač, N.; Chen, K.-C.; Koma, Zs.; Wang, C.-K.; Anders, K.; Höfle, B.

2017-09-01

Information about the 3D structure of understory vegetation is of high relevance in forestry research and management (e.g., for complete biomass estimations). However, it has been hardly investigated systematically with state-of-the-art methods such as static terrestrial laser scanning (TLS) or laser scanning from unmanned aerial vehicle platforms (ULS). A prominent challenge for scanning forests is posed by occlusion, calling for proper TLS scan position or ULS flight line configurations in order to achieve an accurate representation of understory vegetation. The aim of our study is to examine the effect of TLS or ULS scanning strategies on (1) the height of individual understory trees and (2) understory canopy height raster models. We simulate full-waveform TLS and ULS point clouds of a virtual forest plot captured from various combinations of max. 12 TLS scan positions or 3 ULS flight lines. The accuracy of the respective datasets is evaluated with reference values given by the virtually scanned 3D triangle mesh tree models. TLS tree height underestimations range up to 1.84 m (15.30 % of tree height) for single TLS scan positions, but combining three scan positions reduces the underestimation to maximum 0.31 m (2.41 %). Combining ULS flight lines also results in improved tree height representation, with a maximum underestimation of 0.24 m (2.15 %). The presented simulation approach offers a complementary source of information for efficient planning of field campaigns aiming at understory vegetation modelling.

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...

Measurements of auditory-verbal STM span in aphasia: effects of item, task, and lexical impairment.

PubMed

Martin, Nadine; Ayala, Jennifer

2004-06-01

In the first part of this study, we investigated effects of item and task type on span performance in a group of aphasic individuals with word processing and STM deficits. Group analyses revealed significant effects of item on span performance with span being greater for digits than for words. We also investigated associations between subjects' lexical-semantic and phonological processing abilities and performance on four measures of verbal span (digit and word span, each varied for type of response, verbal vs. pointing) as well as one measure of nonverbal span. We predicted and found that the patterns of association between verbal span tasks and lexical abilities reflected the integrity of language processes and representations deployed in each paradigm used to assess span. Performance on the pointing span task, which engages both lexical-semantic and phonological processes, correlated with measures of both lexical-semantic and phonological abilities. Performance on repetition span, which engages primarily input and output phonological processes, correlated with measures of phonological abilities but not measures of lexical-semantic abilities. However, when partial correlations were performed for two subject groups based on their relative preservation of lexical-semantic ability (less or more than phonological ability), repetition span correlated with lexical-semantic measures only in the subgroup with relatively impaired lexical-semantics. Additionally, performance on the nonverbal span task correlated with measures of phonological abilities, suggesting either a general cognitive deficit affecting verbal and nonverbal STM or possibly, the use of a verbal strategy to perform this task. Our discussion focuses on the interpretation of span measurements in clinical practice and research, as well as the implications of these data for theories of short-term memory and word processing.

Associative-memory representations emerge as shared spatial patterns of theta activity spanning the primate temporal cortex

PubMed Central

Nakahara, Kiyoshi; Adachi, Ken; Kawasaki, Keisuke; Matsuo, Takeshi; Sawahata, Hirohito; Majima, Kei; Takeda, Masaki; Sugiyama, Sayaka; Nakata, Ryota; Iijima, Atsuhiko; Tanigawa, Hisashi; Suzuki, Takafumi; Kamitani, Yukiyasu; Hasegawa, Isao

2016-01-01

Highly localized neuronal spikes in primate temporal cortex can encode associative memory; however, whether memory formation involves area-wide reorganization of ensemble activity, which often accompanies rhythmicity, or just local microcircuit-level plasticity, remains elusive. Using high-density electrocorticography, we capture local-field potentials spanning the monkey temporal lobes, and show that the visual pair-association (PA) memory is encoded in spatial patterns of theta activity in areas TE, 36, and, partially, in the parahippocampal cortex, but not in the entorhinal cortex. The theta patterns elicited by learned paired associates are distinct between pairs, but similar within pairs. This pattern similarity, emerging through novel PA learning, allows a machine-learning decoder trained on theta patterns elicited by a particular visual item to correctly predict the identity of those elicited by its paired associate. Our results suggest that the formation and sharing of widespread cortical theta patterns via learning-induced reorganization are involved in the mechanisms of associative memory representation. PMID:27282247

The ARES High-level Intermediate Representation

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

Moss, Nicholas David

The LLVM intermediate representation (IR) lacks semantic constructs for depicting common high-performance operations such as parallel and concurrent execution, communication and synchronization. Currently, representing such semantics in LLVM requires either extending the intermediate form (a signi cant undertaking) or the use of ad hoc indirect means such as encoding them as intrinsics and/or the use of metadata constructs. In this paper we discuss a work in progress to explore the design and implementation of a new compilation stage and associated high-level intermediate form that is placed between the abstract syntax tree and when it is lowered to LLVM's IR. Thismore » highlevel representation is a superset of LLVM IR and supports the direct representation of these common parallel computing constructs along with the infrastructure for supporting analysis and transformation passes on this representation.« less

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.

Optimum Array Processing for Detecting Binary Signals Corrupted by Directional Interference.

DTIC Science & Technology

1972-12-01

specific cases. Two different series representations of a vector random process are discussed in Van Trees [3]. These two methods both require the... spaci ~ng d, etc.) its detection error represents a lower bound for the performance that might be obtained with other types of array processing (such...Middleton, Introduction to Statistical Communication Theory, New York: McGraw-Hill, 1960. 3. H.L. Van Trees , Detection, Estimation, and Modulation Theory

MEqTrees Telescope and Radio-sky Simulations and CPU Benchmarking

NASA Astrophysics Data System (ADS)

Shanmugha Sundaram, G. A.

2009-09-01

MEqTrees is a Python-based implementation of the classical Measurement Equation, wherein the various 2×2 Jones matrices are parametrized representations in the spatial and sky domains for any generic radio telescope. Customized simulations of radio-source sky models and corrupt Jones terms are demonstrated based on a policy framework, with performance estimates derived for array configurations, ``dirty''-map residuals and processing power requirements for such computations on conventional platforms.

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.

Differential involvement of knowledge representation and executive control in episodic memory performance in young and older adults.

PubMed

Bouazzaoui, Badiâa; Fay, Séverine; Taconnat, Laurence; Angel, Lucie; Vanneste, Sandrine; Isingrini, Michel

2013-06-01

Craik and Bialystok (2006, 2008) postulated that examining the evolution of knowledge representation and control processes across the life span could help in understanding age-related cognitive changes. The present study explored the hypothesis that knowledge representation and control processes are differentially involved in the episodic memory performance of young and older adults. Young and older adults were administered a cued-recall task and tests of crystallized knowledge and executive functioning to measure representation and control processes, respectively. Results replicate the classic finding that executive and cued-recall performance decline with age, but crystallized-knowledge performance does not. Factor analysis confirmed the independence of representation and control. Correlation analyses showed that the memory performance of younger adults was correlated with representation but not with control measures, whereas the memory performance of older adults was correlated with both representation and control measures. Regression analyses indicated that the control factor was the main predictor of episodic-memory performance for older adults, with the representation factor adding an independent contribution, but the representation factor was the sole predictor for young adults. This finding supports the view that factors sustaining episodic memory vary from young adulthood to old age; representation was shown to be important throughout adulthood, and control was also important for older adults. The results also indicated that control and representation modulate age-group-related variance in episodic memory.

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.

PubMed

Crampton-Platt, Alex; Timmermans, Martijn J T N; Gimmel, Matthew L; Kutty, Sujatha Narayanan; Cockerill, Timothy D; Vun Khen, Chey; Vogler, Alfried P

2015-09-01

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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.

Modeling biochemical pathways in the gene ontology

DOE PAGES

Hill, David P.; D’Eustachio, Peter; Berardini, Tanya Z.; ...

2016-09-01

The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes inmore » the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.« less

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

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

A Conference on Three-Dimensional Representation held in University of Minnesota on 24-26 May 1989

NASA Astrophysics Data System (ADS)

Biederman, Irving

1989-06-01

This is the final report for a conference grant entitled: A conference on Three-Dimensional Representation. The two and one-half day conference was held at the University of Minn. on May 24 to 26, 1989 to evaluate the current status of problem associated with three-dimensional representations from current computational, psychological, development, and neurophysiological perspectives. Nineteen presentations were made spanning these approaches. One hundred sixty-six individuals attended the conference. Of 44 evaluations received, 75 percent rated the conference as excellent, 20 percent as good, and 5 percent as fair. None rated it poor. The report consists of the original and revised program, conference abstracts evaluation summary and the rooster of attendees.

Crop vulnerability: Carya

USDA-ARS?s Scientific Manuscript database

Long established native tree populations reflect local adaptations. Representation of diverse populations in accessible ex situ collections that link information on phenotypic expression to information on spatial and temporal origination is the most efficient means of preserving and exploring genet...

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.

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

Ronold, K.O.; Nielsen, N.J.R.; Tura, F.

This paper demonstrates how a structural reliability method can be applied as a rational means to analyze free spans of submarine pipelines with respect to failure in ultimate loading, and to establish partial safety factors for design of such free spans against this failure mode. It is important to note that the described procedure shall be considered as an illustration of a structural reliability methodology, and that the results do not represent a set of final design recommendations. A scope of design cases, consisting of a number of available site-specific pipeline spans, is established and is assumed representative for themore » future occurrence of submarine pipeline spans. Probabilistic models for the wave and current loading and its transfer to stresses in the pipe wall of a pipeline span is established together with a stochastic representation of the material resistance. The event of failure in ultimate loading is considered as based on a limit state which is reached when the maximum stress over the design life of the pipeline exceeds the yield strength of the pipe material. The yielding limit state is considered an ultimate limit state (ULS).« less

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

Forest representation of vessels in cone-beam computed tomographic angiography.

PubMed

Chen, Zikuan; Ning, Ruola

2005-01-01

Cone-beam computed tomographic angiography (CBCTA) provides a fast three-dimensional (3D) vascular imaging modality, aiming at digitally representing the spatial vascular structure in an angiographic volume. Due to the finite coverage of cone-beam scan, as well as the volume cropping in volumetric image processing, an angiographic volume may fail to contain a whole vascular tree, but rather consist of a multitude of vessel segments or subtrees. As such, it is convenient to represent multitudinal components by a forest. The vessel tracking issue then becomes component characterization/identification in the forest. The forest representation brings several conveniences for vessel tracking: (1) to sort and count the vessels in an angiographic volume, for example, according to spatial occupancy and skeleton pathlength; (2) to single out a vessel and perform in situ 3D measurement and 3D visualization in the support space; (3) to delineate individual vessels from the original angiographic volume; and (4) to cull the forest by getting rid of non-vessels and small vessels. A 3D skeletonization is used to generate component skeletons. For tree construction from skeletons, we suggest a pathlength-based procedure, which lifts the restrictions of unit-width skeleton and root determination. We experimentally demonstrate the forest representation of a dog's carotid arteries in a CBCTA system. In principle, the forest representation is useful for managing vessels in both 2D angiographic images and 3D angiographic volumes.

Phylogenetic trees in bioinformatics

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

Burr, Tom L

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding themore » best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.« less

Care for women involved with drugs: social representations of nurses.

PubMed

Rodrigues, Andreia Silva; Oliveira, Jeane Freitas de; Suto, Cleuma Sueli Santos; Coutinho, Maria da Penha de Lima; Paiva, Mirian Santos; Souza, Simone Santos

2017-01-01

analyze social representations of nurses related to the care for women involved with drugs. qualitative research founded on the theory of social representations, with 42 nurses from a public maternity ward of Salvador-BA, using identification questionnaire, test of free association of words, and semi-structured interview. We analyzed the structure of social representations and the similarity tree of free evocations, and also analyzed the content of interviews. care for women involved with drugs is represented by a set of words that shows theoretical questions and scientific techniques, but faced with experiences in the training, in the daily work and in ideas and values assigned to the consumption of drugs especially in the gravidic-puerperal period. The social representations of nurses show conflicts between social and cultural aspects around the problem of drugs and the health care provided to women involved with drugs.

Shared Governance at Lincoln University: An Elusive Quarry

ERIC Educational Resources Information Center

DeBoy, James L.

2015-01-01

This paper identifies those factors that led to American Association of University Professors (AAUP) representation at the nation's oldest degree-granting Historically Black College University (HBCU). In the span of 18 months, Lincoln Faculty overwhelmingly embraced unionism when the body agreed to have AAUP as its official agent in the collective…

The Need for Alternative Paradigms in Science and Engineering Education

ERIC Educational Resources Information Center

Baggi, Dennis L.

2007-01-01

There are two main claims in this article. First, that the classic pillars of engineering education, namely, traditional mathematics and differential equations, are merely a particular, if not old-fashioned, representation of a broader mathematical vision, which spans from Turing machine programming and symbolic productions sets to sub-symbolic…

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.

Vision based obstacle detection and grouping for helicopter guidance

NASA Technical Reports Server (NTRS)

Sridhar, Banavar; Chatterji, Gano

1993-01-01

Electro-optical sensors can be used to compute range to objects in the flight path of a helicopter. The computation is based on the optical flow/motion at different points in the image. The motion algorithms provide a sparse set of ranges to discrete features in the image sequence as a function of azimuth and elevation. For obstacle avoidance guidance and display purposes, these discrete set of ranges, varying from a few hundreds to several thousands, need to be grouped into sets which correspond to objects in the real world. This paper presents a new method for object segmentation based on clustering the sparse range information provided by motion algorithms together with the spatial relation provided by the static image. The range values are initially grouped into clusters based on depth. Subsequently, the clusters are modified by using the K-means algorithm in the inertial horizontal plane and the minimum spanning tree algorithms in the image plane. The object grouping allows interpolation within a group and enables the creation of dense range maps. Researchers in robotics have used densely scanned sequence of laser range images to build three-dimensional representation of the outside world. Thus, modeling techniques developed for dense range images can be extended to sparse range images. The paper presents object segmentation results for a sequence of flight images.

Robustness of mission plans for unmanned aircraft

NASA Astrophysics Data System (ADS)

Niendorf, Moritz

This thesis studies the robustness of optimal mission plans for unmanned aircraft. Mission planning typically involves tactical planning and path planning. Tactical planning refers to task scheduling and in multi aircraft scenarios also includes establishing a communication topology. Path planning refers to computing a feasible and collision-free trajectory. For a prototypical mission planning problem, the traveling salesman problem on a weighted graph, the robustness of an optimal tour is analyzed with respect to changes to the edge costs. Specifically, the stability region of an optimal tour is obtained, i.e., the set of all edge cost perturbations for which that tour is optimal. The exact stability region of solutions to variants of the traveling salesman problems is obtained from a linear programming relaxation of an auxiliary problem. Edge cost tolerances and edge criticalities are derived from the stability region. For Euclidean traveling salesman problems, robustness with respect to perturbations to vertex locations is considered and safe radii and vertex criticalities are introduced. For weighted-sum multi-objective problems, stability regions with respect to changes in the objectives, weights, and simultaneous changes are given. Most critical weight perturbations are derived. Computing exact stability regions is intractable for large instances. Therefore, tractable approximations are desirable. The stability region of solutions to relaxations of the traveling salesman problem give under approximations and sets of tours give over approximations. The application of these results to the two-neighborhood and the minimum 1-tree relaxation are discussed. Bounds on edge cost tolerances and approximate criticalities are obtainable likewise. A minimum spanning tree is an optimal communication topology for minimizing the cumulative transmission power in multi aircraft missions. The stability region of a minimum spanning tree is given and tolerances, stability balls, and criticalities are derived. This analysis is extended to Euclidean minimum spanning trees. This thesis aims at enabling increased mission performance by providing means of assessing the robustness and optimality of a mission and methods for identifying critical elements. Examples of the application to mission planning in contested environments, cargo aircraft mission planning, multi-objective mission planning, and planning optimal communication topologies for teams of unmanned aircraft are given.

Extracting the information of coastline shape and its multiple representations

NASA Astrophysics Data System (ADS)

Liu, Ying; Li, Shujun; Tian, Zhen; Chen, Huirong

2007-06-01

According to studying the coastline, a new way of multiple representations is put forward in the paper. That is stimulating human thinking way when they generalized, building the appropriate math model and describing the coastline with graphics, extracting all kinds of the coastline shape information. The coastline automatic generalization will be finished based on the knowledge rules and arithmetic operators. Showing the information of coastline shape by building the curve Douglas binary tree, it can reveal the shape character of coastline not only microcosmically but also macroscopically. Extracting the information of coastline concludes the local characteristic point and its orientation, the curve structure and the topology trait. The curve structure can be divided the single curve and the curve cluster. By confirming the knowledge rules of the coastline generalization, the generalized scale and its shape parameter, the coastline automatic generalization model is established finally. The method of the multiple scale representation of coastline in this paper has some strong points. It is human's thinking mode and can keep the nature character of the curve prototype. The binary tree structure can control the coastline comparability, avoid the self-intersect phenomenon and hold the unanimous topology relationship.

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.

Reticulate classification of mosaic microbial genomes using NeAT website.

PubMed

Lima-Mendez, Gipsi

2012-01-01

The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representations. When LGT contribution to genome evolution cannot be neglected (e.g., for prokaryotes and mobile genetic elements), the tree becomes misleading. Networks appear as an intuitive way to represent both vertical and horizontal relationships, while overlapping groups within such graphs are more suitable for their classification. Here, we describe a method to represent both vertical and horizontal relationships. We start with a set of genomes whose coded proteins have been grouped into families based on sequence similarity. Next, all pairs of genomes are compared, counting the number of proteins classified into the same family. From this comparison, we derive a weighted graph where genomes with a significant number of similar proteins are linked. Finally, we apply a two-step clustering of this graph to produce a classification where nodes can be assigned to multiple clusters. The procedure can be performed using the Network Analysis Tools (NeAT) website.

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.

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.

Object-oriented fault tree evaluation program for quantitative analyses

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1988-01-01

Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

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...

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

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.

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

PubMed Central

Koonin, Eugene V; Wolf, Yuri I

2009-01-01

Background The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. Concept Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs), that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes) and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language). Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or FOL). Search for trends and patterns in the FOL is a productive direction of study that leads to the delineation of ensembles of FUEs that evolve coherently for a certain time span owing to a shared history of vertical inheritance or horizontal gene transfer; these ensembles are commonly known as genomes, taxa, or clades, depending on the level of analysis. A small set of genes (the universal genetic core of life) might show a (mostly) coherent evolutionary trend that transcends the entire history of cellular life forms. However, it might not be useful to denote this trend "the tree of life", or organismal, or species tree because neither organisms nor species are fundamental units of life. Conclusion A logical analysis of the units and processes of biological evolution suggests that the natural fundamental unit of evolution is a FUE, that is, a genetic element with an independent evolutionary history. Evolution of a FUE on the macro scale is naturally represented by a tree. Only the full compendium of trees for individual FUEs (the FOL) is an adequate depiction of the evolution of life. Coherent evolution of FUEs over extended evolutionary intervals is a crucial aspect of the history of life but a "species" or "organismal" tree is not a fundamental concept. Reviewers This articles was reviewed by Valerian Dolja, W. Ford Doolittle, Nicholas Galtier, and William Martin PMID:19788730

Model's sparse representation based on reduced mixed GMsFE basis methods

NASA Astrophysics Data System (ADS)

Jiang, Lijian; Li, Qiuqi

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a large number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.

Model's sparse representation based on reduced mixed GMsFE basis methods

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

Jiang, Lijian, E-mail: ljjiang@hnu.edu.cn; Li, Qiuqi, E-mail: qiuqili@hnu.edu.cn

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a largemore » number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.« less

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.

Anatomical modeling of the bronchial tree

NASA Astrophysics Data System (ADS)

Hentschel, Gerrit; Klinder, Tobias; Blaffert, Thomas; Bülow, Thomas; Wiemker, Rafael; Lorenz, Cristian

2010-02-01

The bronchial tree is of direct clinical importance in the context of respective diseases, such as chronic obstructive pulmonary disease (COPD). It furthermore constitutes a reference structure for object localization in the lungs and it finally provides access to lung tissue in, e.g., bronchoscope based procedures for diagnosis and therapy. This paper presents a comprehensive anatomical model for the bronchial tree, including statistics of position, relative and absolute orientation, length, and radius of 34 bronchial segments, going beyond previously published results. The model has been built from 16 manually annotated CT scans, covering several branching variants. The model is represented as a centerline/tree structure but can also be converted in a surface representation. Possible model applications are either to anatomically label extracted bronchial trees or to improve the tree extraction itself by identifying missing segments or sub-trees, e.g., if located beyond a bronchial stenosis. Bronchial tree labeling is achieved using a naïve Bayesian classifier based on the segment properties contained in the model in combination with tree matching. The tree matching step makes use of branching variations covered by the model. An evaluation of the model has been performed in a leaveone- out manner. In total, 87% of the branches resulting from preceding airway tree segmentation could be correctly labeled. The individualized model enables the detection of missing branches, allowing a targeted search, e.g., a local rerun of the tree-segmentation segmentation.

Knowledge Representation Standards and Interchange Formats for Causal Graphs

NASA Technical Reports Server (NTRS)

Throop, David R.; Malin, Jane T.; Fleming, Land

2005-01-01

In many domains, automated reasoning tools must represent graphs of causally linked events. These include fault-tree analysis, probabilistic risk assessment (PRA), planning, procedures, medical reasoning about disease progression, and functional architectures. Each of these fields has its own requirements for the representation of causation, events, actors and conditions. The representations include ontologies of function and cause, data dictionaries for causal dependency, failure and hazard, and interchange formats between some existing tools. In none of the domains has a generally accepted interchange format emerged. The paper makes progress towards interoperability across the wide range of causal analysis methodologies. We survey existing practice and emerging interchange formats in each of these fields. Setting forth a set of terms and concepts that are broadly shared across the domains, we examine the several ways in which current practice represents them. Some phenomena are difficult to represent or to analyze in several domains. These include mode transitions, reachability analysis, positive and negative feedback loops, conditions correlated but not causally linked and bimodal probability distributions. We work through examples and contrast the differing methods for addressing them. We detail recent work in knowledge interchange formats for causal trees in aerospace analysis applications in early design, safety and reliability. Several examples are discussed, with a particular focus on reachability analysis and mode transitions. We generalize the aerospace analysis work across the several other domains. We also recommend features and capabilities for the next generation of causal knowledge representation standards.

Stable and Dynamic Coding for Working Memory in Primate Prefrontal Cortex

PubMed Central

Watanabe, Kei; Funahashi, Shintaro; Stokes, Mark G.

2017-01-01

Working memory (WM) provides the stability necessary for high-level cognition. Influential theories typically assume that WM depends on the persistence of stable neural representations, yet increasing evidence suggests that neural states are highly dynamic. Here we apply multivariate pattern analysis to explore the population dynamics in primate lateral prefrontal cortex (PFC) during three variants of the classic memory-guided saccade task (recorded in four animals). We observed the hallmark of dynamic population coding across key phases of a working memory task: sensory processing, memory encoding, and response execution. Throughout both these dynamic epochs and the memory delay period, however, the neural representational geometry remained stable. We identified two characteristics that jointly explain these dynamics: (1) time-varying changes in the subpopulation of neurons coding for task variables (i.e., dynamic subpopulations); and (2) time-varying selectivity within neurons (i.e., dynamic selectivity). These results indicate that even in a very simple memory-guided saccade task, PFC neurons display complex dynamics to support stable representations for WM. SIGNIFICANCE STATEMENT Flexible, intelligent behavior requires the maintenance and manipulation of incoming information over various time spans. For short time spans, this faculty is labeled “working memory” (WM). Dominant models propose that WM is maintained by stable, persistent patterns of neural activity in prefrontal cortex (PFC). However, recent evidence suggests that neural activity in PFC is dynamic, even while the contents of WM remain stably represented. Here, we explored the neural dynamics in PFC during a memory-guided saccade task. We found evidence for dynamic population coding in various task epochs, despite striking stability in the neural representational geometry of WM. Furthermore, we identified two distinct cellular mechanisms that contribute to dynamic population coding. PMID:28559375

Modelling Mediterranean agro-ecosystems by including agricultural trees in the LPJmL model

NASA Astrophysics Data System (ADS)

Fader, M.; von Bloh, W.; Shi, S.; Bondeau, A.; Cramer, W.

2015-11-01

In the Mediterranean region, climate and land use change are expected to impact on natural and agricultural ecosystems by warming, reduced rainfall, direct degradation of ecosystems and biodiversity loss. Human population growth and socioeconomic changes, notably on the eastern and southern shores, will require increases in food production and put additional pressure on agro-ecosystems and water resources. Coping with these challenges requires informed decisions that, in turn, require assessments by means of a comprehensive agro-ecosystem and hydrological model. This study presents the inclusion of 10 Mediterranean agricultural plants, mainly perennial crops, in an agro-ecosystem model (Lund-Potsdam-Jena managed Land - LPJmL): nut trees, date palms, citrus trees, orchards, olive trees, grapes, cotton, potatoes, vegetables and fodder grasses. The model was successfully tested in three model outputs: agricultural yields, irrigation requirements and soil carbon density. With the development presented in this study, LPJmL is now able to simulate in good detail and mechanistically the functioning of Mediterranean agriculture with a comprehensive representation of ecophysiological processes for all vegetation types (natural and agricultural) and in a consistent framework that produces estimates of carbon, agricultural and hydrological variables for the entire Mediterranean basin. This development paves the way for further model extensions aiming at the representation of alternative agro-ecosystems (e.g. agroforestry), and opens the door for a large number of applications in the Mediterranean region, for example assessments of the consequences of land use transitions, the influence of management practices and climate change impacts.

Application of a Hybrid Forest Growth Model to Evaluate Climate Change Impacts on Productivity, Nutrient Cycling and Mortality in a Montane Forest Ecosystem.

PubMed

Seely, Brad; Welham, Clive; Scoullar, Kim

2015-01-01

Climate change introduces considerable uncertainty in forest management planning and outcomes, potentially undermining efforts at achieving sustainable practices. Here, we describe the development and application of the FORECAST Climate model. Constructed using a hybrid simulation approach, the model includes an explicit representation of the effect of temperature and moisture availability on tree growth and survival, litter decomposition, and nutrient cycling. The model also includes a representation of the impact of increasing atmospheric CO2 on water use efficiency, but no direct CO2 fertilization effect. FORECAST Climate was evaluated for its ability to reproduce the effects of historical climate on Douglas-fir and lodgepole pine growth in a montane forest in southern British Columbia, Canada, as measured using tree ring analysis. The model was subsequently used to project the long-term impacts of alternative future climate change scenarios on forest productivity in young and established stands. There was a close association between predicted sapwood production and measured tree ring chronologies, providing confidence that model is able to predict the relative impact of annual climate variability on tree productivity. Simulations of future climate change suggest a modest increase in productivity in young stands of both species related to an increase in growing season length. In contrast, results showed a negative impact on stemwood biomass production (particularly in the case of lodgepole pine) for established stands due to increased moisture stress mortality.

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

PubMed

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

2009-12-03

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

Application of a Hybrid Forest Growth Model to Evaluate Climate Change Impacts on Productivity, Nutrient Cycling and Mortality in a Montane Forest Ecosystem

PubMed Central

Seely, Brad; Welham, Clive; Scoullar, Kim

2015-01-01

Climate change introduces considerable uncertainty in forest management planning and outcomes, potentially undermining efforts at achieving sustainable practices. Here, we describe the development and application of the FORECAST Climate model. Constructed using a hybrid simulation approach, the model includes an explicit representation of the effect of temperature and moisture availability on tree growth and survival, litter decomposition, and nutrient cycling. The model also includes a representation of the impact of increasing atmospheric CO2 on water use efficiency, but no direct CO2 fertilization effect. FORECAST Climate was evaluated for its ability to reproduce the effects of historical climate on Douglas-fir and lodgepole pine growth in a montane forest in southern British Columbia, Canada, as measured using tree ring analysis. The model was subsequently used to project the long-term impacts of alternative future climate change scenarios on forest productivity in young and established stands. There was a close association between predicted sapwood production and measured tree ring chronologies, providing confidence that model is able to predict the relative impact of annual climate variability on tree productivity. Simulations of future climate change suggest a modest increase in productivity in young stands of both species related to an increase in growing season length. In contrast, results showed a negative impact on stemwood biomass production (particularly in the case of lodgepole pine) for established stands due to increased moisture stress mortality. PMID:26267446

Modelling Mediterranean agro-ecosystems by including agricultural trees in the LPJmL model

NASA Astrophysics Data System (ADS)

Fader, M.; von Bloh, W.; Shi, S.; Bondeau, A.; Cramer, W.

2015-06-01

Climate and land use change in the Mediterranean region is expected to affect natural and agricultural ecosystems by decreases in precipitation, increases in temperature as well as biodiversity loss and anthropogenic degradation of natural resources. Demographic growth in the Eastern and Southern shores will require increases in food production and put additional pressure on agro-ecosystems and water resources. Coping with these challenges requires informed decisions that, in turn, require assessments by means of a comprehensive agro-ecosystem and hydrological model. This study presents the inclusion of 10 Mediterranean agricultural plants, mainly perennial crops, in an agro-ecosystem model (LPJmL): nut trees, date palms, citrus trees, orchards, olive trees, grapes, cotton, potatoes, vegetables and fodder grasses. The model was successfully tested in three model outputs: agricultural yields, irrigation requirements and soil carbon density. With the development presented in this study, LPJmL is now able to simulate in good detail and mechanistically the functioning of Mediterranean agriculture with a comprehensive representation of ecophysiological processes for all vegetation types (natural and agricultural) and in a consistent framework that produces estimates of carbon, agricultural and hydrological variables for the entire Mediterranean basin. This development pave the way for further model extensions aiming at the representation of alternative agro-ecosystems (e.g. agroforestry), and opens the door for a large number of applications in the Mediterranean region, for example assessments on the consequences of land use transitions, the influence of management practices and climate change impacts.

Pre-rain green-up is ubiquitous across southern tropical Africa: implications for temporal niche separation and model representation.

PubMed

Ryan, Casey M; Williams, Mathew; Grace, John; Woollen, Emily; Lehmann, Caroline E R

2017-01-01

Tree phenology mediates land-atmosphere mass and energy exchange and is a determinant of ecosystem structure and function. In the dry tropics, including African savannas, many trees grow new leaves during the dry season - weeks or months before the rains typically start. This syndrome of pre-rain green-up has long been recognized at small scales, but the high spatial and interspecific variability in leaf phenology has precluded regional generalizations. We used remote sensing data to show that this precocious phenology is ubiquitous across the woodlands and savannas of southern tropical Africa. In 70% of the study area, green-up preceded rain onset by > 20 d (42% > 40 d). All the main vegetation formations exhibited pre-rain green-up, by as much as 53 ± 18 d (in the wet miombo). Green-up showed low interannual variability (SD between years = 11 d), and high spatial variability (> 100 d). These results are consistent with a high degree of local phenological adaptation, and an insolation trigger of green-up. Tree-tree competition and niche separation may explain the ubiquity of this precocious phenology. The ubiquity of pre-rain green-up described here challenges existing model representations and suggests resistance (but not necessarily resilience) to the delay in rain onset predicted under climate change. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

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.

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.

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.

Simulation of multivariate stationary stochastic processes using dimension-reduction representation methods

NASA Astrophysics Data System (ADS)

Liu, Zhangjun; Liu, Zenghui; Peng, Yongbo

2018-03-01

In view of the Fourier-Stieltjes integral formula of multivariate stationary stochastic processes, a unified formulation accommodating spectral representation method (SRM) and proper orthogonal decomposition (POD) is deduced. By introducing random functions as constraints correlating the orthogonal random variables involved in the unified formulation, the dimension-reduction spectral representation method (DR-SRM) and the dimension-reduction proper orthogonal decomposition (DR-POD) are addressed. The proposed schemes are capable of representing the multivariate stationary stochastic process with a few elementary random variables, bypassing the challenges of high-dimensional random variables inherent in the conventional Monte Carlo methods. In order to accelerate the numerical simulation, the technique of Fast Fourier Transform (FFT) is integrated with the proposed schemes. For illustrative purposes, the simulation of horizontal wind velocity field along the deck of a large-span bridge is proceeded using the proposed methods containing 2 and 3 elementary random variables. Numerical simulation reveals the usefulness of the dimension-reduction representation methods.

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

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.

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.

Protein space: a natural method for realizing the nature of protein universe.

PubMed

Yu, Chenglong; Deng, Mo; Cheng, Shiu-Yuen; Yau, Shek-Chung; He, Rong L; Yau, Stephen S-T

2013-02-07

Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe. Copyright © 2012 Elsevier Ltd. All rights reserved.

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

PubMed Central

Holden, Brian J; Pinney, John W; Lovell, Simon C; Amoutzias, Grigoris D; Robertson, David L

2007-01-01

Background Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH) family of transcription factors as an example. Results Network representations that arrange nodes (proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available. PMID:17683601

Spatial modeling and classification of corneal shape.

PubMed

Marsolo, Keith; Twa, Michael; Bullimore, Mark A; Parthasarathy, Srinivasan

2007-03-01

One of the most promising applications of data mining is in biomedical data used in patient diagnosis. Any method of data analysis intended to support the clinical decision-making process should meet several criteria: it should capture clinically relevant features, be computationally feasible, and provide easily interpretable results. In an initial study, we examined the feasibility of using Zernike polynomials to represent biomedical instrument data in conjunction with a decision tree classifier to distinguish between the diseased and non-diseased eyes. Here, we provide a comprehensive follow-up to that work, examining a second representation, pseudo-Zernike polynomials, to determine whether they provide any increase in classification accuracy. We compare the fidelity of both methods using residual root-mean-square (rms) error and evaluate accuracy using several classifiers: neural networks, C4.5 decision trees, Voting Feature Intervals, and Naïve Bayes. We also examine the effect of several meta-learning strategies: boosting, bagging, and Random Forests (RFs). We present results comparing accuracy as it relates to dataset and transformation resolution over a larger, more challenging, multi-class dataset. They show that classification accuracy is similar for both data transformations, but differs by classifier. We find that the Zernike polynomials provide better feature representation than the pseudo-Zernikes and that the decision trees yield the best balance of classification accuracy and interpretability.

Fast correspondences search in anatomical trees

NASA Astrophysics Data System (ADS)

dos Santos, Thiago R.; Gergel, Ingmar; Meinzer, Hans-Peter; Maier-Hein, Lena

2010-03-01

Registration of multiple medical images commonly comprises the steps feature extraction, correspondences search and transformation computation. In this paper, we present a new method for a fast and pose independent search of correspondences using as features anatomical trees such as the bronchial system in the lungs or the vessel system in the liver. Our approach scores the similarities between the trees' nodes (bifurcations) taking into account both, topological properties extracted from their graph representations and anatomical properties extracted from the trees themselves. The node assignment maximizes the global similarity (sum of the scores of each pair of assigned nodes), assuring that the matches are distributed throughout the trees. Furthermore, the proposed method is able to deal with distortions in the data, such as noise, motion, artifacts, and problems associated with the extraction method, such as missing or false branches. According to an evaluation on swine lung data sets, the method requires less than one second on average to compute the matching and yields a high rate of correct matches compared to state of the art work.

Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty.

PubMed

Blomberg, S

2000-11-01

Currently available programs for the comparative analysis of phylogenetic data do not perform optimally when the phylogeny is not completely specified (i.e. the phylogeny contains polytomies). Recent literature suggests that a better way to analyse the data would be to create random trees from the known phylogeny that are fully-resolved but consistent with the known tree. A computer program is presented, Fels-Rand, that performs such analyses. A randomisation procedure is used to generate trees that are fully resolved but whose structure is consistent with the original tree. Statistics are then calculated on a large number of these randomly-generated trees. Fels-Rand uses the object-oriented features of Xlisp-Stat to manipulate internal tree representations. Xlisp-Stat's dynamic graphing features are used to provide heuristic tools to aid in analysis, particularly outlier analysis. The usefulness of Xlisp-Stat as a system for phylogenetic computation is discussed. Available from the author or at http://www.uq.edu.au/~ansblomb/Fels-Rand.sit.hqx. Xlisp-Stat is available from http://stat.umn.edu/~luke/xls/xlsinfo/xlsinfo.html. s.blomberg@abdn.ac.uk

treespace: Statistical exploration of landscapes of phylogenetic trees.

PubMed

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

2017-11-01

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Selection criteria for forested natural areas in New England, USA

Treesearch

William B. Leak; Mariko Yamasaki; Marie-Louise Smith; David T. Funk

1994-01-01

The selection of forested natural areas for research and educational purposes is discussed. Five factors are important: sufficient size; representation of typical communities and sites; documented disturbance histories; acceptable current condition in terms of age, tree size, and successional stage; and administrative feasibility.

A poroelastic model coupled to a fluid network with applications in lung modelling.

PubMed

Berger, Lorenz; Bordas, Rafel; Burrowes, Kelly; Grau, Vicente; Tavener, Simon; Kay, David

2016-01-01

We develop a lung ventilation model based on a continuum poroelastic representation of lung parenchyma that is strongly coupled to a pipe network representation of the airway tree. The continuous system of equations is discretized using a low-order stabilised finite element method. The framework is applied to a realistic lung anatomical model derived from computed tomography data and an artificially generated airway tree to model the conducting airway region. Numerical simulations produce physiologically realistic solutions and demonstrate the effect of airway constriction and reduced tissue elasticity on ventilation, tissue stress and alveolar pressure distribution. The key advantage of the model is the ability to provide insight into the mutual dependence between ventilation and deformation. This is essential when studying lung diseases, such as chronic obstructive pulmonary disease and pulmonary fibrosis. Thus the model can be used to form a better understanding of integrated lung mechanics in both the healthy and diseased states. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Accurate reconstruction in digital holographic microscopy using Fresnel dual-tree complex wavelet transform

NASA Astrophysics Data System (ADS)

Zhang, Xiaolei; Zhang, Xiangchao; Yuan, He; Zhang, Hao; Xu, Min

2018-02-01

Digital holography is a promising measurement method in the fields of bio-medicine and micro-electronics. But the captured images of digital holography are severely polluted by the speckle noise because of optical scattering and diffraction. Via analyzing the properties of Fresnel diffraction and the topographies of micro-structures, a novel reconstruction method based on the dual-tree complex wavelet transform (DT-CWT) is proposed. This algorithm is shiftinvariant and capable of obtaining sparse representations for the diffracted signals of salient features, thus it is well suited for multiresolution processing of the interferometric holograms of directional morphologies. An explicit representation of orthogonal Fresnel DT-CWT bases and a specific filtering method are developed. This method can effectively remove the speckle noise without destroying the salient features. Finally, the proposed reconstruction method is compared with the conventional Fresnel diffraction integration and Fresnel wavelet transform with compressive sensing methods to validate its remarkable superiority on the aspects of topography reconstruction and speckle removal.

Beyond Capacity Limitations: Determinants of Word Recall Performance on Verbal Working Memory Span Tasks in Children With SLI

PubMed Central

Mainela-Arnold, Elina; Evans, Julia L.

2016-01-01

Reduced verbal working memory capacity has been proposed as a possible account of language impairments in specific language impairment (SLI). Studies have shown, however, that differences in strength of linguistic representations in the form of word frequency affect list recall and performance on verbal working memory tasks. This suggests that verbal memory capacity and long-term linguistic knowledge may not be distinct constructs. It has been suggested that linguistic representations in SLI are weak in ways that result in a breakdown in language processing on tasks that require manipulation of unfamiliar material. In this study, the effects of word frequency, long-term linguistic knowledge, and serial order position on recall performance in the competing language processing task (CLPT) were investigated in 10 children with SLI and 10 age-matched peers (age 8 years 6 months to 12 years 4 months). The children with SLI recalled significantly fewer target words on the CLPT as compared with their age-matched controls. The SLI group did not differ, however, in their ability to recall target words having high word frequency but were significantly poorer in their ability to recall words on the CLPT having low word frequency. Differences in receptive and expressive language abilities also appeared closely related to performance on the CLPT, suggesting that working memory capacity is not distinct from language knowledge and that degraded linguistic representations may have an effect on performance on verbal working memory span tasks in children with SLI. PMID:16378481

Adaptive zero-tree structure for curved wavelet image coding

NASA Astrophysics Data System (ADS)

Zhang, Liang; Wang, Demin; Vincent, André

2006-02-01

We investigate the issue of efficient data organization and representation of the curved wavelet coefficients [curved wavelet transform (WT)]. We present an adaptive zero-tree structure that exploits the cross-subband similarity of the curved wavelet transform. In the embedded zero-tree wavelet (EZW) and the set partitioning in hierarchical trees (SPIHT), the parent-child relationship is defined in such a way that a parent has four children, restricted to a square of 2×2 pixels, the parent-child relationship in the adaptive zero-tree structure varies according to the curves along which the curved WT is performed. Five child patterns were determined based on different combinations of curve orientation. A new image coder was then developed based on this adaptive zero-tree structure and the set-partitioning technique. Experimental results using synthetic and natural images showed the effectiveness of the proposed adaptive zero-tree structure for encoding of the curved wavelet coefficients. The coding gain of the proposed coder can be up to 1.2 dB in terms of peak SNR (PSNR) compared to the SPIHT coder. Subjective evaluation shows that the proposed coder preserves lines and edges better than the SPIHT coder.

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M

2018-06-23

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Wood phenology: from organ-scale processes to terrestrial ecosystem models

NASA Astrophysics Data System (ADS)

Delpierre, Nicolas; Guillemot, Joannès

2016-04-01

In temperate and boreal trees, a dormancy period prevents organ development during adverse climatic conditions. Whereas the phenology of leaves and flowers has received considerable attention, to date, little is known regarding the phenology of other tree organs such as wood, fine roots, fruits and reserve compounds. In this presentation, we review both the role of environmental drivers in determining the phenology of wood and the models used to predict its phenology in temperate and boreal forest trees. Temperature is a key driver of the resumption of wood activity in spring. There is no such clear dominant environmental cue involved in the cessation of wood formation in autumn, but temperature and water stress appear as prominent factors. We show that wood phenology is a key driver of the interannual variability of wood growth in temperate tree species. Incorporating representations of wood phenology in a terrestrial ecosystem model substantially improved the simulation of wood growth under current climate.

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

2011-01-01

Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. PMID:22165819

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

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

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

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...

E-Learning Technologies: Employing Matlab Web Server to Facilitate the Education of Mathematical Programming

ERIC Educational Resources Information Center

Karagiannis, P.; Markelis, I.; Paparrizos, K.; Samaras, N.; Sifaleras, A.

2006-01-01

This paper presents new web-based educational software (webNetPro) for "Linear Network Programming." It includes many algorithms for "Network Optimization" problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such…

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

The Emergence of Organizing Structure in Conceptual Representation

ERIC Educational Resources Information Center

Lake, Brenden M.; Lawrence, Neil D.; Tenenbaum, Joshua B.

2018-01-01

Both scientists and children make important structural discoveries, yet their computational underpinnings are not well understood. Structure discovery has previously been formalized as probabilistic inference about the right structural form--where form could be a tree, ring, chain, grid, etc. (Kemp & Tenenbaum, 2008). Although this approach…

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.

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles

PubMed Central

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models. PMID:26393926

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles.

PubMed

Gatziolis, Demetrios; Lienard, Jean F; Vogs, Andre; Strigul, Nikolay S

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models.

MATERNAL REPRESENTATIONS AND INFANT ATTACHMENT: AN EXAMINATION OF THE PROTOTYPE HYPOTHESIS.

PubMed

Madigan, Sheri; Hawkins, Erinn; Plamondon, Andre; Moran, Greg; Benoit, Diane

2015-01-01

The prototype hypothesis suggests that attachment representations derived in infancy continue to influence subsequent relationships over the life span, including those formed with one's own children. In the current study, we test the prototype hypothesis by exploring (a) whether child-specific representations following actual experience in interaction with a specific child impacts caregiver-child attachment over and above the prenatal forecast of that representation and (b) whether maternal attachment representations exert their influence on infant attachment via the more child-specific representation of that relationship. In a longitudinal study of 84 mother-infant dyads, mothers' representations of their attachment history were obtained prenatally with the Adult Attachment Interview (AAI; M. Main, R. Goldwyn, & E. Hesse, 2002), representations of relationship with a specific child were assessed with the Working Model of the Child Interview (WMCI; C.H. Zeanah, D. Benoit, & L. Barton, 1986), collected both prenatally and again at infant age 11 months, and infant attachment was assessed in the Strange Situation Procedure (M.D.S. Ainsworth, M.C. Blehar, E. Walters, & S. Wall, 1978) when infants were 11 months of age. Consistent with the prototype hypothesis, considerable correspondence was found between mothers' AAI and WMCI classifications. A mediation analysis showed that WMCI fully accounted for the association between AAI and infant attachment. Postnatal WMCI measured at 11 months' postpartum did not add to the prediction of infant attachment, over and above that explained by the prenatal WMCI. Implications for these findings are discussed. © 2015 Michigan Association for Infant Mental Health.

Beyond Low-Rank Representations: Orthogonal clustering basis reconstruction with optimized graph structure for multi-view spectral clustering.

PubMed

Wang, Yang; Wu, Lin

2018-07-01

Low-Rank Representation (LRR) is arguably one of the most powerful paradigms for Multi-view spectral clustering, which elegantly encodes the multi-view local graph/manifold structures into an intrinsic low-rank self-expressive data similarity embedded in high-dimensional space, to yield a better graph partition than their single-view counterparts. In this paper we revisit it with a fundamentally different perspective by discovering LRR as essentially a latent clustered orthogonal projection based representation winged with an optimized local graph structure for spectral clustering; each column of the representation is fundamentally a cluster basis orthogonal to others to indicate its members, which intuitively projects the view-specific feature representation to be the one spanned by all orthogonal basis to characterize the cluster structures. Upon this finding, we propose our technique with the following: (1) We decompose LRR into latent clustered orthogonal representation via low-rank matrix factorization, to encode the more flexible cluster structures than LRR over primal data objects; (2) We convert the problem of LRR into that of simultaneously learning orthogonal clustered representation and optimized local graph structure for each view; (3) The learned orthogonal clustered representations and local graph structures enjoy the same magnitude for multi-view, so that the ideal multi-view consensus can be readily achieved. The experiments over multi-view datasets validate its superiority, especially over recent state-of-the-art LRR models. Copyright © 2018 Elsevier Ltd. All rights reserved.

The nature and development of preservice science teachers' conceptions of subject matter and pedagogy

NASA Astrophysics Data System (ADS)

Lederman, Norman G.; Gess-Newsome, Julie; Latz, Mark S.

The purpose of this study was to assess the development and changes in preservice science teachers' subject matter and pedagogy knowledge structures as they proceeded through a professional teacher education program. Twelve secondary preservice science teachers were asked to create representations of their subject matter and pedagogy knowledge structures periodically (four times spanning the entirety of their subject-specific teacher education program) and participate in a videotaped interview concerning the eight knowledge structure representations immediately following student teaching. Qualitative analyses of knowledge structure representations and transcribed interviews within and between subjects were performed by one of the researchers and blindly corroborated by the other two researchers. Initial knowledge structure representations were typically linear and lacked coherence. Both types of knowledge structure representations were highly susceptible to change as a consequence of the act of teaching. Although there was some overlap between subject matter and pedagogy knowledge structures, they were reported to exert separate influences on classroom practice, with the pedagogy knowledge structure having primary influence on instructional decisions. Furthermore, the complexity of one's subject matter structure appeared to be a critical factor in determining whether the structure directly influences classroom practice.Received: 5 February 1993; Revised: 28 July 1993;

Parallel, multi-stage processing of colors, faces and shapes in macaque inferior temporal cortex

PubMed Central

Lafer-Sousa, Rosa; Conway, Bevil R.

2014-01-01

Visual-object processing culminates in inferior temporal (IT) cortex. To assess the organization of IT, we measured fMRI responses in alert monkey to achromatic images (faces, fruit, bodies, places) and colored gratings. IT contained multiple color-biased regions, which were typically ventral to face patches and, remarkably, yoked to them, spaced regularly at four locations predicted by known anatomy. Color and face selectivity increased for more anterior regions, indicative of a broad hierarchical arrangement. Responses to non-face shapes were found across IT, but were stronger outside color-biased regions and face patches, consistent with multiple parallel streams. IT also contained multiple coarse eccentricity maps: face patches overlapped central representations; color-biased regions spanned mid-peripheral representations; and place-biased regions overlapped peripheral representations. These results suggest that IT comprises parallel, multi-stage processing networks subject to one organizing principle. PMID:24141314

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.

Non Temporal Determinants of Bilingual Memory Capacity: The Role of Long-Term Representations and Fluency.

ERIC Educational Resources Information Center

Chincotta, Dino; Underwood, Geoffrey

1998-01-01

Examined the view that the variation in bilingual short-term memory capacity is determined by differential rates of subvocal rehearsal between the languages. Auditory memory span and articulation time were measured for three bilingual groups who spoke Finnish at home and Swedish at school, and either Finnish of Swedish in both the home and the…

Beyond Capacity Limitations: Determinants of Word Recall Performance on Verbal Working Memory Span Tasks in Children with SLI

ERIC Educational Resources Information Center

Mainela-Arnold, Elina; Evans, Julia L.

2005-01-01

Reduced verbal working memory capacity has been proposed as a possible account of language impairments in specific language impairment (SLI). Studies have shown, however, that differences in strength of linguistic representations in the form of word frequency affect list recall and performance on verbal working memory tasks. This suggests that…

The Contribution of Symbolic Skills to the Development of an Explicit Theory of Mind

ERIC Educational Resources Information Center

Lillard, Angeline S.; Kavanaugh, Robert D.

2014-01-01

Theorists have speculated about the symbolic underpinnings of theory of mind (ToM), but no study has examined them across the main developmental span of ToM. Here, the onset of symbolic understandings in three domains (pretend play, language, and understanding representations) and ToM was examined. Fifty-eight children were tested on batteries of…

Multi-scale enhancement of climate prediction over land by improving the model sensitivity to vegetation variability

NASA Astrophysics Data System (ADS)

Alessandri, A.; Catalano, F.; De Felice, M.; Hurk, B. V. D.; Doblas-Reyes, F. J.; Boussetta, S.; Balsamo, G.; Miller, P. A.

2017-12-01

Here we demonstrate, for the first time, that the implementation of a realistic representation of vegetation in Earth System Models (ESMs) can significantly improve climate simulation and prediction across multiple time-scales. The effective sub-grid vegetation fractional coverage vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the surface resistance to evapotranspiration, albedo, roughness lenght, and soil field capacity. To adequately represent this effect in the EC-Earth ESM, we included an exponential dependence of the vegetation cover on the Leaf Area Index.By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (20th Century) simulations and retrospective predictions to the decadal (5-years), seasonal (2-4 months) and weather (4 days) time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation-cover consistently correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste Brazil and South East Asia, mainly related to improved performance in the surface evapotranspiration.Above results are discussed in a peer-review paper just being accepted for publication on Climate Dynamics (Alessandri et al., 2017; doi:10.1007/s00382-017-3766-y).

Conceptual and Linguistic Representations of Kinds and Classes

ERIC Educational Resources Information Center

Prasada, Sandeep; Hennefield, Laura; Otap, Daniel

2012-01-01

We investigate the hypothesis that our conceptual systems provide two formally distinct ways of representing categories by investigating the manner in which lexical nominals (e.g., "tree," "picnic table") and phrasal nominals (e.g., "black bird," "birds that like rice") are interpreted. Four experiments found that lexical nominals may be mapped…

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

The Development of Shared Liking of Representational but not Abstract Art in Primary School Children and Their Justifications for Liking

PubMed Central

Rodway, Paul; Kirkham, Julie; Schepman, Astrid; Lambert, Jordana; Locke, Anastasia

2016-01-01

Understanding how aesthetic preferences are shared among individuals, and its developmental time course, is a fundamental question in aesthetics. It has been shown that semantic associations, in response to representational artworks, overlap more strongly among individuals than those generated by abstract artworks and that the emotional valence of the associations also overlaps more for representational artworks. This valence response may be a key driver in aesthetic appreciation. The current study tested predictions derived from the semantic association account in a developmental context. Twenty 4-, 6-, 8- and 10-year-old children (n = 80) were shown 20 artworks (10 representational, 10 abstract) and were asked to rate each artwork and to explain their decision. Cross-observer agreement in aesthetic preferences increased with age from 4–8 years for both abstract and representational art. However, after age 6 the level of shared appreciation for representational and abstract artworks diverged, with significantly higher levels of agreement for representational than abstract artworks at age 8 and 10. The most common justifications for representational artworks involved subject matter, while for abstract artworks formal artistic properties and color were the most commonly used justifications. Representational artwork also showed a significantly higher proportion of associations and emotional responses than abstract artworks. In line with predictions from developmental cognitive neuroscience, references to the artist as an agent increased between ages 4 and 6 and again between ages 6 and 8, following the development of Theory of Mind. The findings support the view that increased experience with representational content during the life span reduces inter-individual variation in aesthetic appreciation and increases shared preferences. In addition, brain and cognitive development appear to impact on art appreciation at milestone ages. PMID:26903834

The Development of Shared Liking of Representational but not Abstract Art in Primary School Children and Their Justifications for Liking.

PubMed

Rodway, Paul; Kirkham, Julie; Schepman, Astrid; Lambert, Jordana; Locke, Anastasia

2016-01-01

Understanding how aesthetic preferences are shared among individuals, and its developmental time course, is a fundamental question in aesthetics. It has been shown that semantic associations, in response to representational artworks, overlap more strongly among individuals than those generated by abstract artworks and that the emotional valence of the associations also overlaps more for representational artworks. This valence response may be a key driver in aesthetic appreciation. The current study tested predictions derived from the semantic association account in a developmental context. Twenty 4-, 6-, 8- and 10-year-old children (n = 80) were shown 20 artworks (10 representational, 10 abstract) and were asked to rate each artwork and to explain their decision. Cross-observer agreement in aesthetic preferences increased with age from 4-8 years for both abstract and representational art. However, after age 6 the level of shared appreciation for representational and abstract artworks diverged, with significantly higher levels of agreement for representational than abstract artworks at age 8 and 10. The most common justifications for representational artworks involved subject matter, while for abstract artworks formal artistic properties and color were the most commonly used justifications. Representational artwork also showed a significantly higher proportion of associations and emotional responses than abstract artworks. In line with predictions from developmental cognitive neuroscience, references to the artist as an agent increased between ages 4 and 6 and again between ages 6 and 8, following the development of Theory of Mind. The findings support the view that increased experience with representational content during the life span reduces inter-individual variation in aesthetic appreciation and increases shared preferences. In addition, brain and cognitive development appear to impact on art appreciation at milestone ages.

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...

Workshop on AI (Artificial Intelligence) and Simulation (2nd) Held in Seattle, Washington on 14 July 1987,

DTIC Science & Technology

1987-07-01

position of the camshaft (for example), the position of each other kinematic pair will have a definite computable value. Thus the only state variables needed...DF CONNROD _CON ROD DIF C OD WF CYL /N. D I T.~ UN ,BLO CT!L \\ CYL C"YL CYL Y I C BLO"cB BLO CYL BLO Figure 2 CSG Tree for Crank .Mechanism program...ships plate. The actual representation is a binary tree who-e - internal nodes are set operation, and rigid motions and The first step for kinematic

On the detection of pornographic digital images

NASA Astrophysics Data System (ADS)

Schettini, Raimondo; Brambilla, Carla; Cusano, Claudio; Ciocca, Gianluigi

2003-06-01

The paper addresses the problem of distinguishing between pornographic and non-pornographic photographs, for the design of semantic filters for the web. Both, decision forests of trees built according to CART (Classification And Regression Trees) methodology and Support Vectors Machines (SVM), have been used to perform the classification. The photographs are described by a set of low-level features, features that can be automatically computed simply on gray-level and color representation of the image. The database used in our experiments contained 1500 photographs, 750 of which labeled as pornographic on the basis of the independent judgement of several viewers.

At-Least Version of the Generalized Minimum Spanning Tree Problem: Optimization Through Ant Colony System and Genetic Algorithms

NASA Technical Reports Server (NTRS)

Janich, Karl W.

2005-01-01

The At-Least version of the Generalized Minimum Spanning Tree Problem (L-GMST) is a problem in which the optimal solution connects all defined clusters of nodes in a given network at a minimum cost. The L-GMST is NPHard; therefore, metaheuristic algorithms have been used to find reasonable solutions to the problem as opposed to computationally feasible exact algorithms, which many believe do not exist for such a problem. One such metaheuristic uses a swarm-intelligent Ant Colony System (ACS) algorithm, in which agents converge on a solution through the weighing of local heuristics, such as the shortest available path and the number of agents that recently used a given path. However, in a network using a solution derived from the ACS algorithm, some nodes may move around to different clusters and cause small changes in the network makeup. Rerunning the algorithm from the start would be somewhat inefficient due to the significance of the changes, so a genetic algorithm based on the top few solutions found in the ACS algorithm is proposed to quickly and efficiently adapt the network to these small changes.

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.

Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.

PubMed

Nye, Tom M W; Tang, Xiaoxian; Weyenberg, Grady; Yoshida, Ruriko

2017-12-01

Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees, one for each gene in the analysis. Analysis of samples of trees is difficult due to the multi-dimensionality of the space of possible trees. In Euclidean spaces, principal component analysis is a popular method of reducing high-dimensional data to a low-dimensional representation that preserves much of the sample's structure. However, the space of all phylogenetic trees on a fixed set of species does not form a Euclidean vector space, and methods adapted to tree space are needed. Previous work introduced the notion of a principal geodesic in this space, analogous to the first principal component. Here we propose a geometric object for tree space similar to the [Formula: see text]th principal component in Euclidean space: the locus of the weighted Fréchet mean of [Formula: see text] vertex trees when the weights vary over the [Formula: see text]-simplex. We establish some basic properties of these objects, in particular showing that they have dimension [Formula: see text], and propose algorithms for projection onto these surfaces and for finding the principal locus associated with a sample of trees. Simulation studies demonstrate that these algorithms perform well, and analyses of two datasets, containing Apicomplexa and African coelacanth genomes respectively, reveal important structure from the second principal components.

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.

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Multi-hop path tracing of mobile robot with multi-range image

NASA Astrophysics Data System (ADS)

Choudhury, Ramakanta; Samal, Chandrakanta; Choudhury, Umakanta

2010-02-01

It is well known that image processing depends heavily upon image representation technique . This paper intends to find out the optimal path of mobile robots for a specified area where obstacles are predefined as well as modified. Here the optimal path is represented by using the Quad tree method. Since there has been rising interest in the use of quad tree, we have tried to use the successive subdivision of images into quadrants from which the quad tree is developed. In the quad tree, obstacles-free area and the partial filled area are represented with different notations. After development of quad tree the algorithm is used to find the optimal path by employing neighbor finding technique, with a view to move the robot from the source to destination. The algorithm, here , permeates through the entire tree, and tries to locate the common ancestor for computation. The computation and the algorithm, aim at easing the ability of the robot to trace the optimal path with the help of adjacencies between the neighboring nodes as well as determining such adjacencies in the horizontal, vertical and diagonal directions. In this paper efforts have been made to determine the movement of the adjacent block in the quad tree and to detect the transition between the blocks equal size and finally generate the result.

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

PubMed Central

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-01-01

Background The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. Results We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. Conclusion By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development. PMID:16740163

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

PubMed

Boyle, Thomas J; Bao, Zhirong; Murray, John I; Araya, Carlos L; Waterston, Robert H

2006-06-01

The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

Dioxins and congener-specific polychlorinated biphenyls in three avian species from the Wisconsin River, Wisconsin

USGS Publications Warehouse

Custer, T.W.; Custer, Christine M.; Hines, Randy K.

2002-01-01

Sediments from the Wisconsin River, WI, USA are contaminated with 2,3,7,8-tetrachloro-p-dioxin (TCDD) and polychlorinated biphenyls (PCBs). Wet weight concentrations of TCDD and PCBs in eggs were at background levels and highest in the piscivorous hooded merganser (Lophodytes cucullatus; geometric MEAN=7 pg/g TCDD and 0.92 I?g/g PCBs) and lowest in the omnivorous wood duck (Aix sponsa) (<1 pg/g and 0.07 I?g/g); concentrations in eggs of the insectivorous tree swallow (Tachycineta bicolor) were intermediate (<1 pg/g and 0.33 I?g/g). Positive accumulation rates of TCDD (8a??19 pg/day) and PCBs (0.4a??0.7 I?g/day) in tree swallow nestlings suggest that the Wisconsin River is the source of these contaminants for tree swallow nestlings. The lower representation of trichlorobiphenyls and tetrachorobiphenyls in hooded merganser eggs compared to wood duck or tree swallow eggs suggests that the hooded merganser or its diet has a greater ability to metabolize lower-numbered PCB congeners than wood ducks or tree swallows.

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.

High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.

PubMed

Brousseau, Louise; Tinaut, Alexandra; Duret, Caroline; Lang, Tiange; Garnier-Gere, Pauline; Scotti, Ivan

2014-03-27

The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.

Reconstruction of forest geometries from terrestrial laser scanning point clouds for canopy radiative transfer modelling

NASA Astrophysics Data System (ADS)

Bremer, Magnus; Schmidtner, Korbinian; Rutzinger, Martin

2015-04-01

The architecture of forest canopies is a key parameter for forest ecological issues helping to model the variability of wood biomass and foliage in space and time. In order to understand the nature of subpixel effects of optical space-borne sensors with coarse spatial resolution, hypothetical 3D canopy models are widely used for the simulation of radiative transfer in forests. Thereby, radiation is traced through the atmosphere and canopy geometries until it reaches the optical sensor. For a realistic simulation scene we decompose terrestrial laser scanning point cloud data of leaf-off larch forest plots in the Austrian Alps and reconstruct detailed model ready input data for radiative transfer simulations. The point clouds are pre-classified into primitive classes using Principle Component Analysis (PCA) using scale adapted radius neighbourhoods. Elongated point structures are extracted as tree trunks. The tree trunks are used as seeds for a Dijkstra-growing procedure, in order to obtain single tree segmentation in the interlinked canopies. For the optimized reconstruction of branching architectures as vector models, point cloud skeletonisation is used in combination with an iterative Dijkstra-growing and by applying distance constraints. This allows conducting a hierarchical reconstruction preferring the tree trunk and higher order branches and avoiding over-skeletonization effects. Based on the reconstructed branching architectures, larch needles are modelled based on the hierarchical level of branches and the geometrical openness of the canopy. For radiative transfer simulations, branch architectures are used as mesh geometries representing branches as cylindrical pipes. Needles are either used as meshes or as voxel-turbids. The presented workflow allows an automatic classification and single tree segmentation in interlinked canopies. The iterative Dijkstra-growing using distance constraints generated realistic reconstruction results. As the mesh representation of branches proved to be sufficient for the simulation approach, the modelling of huge amounts of needles is much more efficient in voxel-turbid representation.

Modeling the Neurodynamics of Submarine Piloting and Navigation Teams

DTIC Science & Technology

2014-05-07

phenomena. The Hurst exponent , H, which is commonly used in a number of scientific fields, provides an estimate of correlation overtime scales...times series for a SPAN performance and CWT representation. The CWT is superimposed by scaling exponent trend near a time of stress. Scaling... exponents at the outset correspond to corrective or anticorrelated behavior. Scaling exponents increase throughout as the team manages the incident and

Stakeholder Collaboration in Air Force Acquisition: Adaptive Design Using System Representations

DTIC Science & Technology

2003-06-01

261 Figure 6.10. Notional efficacy of SR and analysis for different emphasis areas…...….264 Figure 7.1. Adaptive functions during...closer collaboration spanning requirements activities in the user community and acquisition activities . Drafts in 2003 of new versions of DoD...come to grips with the necessary changes in their activities and processes to effectively implement these objectives. As this research effort

Phonological similarity in working memory span tasks.

PubMed

Chow, Michael; Macnamara, Brooke N; Conway, Andrew R A

2016-08-01

In a series of four experiments, we explored what conditions are sufficient to produce a phonological similarity facilitation effect in working memory span tasks. By using the same set of memoranda, but differing the secondary-task requirements across experiments, we showed that a phonological similarity facilitation effect is dependent upon the semantic relationship between the memoranda and the secondary-task stimuli, and is robust to changes in the representation, ordering, and pool size of the secondary-task stimuli. These findings are consistent with interference accounts of memory (Brown, Neath, & Chater, Psychological Review, 114, 539-576, 2007; Oberauer, Lewandowsky, Farrell, Jarrold, & Greaves, Psychonomic Bulletin & Review, 19, 779-819, 2012), whereby rhyming stimuli provide a form of categorical similarity that allows distractors to be excluded from retrieval at recall.

A framework for incorporating the effects of hydrodynamic stresses on forest photosynthesis and evaporation

NASA Astrophysics Data System (ADS)

Matheny, A. M.; Bohrer, G.; Thompsen, J.; Frasson, R.; Frasson, C. D.; Ivanov, V. Y.

2012-12-01

Hydraulic limitations are known to control transpiration in forest ecosystems when the soil is drying or when the vapor pressure deficit between the air and stomata (VPD) is very large, but they can also impact stomatal apertures under conditions of adequate soil moisture and lower evaporative demand. We use the NACP flux measurements and models dataset for multiple site/model intercomparisons to evaluate the degree to which currently un-resolved high-frequency (sub-daily) hydrodynamic stresses affect the error in model prediction of latent heat flux. We find that many site-model combinations are characterized by a typical pattern of overestimation of afternoon flux and a corresponding underestimation of pre-noon flux. We hypothesize that this pattern is a result of un-resolved afternoon stomata closure due to hydrodynamic stresses. In a forest plot at the University of Michigan Biological Station, we use measurements of leaf-level stomata conductance and water potential to demonstrate that trees of similar type - mid-late successional deciduous trees - have very different hydrodynamic strategies that lead to differences in their temporal patterns of stomata conductance. We found that red oak trees continue transpiring despite a large stem-water deficit while red maple trees regulate stomata to maintain a high water potential. Red oaks, which are ring porous, are also able to access more soil water, assumingly from deeper ground layers and have higher conductivity, compared with the maples, which are diffuse porous. These differences will lead to large differences in stomata conductance and water use based on the species composition of the forest. We also demonstrate that the size and shape of the tree stem-branch system may lead to differences in the extent of hydrodynamic stress, which may change the forest respiration patterns as the forest grows and ages. We propose a framework to resolve tree hydrodynamics in global and regional models. It is based on the Finite-Elements Tree-Crown Hydrodynamics model (FETCH) combined with a statistical functional-type/hydraulic-type/size representation of the trees in the forest. Lidar and multi-spectral images of the forest can be used to obtain numerical distributions of species and size of individual tree crowns needed to initialize such simulations. FETCH simulates water flow through the tree as a simplified system of porous media conduits. It explicitly resolves spatiotemporal hydraulic stresses throughout the tree's hydraulic system that cannot be easily represented using other stomatal-conductance models. It uses a physical representation of water flow in a 3-D tree-stem-branch system assuming the xylem is a porous media. Empirical equations relate water potential at the branch-tips to stomata conductance at leaves connected to these branches. FETCH calculates the hydrodynamic stress related closure of stomata, provided the atmospheric and biological variables from the global model, and could replace the current empirical formulation for stomata adjustment based on soil moisture.

The Attachment Doll Play Assessment: Predictive Validity with Concurrent Mother-Child Interaction and Maternal Caregiving Representations

PubMed Central

George, Carol; Solomon, Judith

2016-01-01

Attachment is central to the development of children’s regulatory processes. It has been associated with developmental and psychiatric health across the life span, especially emotional and behavioral regulation of negative affect when stressed (Schore, 2001; Schore and Schore, 2008). Assessment of attachment patterns provides a critical frame for understanding emerging developmental competencies and formulating treatment and intervention. Play-based attachment assessments provide access to representational models of attachment, which are regarded in attachment theory as the central organizing mechanisms associated with stability or change (Bowlby, 1969/1982; Bretherton and Munholland, 2008). The Attachment Doll Play Assessment (ADPA, George and Solomon, 1990–2016; Solomon et al., 1995) is a prominent established representational attachment measure for children aged early latency through childhood. This study examines the predictive validity of the ADPA to caregiving accessibility and responsiveness assessed from mother-child interaction and maternal representation. Sixty nine mothers and their 5–7-year-old children participated in this study. Mother-child interaction was observed during a pre-separation dyadic interaction task. Caregiving representations were rated from the Caregiving Interview (George and Solomon, 1988/1993/2005/2007). Child security with mother was associated with positive dyadic interaction and flexibly integrated maternal caregiving representations. Child controlling/disorganized attachments were significantly associated with problematic dyadic interaction and dysregulated-helpless maternal caregiving representations. The clinical implications and the use of the ADPA in clinical and educational settings are discussed. PMID:27803683

The Attachment Doll Play Assessment: Predictive Validity with Concurrent Mother-Child Interaction and Maternal Caregiving Representations.

PubMed

George, Carol; Solomon, Judith

2016-01-01

Attachment is central to the development of children's regulatory processes. It has been associated with developmental and psychiatric health across the life span, especially emotional and behavioral regulation of negative affect when stressed (Schore, 2001; Schore and Schore, 2008). Assessment of attachment patterns provides a critical frame for understanding emerging developmental competencies and formulating treatment and intervention. Play-based attachment assessments provide access to representational models of attachment, which are regarded in attachment theory as the central organizing mechanisms associated with stability or change (Bowlby, 1969/1982; Bretherton and Munholland, 2008). The Attachment Doll Play Assessment (ADPA, George and Solomon, 1990-2016; Solomon et al., 1995) is a prominent established representational attachment measure for children aged early latency through childhood. This study examines the predictive validity of the ADPA to caregiving accessibility and responsiveness assessed from mother-child interaction and maternal representation. Sixty nine mothers and their 5-7-year-old children participated in this study. Mother-child interaction was observed during a pre-separation dyadic interaction task. Caregiving representations were rated from the Caregiving Interview (George and Solomon, 1988/1993/2005/2007). Child security with mother was associated with positive dyadic interaction and flexibly integrated maternal caregiving representations. Child controlling/disorganized attachments were significantly associated with problematic dyadic interaction and dysregulated-helpless maternal caregiving representations. The clinical implications and the use of the ADPA in clinical and educational settings are discussed.

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.

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.

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.

Production of Non-Canonical Sentences in Agrammatic Aphasia: Limits in Representation or Rule Application?

ERIC Educational Resources Information Center

Burchert, Frank; Meissner, Nadine; De Bleser, Ria

2008-01-01

The study reported here compares two linguistically informed hypotheses on agrammatic sentence production, the TPH [Friedmann, N., & Grodzinsky, Y. (1997). "Tense and agreement in agrammatic production: Pruning the syntactic tree." "Brain and Language," 56, 397-425.] and the DOP [Bastiaanse, R., & van Zonneveld, R. (2005). "Sentence production…

Multiple Object Retrieval in Image Databases Using Hierarchical Segmentation Tree

ERIC Educational Resources Information Center

Chen, Wei-Bang

2012-01-01

The purpose of this research is to develop a new visual information analysis, representation, and retrieval framework for automatic discovery of salient objects of user's interest in large-scale image databases. In particular, this dissertation describes a content-based image retrieval framework which supports multiple-object retrieval. The…

CHINESE GRAMMARS AND THE COMPUTER AT THE OHIO STATE UNIVERSITY. PRELIMINARY REPORT.

ERIC Educational Resources Information Center

MEYERS, L.F.; YANG, J.

SAMPLE OUTPUT SENTENCES OF VARIOUS COMIT AND SNOBOL PROGRAMS FOR TESTING A CHINESE GENERATIVE GRAMMAR ARE PRESENTED. THE GRAMMAR CHOSEN FOR EXPERIMENTATION IS A PRELIMINARY VERSION OF A TRANSFORMATIONAL GRAMMAR. ALL OF THE COMIT PROGRAMS AND ONE OF THE SNOBOL PROGRAMS USE A LINEARIZED REPRESENTATION OF TREE STRUCTURES, WITH ADDITIONAL NUMERICAL…

A Comparison of Two Scoring Methods for an Automated Speech Scoring System

ERIC Educational Resources Information Center

Xi, Xiaoming; Higgins, Derrick; Zechner, Klaus; Williamson, David

2012-01-01

This paper compares two alternative scoring methods--multiple regression and classification trees--for an automated speech scoring system used in a practice environment. The two methods were evaluated on two criteria: construct representation and empirical performance in predicting human scores. The empirical performance of the two scoring models…

Gravitational and Magnetic Anomaly Inversion Using a Tree-Based Geometry Representation

DTIC Science & Technology

2009-06-01

find successive mini- ized vectors. Throughout this paper, the term iteration refers to a ingle loop through a stage of the global scheme, not...BOX 12211 RESEARCH TRIANGLE PARK NC 27709-2211 5 NAVAL RESEARCH LAB E R FRANCHI CODE 7100 M H ORR CODE 7120 J A BUCARO CODE 7130

The Application of Morpho-Syntactic Language Processing to Effective Phrase Matching.

ERIC Educational Resources Information Center

Sheridan, Paraic; Smeaton, Alan F.

1992-01-01

Describes a process of morpho-syntactic language analysis for information retrieval. Tree Structured Analytics (TSA) used for text representation is summarized; the matching process developed for such structures is outlined with an example appended; and experiments carried out to evaluate the effectiveness of TSA matching are discussed. (26…

Continental-scale temperature covariance in proxy reconstructions and climate models

NASA Astrophysics Data System (ADS)

Hartl-Meier, Claudia; Büntgen, Ulf; Smerdon, Jason; Zorita, Eduardo; Krusic, Paul; Ljungqvist, Fredrik; Schneider, Lea; Esper, Jan

2017-04-01

Inter-continental temperature variability over the past millennium has been reported to be more coherent in climate model simulations than in multi-proxy-based reconstructions, a finding that undermines the representation of spatial variability in either of these approaches. We assess the covariance of summer temperatures among Northern Hemisphere continents by comparing tree-ring based temperature reconstructions with state-of-the-art climate model simulations over the past millennium. We find inter-continental temperature covariance to be larger in tree-ring-only reconstructions compared to those derived from multi-proxy networks, thus enhancing the agreement between proxy- and model-based spatial representations. A detailed comparison of simulated temperatures, however, reveals substantial spread among the models. Over the past millennium, inter-continental temperature correlations are driven by the cooling after major volcanic eruptions in 1257, 1452, 1601, and 1815. The coherence of these synchronizing events appears to be elevated in several climate simulations relative to their own covariance baselines and the proxy reconstructions, suggesting these models overestimate the amplitude of cooling in response to volcanic forcing at large spatial scales.

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

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.

Group-sparse representation with dictionary learning for medical image denoising and fusion.

PubMed

Li, Shutao; Yin, Haitao; Fang, Leyuan

2012-12-01

Recently, sparse representation has attracted a lot of interest in various areas. However, the standard sparse representation does not consider the intrinsic structure, i.e., the nonzero elements occur in clusters, called group sparsity. Furthermore, there is no dictionary learning method for group sparse representation considering the geometrical structure of space spanned by atoms. In this paper, we propose a novel dictionary learning method, called Dictionary Learning with Group Sparsity and Graph Regularization (DL-GSGR). First, the geometrical structure of atoms is modeled as the graph regularization. Then, combining group sparsity and graph regularization, the DL-GSGR is presented, which is solved by alternating the group sparse coding and dictionary updating. In this way, the group coherence of learned dictionary can be enforced small enough such that any signal can be group sparse coded effectively. Finally, group sparse representation with DL-GSGR is applied to 3-D medical image denoising and image fusion. Specifically, in 3-D medical image denoising, a 3-D processing mechanism (using the similarity among nearby slices) and temporal regularization (to perverse the correlations across nearby slices) are exploited. The experimental results on 3-D image denoising and image fusion demonstrate the superiority of our proposed denoising and fusion approaches.

Verbal short-term memory in Down's syndrome: an articulatory loop deficit?

PubMed

Vicari, S; Marotta, L; Carlesimo, G A

2004-02-01

Verbal short-term memory, as measured by digit or word span, is generally impaired in individuals with Down's syndrome (DS) compared to mental age-matched controls. Moving from the working memory model, the present authors investigated the hypothesis that impairment in some of the articulatory loop sub-components is at the base of the deficient maintenance and recall of phonological representations in individuals with DS. Two experiments were carried out in a group of adolescents with DS and in typically developing children matched for mental age. In the first experiment, the authors explored the reliance of these subjects on the subvocal rehearsal mechanism during a word-span task and the effects produced by varying the frequency of occurrence of the words on the extension of the word span. In the second experiment, they investigated the functioning of the phonological store component of the articulatory loop in more detail. A reduced verbal span in DS was confirmed. Neither individuals with DS nor controls engaged in spontaneous subvocal rehearsal. Moreover, the data provide little support for defective functioning of the phonological store in DS. No evidence was found suggesting that a dysfunction of the articulatory loop and lexical-semantic competence significantly contributed to verbal span reduction in subjects with DS. Alternative explanations of defective verbal short-term memory in DS, such as a central executive system impairment, must be considered.

A prognostic pollen emissions model for climate models (PECM1.0)

NASA Astrophysics Data System (ADS)

Wozniak, Matthew C.; Steiner, Allison L.

2017-11-01

We develop a prognostic model called Pollen Emissions for Climate Models (PECM) for use within regional and global climate models to simulate pollen counts over the seasonal cycle based on geography, vegetation type, and meteorological parameters. Using modern surface pollen count data, empirical relationships between prior-year annual average temperature and pollen season start dates and end dates are developed for deciduous broadleaf trees (Acer, Alnus, Betula, Fraxinus, Morus, Platanus, Populus, Quercus, Ulmus), evergreen needleleaf trees (Cupressaceae, Pinaceae), grasses (Poaceae; C3, C4), and ragweed (Ambrosia). This regression model explains as much as 57 % of the variance in pollen phenological dates, and it is used to create a climate-flexible phenology that can be used to study the response of wind-driven pollen emissions to climate change. The emissions model is evaluated in the Regional Climate Model version 4 (RegCM4) over the continental United States by prescribing an emission potential from PECM and transporting pollen as aerosol tracers. We evaluate two different pollen emissions scenarios in the model using (1) a taxa-specific land cover database, phenology, and emission potential, and (2) a plant functional type (PFT) land cover, phenology, and emission potential. The simulated surface pollen concentrations for both simulations are evaluated against observed surface pollen counts in five climatic subregions. Given prescribed pollen emissions, the RegCM4 simulates observed concentrations within an order of magnitude, although the performance of the simulations in any subregion is strongly related to the land cover representation and the number of observation sites used to create the empirical phenological relationship. The taxa-based model provides a better representation of the phenology of tree-based pollen counts than the PFT-based model; however, we note that the PFT-based version provides a useful and climate-flexible emissions model for the general representation of the pollen phenology over the United States.

Conformal geodesics in spherically symmetric vacuum spacetimes with cosmological constant

NASA Astrophysics Data System (ADS)

García-Parrado Gómez-Lobo, A.; Gasperín, E.; Valiente Kroon, J. A.

2018-02-01

An analysis of conformal geodesics in the Schwarzschild–de Sitter and Schwarzschild–anti-de Sitter families of spacetimes is given. For both families of spacetimes we show that initial data on a spacelike hypersurface can be given such that the congruence of conformal geodesics arising from this data cover the whole maximal extension of canonical conformal representations of the spacetimes without forming caustic points. For the Schwarzschild–de Sitter family, the resulting congruence can be used to obtain global conformal Gaussian systems of coordinates of the conformal representation. In the case of the Schwarzschild–anti-de Sitter family, the natural parameter of the curves only covers a restricted time span so that these global conformal Gaussian systems do not exist.

Protein sequence comparison based on K-string dictionary.

PubMed

Yu, Chenglong; He, Rong L; Yau, Stephen S-T

2013-10-25

The current K-string-based protein sequence comparisons require large amounts of computer memory because the dimension of the protein vector representation grows exponentially with K. In this paper, we propose a novel concept, the "K-string dictionary", to solve this high-dimensional problem. It allows us to use a much lower dimensional K-string-based frequency or probability vector to represent a protein, and thus significantly reduce the computer memory requirements for their implementation. Furthermore, based on this new concept, we use Singular Value Decomposition to analyze real protein datasets, and the improved protein vector representation allows us to obtain accurate gene trees. © 2013.

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.

Community representation in hospital decision making: a literature review.

PubMed

Murray, Zoë

2015-06-01

Advancing quality in health services requires structures and processes that are informed by consumer input. Although this agenda is well recognised, few researchers have focussed on the establishment and maintenance of customer input throughout the structures and processes used to produce high-quality, safe care. We present an analysis of literature outlining the barriers and enablers involved in community representation in hospital governance. The review aimed to explore how community representation in hospital governance is achieved. Studies spanning 1997-2012 were analysed using Donabedian' s model of quality systems as a guide for categories of interest: structure, in relation to administration of quality; process, which is particularly concerned with cooperation and culture; and outcome, considered, in this case, to be the achievement of effective community representation on quality of care. There are limited published studies on community representation in hospital governance in Australia. What can be gleaned from the literature is: 1) quality subcommittees set up to assist Hospital Boards are a key structure for involving community representation in decision making around quality of care, and 2) there are a number of challenges to effectively developing the process of community representation in hospital governance: ambiguity and the potential for escalated indecision; inadequate value and consideration given to it by decision makers resulting in a lack of time and resources needed to support the community engagement strategy (time, facilitation, budgets); poor support and attitude amongst staff; and consumer issues, such as feeling isolated and intimidated by expert opinion. The analysis indicates that: quality subcommittees set up to assist boards are a key structure for involving community representation in decision making around quality of care. There are clearly a number of challenges to effectively developing the process of community representation in hospital governance, associated with ambiguity, organisational and consumer issues. For an inclusive agenda to real life, work must be done on understanding the representatives' role and the decision making process, adequately supporting the representational process, and developing organisational cooperation and culture regarding community representation.

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.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

Visualizing the Bayesian 2-test case: The effect of tree diagrams on medical decision making.

PubMed

Binder, Karin; Krauss, Stefan; Bruckmaier, Georg; Marienhagen, Jörg

2018-01-01

In medicine, diagnoses based on medical test results are probabilistic by nature. Unfortunately, cognitive illusions regarding the statistical meaning of test results are well documented among patients, medical students, and even physicians. There are two effective strategies that can foster insight into what is known as Bayesian reasoning situations: (1) translating the statistical information on the prevalence of a disease and the sensitivity and the false-alarm rate of a specific test for that disease from probabilities into natural frequencies, and (2) illustrating the statistical information with tree diagrams, for instance, or with other pictorial representation. So far, such strategies have only been empirically tested in combination for "1-test cases", where one binary hypothesis ("disease" vs. "no disease") has to be diagnosed based on one binary test result ("positive" vs. "negative"). However, in reality, often more than one medical test is conducted to derive a diagnosis. In two studies, we examined a total of 388 medical students from the University of Regensburg (Germany) with medical "2-test scenarios". Each student had to work on two problems: diagnosing breast cancer with mammography and sonography test results, and diagnosing HIV infection with the ELISA and Western Blot tests. In Study 1 (N = 190 participants), we systematically varied the presentation of statistical information ("only textual information" vs. "only tree diagram" vs. "text and tree diagram in combination"), whereas in Study 2 (N = 198 participants), we varied the kinds of tree diagrams ("complete tree" vs. "highlighted tree" vs. "pruned tree"). All versions were implemented in probability format (including probability trees) and in natural frequency format (including frequency trees). We found that natural frequency trees, especially when the question-related branches were highlighted, improved performance, but that none of the corresponding probabilistic visualizations did.

Representations of everyday life: a proposal for capturing social values from the Marxist perspective of knowledge production.

PubMed

Soares, Cássia Baldini; Santos, Vilmar Ezequiel Dos; Campos, Célia Maria Sivalli; Lachtim, Sheila Aparecida Ferreira; Campos, Fernanda Cristina

2011-12-01

We propose from the Marxist perspective of the construction of knowledge, a theoretical and methodological framework for understanding social values by capturing everyday representations. We assume that scientific research brings together different dimensions: epistemological, theoretical and methodological that consistently to the other instances, proposes a set of operating procedures and techniques for capturing and analyzing the reality under study in order to expose the investigated object. The study of values reveals the essentiality of the formation of judgments and choices, there are values that reflect the dominant ideology, spanning all social classes, but there are values that reflect class interests, these are not universal, they are formed in relationships and social activities. Basing on the Marxist theory of consciousness, representations are discursive formulations of everyday life - opinion or conviction - issued by subjects about their reality, being a coherent way of understanding and exposure social values: focus groups show is suitable for grasping opinions while interviews show potential to expose convictions.

Geographers of Mars: cartographic inscription and exploration narrative in late Victorian representations of the red planet.

PubMed

Lane, K Maria D

2005-12-01

Over two decades spanning the turn of the twentieth century, astronomers' claims about the landscape and climate of Mars spurred widespread scientific and popular interest in the possibility that the red planet might be inhabited. This essay offers a new explanation for the power with which the notion of an inhabited Mars gripped noted scholars and everyday citizens on both sides of the Atlantic. Rather than pointing to a rekindling of age-old philosophical interest in the plurality of worlds, it argues that turn-of-the-century scientific narratives about Mars derived much of their power and popularity from ties with the newly established discipline of geography. From mapmaking to travelogue-style writing, astronomers borrowed powerful representational strategies from the discipline of geography to legitimize their claims about the red planet. In making the link between geographical and astronomical science more explicit, the essay further suggests that turn-of-the-century representations of Mars could be productively recontextualized alongside geographical works produced in the same period.

Drivers and mechanisms of tree mortality in moist tropical forests.

PubMed

McDowell, Nate; Allen, Craig D; Anderson-Teixeira, Kristina; Brando, Paulo; Brienen, Roel; Chambers, Jeff; Christoffersen, Brad; Davies, Stuart; Doughty, Chris; Duque, Alvaro; Espirito-Santo, Fernando; Fisher, Rosie; Fontes, Clarissa G; Galbraith, David; Goodsman, Devin; Grossiord, Charlotte; Hartmann, Henrik; Holm, Jennifer; Johnson, Daniel J; Kassim, Abd Rahman; Keller, Michael; Koven, Charlie; Kueppers, Lara; Kumagai, Tomo'omi; Malhi, Yadvinder; McMahon, Sean M; Mencuccini, Maurizio; Meir, Patrick; Moorcroft, Paul; Muller-Landau, Helene C; Phillips, Oliver L; Powell, Thomas; Sierra, Carlos A; Sperry, John; Warren, Jeff; Xu, Chonggang; Xu, Xiangtao

2018-02-16

Tree mortality rates appear to be increasing in moist tropical forests (MTFs) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and identify the next steps for improved understanding and reduced prediction. Increasing mortality rates are associated with rising temperature and vapor pressure deficit, liana abundance, drought, wind events, fire and, possibly, CO 2 fertilization-induced increases in stand thinning or acceleration of trees reaching larger, more vulnerable heights. The majority of these mortality drivers may kill trees in part through carbon starvation and hydraulic failure. The relative importance of each driver is unknown. High species diversity may buffer MTFs against large-scale mortality events, but recent and expected trends in mortality drivers give reason for concern regarding increasing mortality within MTFs. Models of tropical tree mortality are advancing the representation of hydraulics, carbon and demography, but require more empirical knowledge regarding the most common drivers and their subsequent mechanisms. We outline critical datasets and model developments required to test hypotheses regarding the underlying causes of increasing MTF mortality rates, and improve prediction of future mortality under climate change. No claim to original US government works New Phytologist © 2018 New Phytologist Trust.

Tree-hierarchy of DNA and distribution of Holliday junctions.

PubMed

Rozikov, U A

2017-12-01

We define a DNA as a sequence of [Formula: see text]'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy has property that each vertex of the Cayley tree belongs only to one of DNA. Then we give a model (energy, Hamiltonian) of this set of DNAs by an analogue of Ising model with three spin values (considered as DNA base pairs) on a set of admissible configurations. To study thermodynamic properties of the model of DNAs we describe corresponding translation invariant Gibbs measures (TIGM) of the model on the Cayley tree of order two. We show that there is a critical temperature [Formula: see text] such that (i) if temperature [Formula: see text] then there exists unique TIGM; (ii) if [Formula: see text] then there are two TIGMs; (iii) if [Formula: see text] then there are three TIGMs. Each such measure describes a phase of the set of DNAs. We use these results to study distributions of Holliday junctions and branches of DNAs. In case of very high and very low temperatures we give stationary distributions and typical configurations of the Holliday junctions.

Sample-Based Surface Coloring

PubMed Central

Bürger, Kai; Krüger, Jens; Westermann, Rüdiger

2011-01-01

In this paper, we present a sample-based approach for surface coloring, which is independent of the original surface resolution and representation. To achieve this, we introduce the Orthogonal Fragment Buffer (OFB)—an extension of the Layered Depth Cube—as a high-resolution view-independent surface representation. The OFB is a data structure that stores surface samples at a nearly uniform distribution over the surface, and it is specifically designed to support efficient random read/write access to these samples. The data access operations have a complexity that is logarithmic in the depth complexity of the surface. Thus, compared to data access operations in tree data structures like octrees, data-dependent memory access patterns are greatly reduced. Due to the particular sampling strategy that is employed to generate an OFB, it also maintains sample coherence, and thus, exhibits very good spatial access locality. Therefore, OFB-based surface coloring performs significantly faster than sample-based approaches using tree structures. In addition, since in an OFB, the surface samples are internally stored in uniform 2D grids, OFB-based surface coloring can efficiently be realized on the GPU to enable interactive coloring of high-resolution surfaces. On the OFB, we introduce novel algorithms for color painting using volumetric and surface-aligned brushes, and we present new approaches for particle-based color advection along surfaces in real time. Due to the intermediate surface representation we choose, our method can be used to color polygonal surfaces as well as any other type of surface that can be sampled. PMID:20616392

Recognition of Natural Scenes from Global Properties: Seeing the Forest without Representing the Trees

ERIC Educational Resources Information Center

Greene, Michelle R.; Oliva, Aude

2009-01-01

Human observers are able to rapidly and accurately categorize natural scenes, but the representation mediating this feat is still unknown. Here we propose a framework of rapid scene categorization that does not segment a scene into objects and instead uses a vocabulary of global, ecological properties that describe spatial and functional aspects…

Case Designs for Ill-Structured Problems: Analysis and Implications for Practice

ERIC Educational Resources Information Center

Dabbagh, Nada; Blijd, Cecily Williams

2009-01-01

This study is a third in a series of studies that examined students' information seeking and problem solving behaviors while interacting with one of two types of web-based representations of an ill-structured instructional design case: hierarchical (tree-like) and heterarchical (network-like). A Java program was used to track students' hypermedia…

On the Existence of Simultaneous Edge Disjoint Realizations of Degree Sequences with ’Few’ Edges

DTIC Science & Technology

1975-08-01

constructing graphs and digraphs with given valences and factors. Discrete Math . 6 (1973) 79-88. 3. M. Keren, Realization of a sun of sequences by a sum...appear. 5. S. Kundu, The k factor conjecture is true. Discrete Math . 6 (1973) 367-376. 6. S. Kundu, Disjoint representation of tree realizable

Multi-Sensor Scene Synthesis and Analysis

DTIC Science & Technology

1981-09-01

Quad Trees for Image Representation and Processing ...... ... 126 2.6.2 Databases ..... ..... ... ..... ... ..... ..... 138 2.6.2.1 Definitions and...Basic Concepts ....... 138 2.6.3 Use of Databases in Hierarchical Scene Analysis ...... ... ..................... 147 2.6.4 Use of Relational Tables...Multisensor Image Database Systems (MIDAS) . 161 2.7.2 Relational Database System for Pictures .... ..... 168 2.7.3 Relational Pictorial Database

Expressivity in Children's Drawings: A Longitudinal Analysis.

ERIC Educational Resources Information Center

Ives, William

This paper reports a follow-up study of 5-, 7-, and 9-year-old subjects who had participated in an investigation of the nature of children's and adults' ability to graphically represent expressive qualities (i.e., happy, sad, angry, loud, quiet, hard). In the original study, the use of literal representation (such as a smiling face on a tree) and…

Conservation priorities for tree crop wild relatives in the United States

Treesearch

Colin K. Khoury; Stephanie L. Greene; Karen A. Williams; Chrystian C. Sosa; Chris Richards

2017-01-01

Crop wild relatives native to the United States have proved useful as genetic resources in breeding more productive, nutritious, and resilient crops. Their utilization is expected to increase with better information about the species and improving breeding tools. But this utilization may be constrained by their limited representation in genebanks and the ongoing loss...

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.

A CFD study on the effectiveness of trees to disperse road traffic emissions at a city scale

NASA Astrophysics Data System (ADS)

Jeanjean, A. P. R.; Hinchliffe, G.; McMullan, W. A.; Monks, P. S.; Leigh, R. J.

2015-11-01

This paper focuses on the effectiveness of trees at dispersing road traffic emissions on a city scale. CFD simulations of air-pollutant concentrations were performed using the OpenFOAM software platform using the k-ε model. Results were validated against the CODASC wind tunnel database before being applied to a LIDAR database of buildings and trees representing the City of Leicester (UK). Most other CFD models in the literature typically use idealised buildings to model wind flow and pollution dispersion. However, the methodology used in this study uses real buildings and trees data from LIDAR to reconstruct a 3D representation of Leicester City Centre. It focuses on a 2 × 2 km area which is on a scale larger than those usually used in other CFD studies. Furthermore, the primary focus of this study is on the interaction of trees with wind flow dynamics. It was found that in effect, trees have a regionally beneficial impact on road traffic emissions by increasing turbulence and reducing ambient concentrations of road traffic emissions by 7% at pedestrian height on average. This was an important result given that previous studies generally concluded that trees trapped pollution by obstructing wind flow in street canyons. Therefore, this study is novel both in its methodology and subsequent results, highlighting the importance of combining local and regional scale models for assessing the impact of trees in urban planning.

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.

A combined model of sensory and cognitive representations underlying tonal expectations in music: from audio signals to behavior.

PubMed

Collins, Tom; Tillmann, Barbara; Barrett, Frederick S; Delbé, Charles; Janata, Petr

2014-01-01

Listeners' expectations for melodies and harmonies in tonal music are perhaps the most studied aspect of music cognition. Long debated has been whether faster response times (RTs) to more strongly primed events (in a music theoretic sense) are driven by sensory or cognitive mechanisms, such as repetition of sensory information or activation of cognitive schemata that reflect learned tonal knowledge, respectively. We analyzed over 300 stimuli from 7 priming experiments comprising a broad range of musical material, using a model that transforms raw audio signals through a series of plausible physiological and psychological representations spanning a sensory-cognitive continuum. We show that RTs are modeled, in part, by information in periodicity pitch distributions, chroma vectors, and activations of tonal space--a representation on a toroidal surface of the major/minor key relationships in Western tonal music. We show that in tonal space, melodies are grouped by their tonal rather than timbral properties, whereas the reverse is true for the periodicity pitch representation. While tonal space variables explained more of the variation in RTs than did periodicity pitch variables, suggesting a greater contribution of cognitive influences to tonal expectation, a stepwise selection model contained variables from both representations and successfully explained the pattern of RTs across stimulus categories in 4 of the 7 experiments. The addition of closure--a cognitive representation of a specific syntactic relationship--succeeded in explaining results from all 7 experiments. We conclude that multiple representational stages along a sensory-cognitive continuum combine to shape tonal expectations in music. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Modeling the temporal dynamics of nonstructural carbohydrate pools in forest trees

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

Richardson, Andrew D.

Trees store carbohydrates, in the form of sugars and starch, as reserves to be used to power both future growth as well as to support day-to-day metabolic functions. These reserves are particularly important in the context of how trees cope with disturbance and stress—for example, as related to pest outbreaks, wind or ice damage, and extreme climate events. In this project, we measured the size of carbon reserves in forest trees, and determined how quickly these reserves are used and replaced—i.e., their “turnover time”. Our work was conducted at Harvard Forest, a temperate deciduous forest in central Massachusetts. Through fieldmore » sampling, laboratory-based chemical analyses, and allometric modeling, we scaled these measurements up to whole-tree NSC budgets. We used these data to test and improve computer simulation models of carbon flow through forest ecosystems. Our modeling focused on the mathematical representation of these stored carbon reserves, and we examined the sensitivity of model performance to different model structures. This project contributes to DOE’s goal to improve next-generation models of the earth system, and to understand the impacts of climate change on terrestrial ecosystems.« less

Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data.

PubMed

Zhang, Peng; Li, Houqiang; Wang, Honghui; Wong, Stephen T C; Zhou, Xiaobo

2011-01-01

Peak detection is one of the most important steps in mass spectrometry (MS) analysis. However, the detection result is greatly affected by severe spectrum variations. Unfortunately, most current peak detection methods are neither flexible enough to revise false detection results nor robust enough to resist spectrum variations. To improve flexibility, we introduce peak tree to represent the peak information in MS spectra. Each tree node is a peak judgment on a range of scales, and each tree decomposition, as a set of nodes, is a candidate peak detection result. To improve robustness, we combine peak detection and common peak alignment into a closed-loop framework, which finds the optimal decomposition via both peak intensity and common peak information. The common peak information is derived and loopily refined from the density clustering of the latest peak detection result. Finally, we present an improved ant colony optimization biomarker selection method to build a whole MS analysis system. Experiment shows that our peak detection method can better resist spectrum variations and provide higher sensitivity and lower false detection rates than conventional methods. The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data.

Classification of Parkinsonian syndromes from FDG-PET brain data using decision trees with SSM/PCA features.

PubMed

Mudali, D; Teune, L K; Renken, R J; Leenders, K L; Roerdink, J B T M

2015-01-01

Medical imaging techniques like fluorodeoxyglucose positron emission tomography (FDG-PET) have been used to aid in the differential diagnosis of neurodegenerative brain diseases. In this study, the objective is to classify FDG-PET brain scans of subjects with Parkinsonian syndromes (Parkinson's disease, multiple system atrophy, and progressive supranuclear palsy) compared to healthy controls. The scaled subprofile model/principal component analysis (SSM/PCA) method was applied to FDG-PET brain image data to obtain covariance patterns and corresponding subject scores. The latter were used as features for supervised classification by the C4.5 decision tree method. Leave-one-out cross validation was applied to determine classifier performance. We carried out a comparison with other types of classifiers. The big advantage of decision tree classification is that the results are easy to understand by humans. A visual representation of decision trees strongly supports the interpretation process, which is very important in the context of medical diagnosis. Further improvements are suggested based on enlarging the number of the training data, enhancing the decision tree method by bagging, and adding additional features based on (f)MRI data.

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.

Pattern Matcher for Trees Constructed from Lists

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

A software library has been developed that takes a high-level description of a pattern to be satisfied and applies it to a target. If the two match, it returns success; otherwise, it indicates a failure. The target is semantically a tree that is constructed from elements of terminal and non-terminal nodes represented through lists and symbols. Additionally, functionality is provided for finding the element in a set that satisfies a given pattern and doing a tree search, finding all occurrences of leaf nodes that match a given pattern. This process is valuable because it is a new algorithmic approach that significantly improves the productivity of the programmers and has the potential of making their resulting code more efficient by the introduction of a novel semantic representation language. This software has been used in many applications delivered to NASA and private industry, and the cost savings that have resulted from it are significant.

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.

The interaction of short-term and long-term memory in phonetic category formation

NASA Astrophysics Data System (ADS)

Harnsberger, James D.

2002-05-01

This study examined the role that short-term memory capacity plays in the relationship between novel stimuli (e.g., non-native speech sounds, native nonsense words) and phonetic categories in long-term memory. Thirty native speakers of American English were administered five tests: categorial AXB discrimination using nasal consonants from Malayalam; categorial identification, also using Malayalam nasals, which measured the influence of phonetic categories in long-term memory; digit span; nonword span, a short-term memory measure mediated by phonetic categories in long-term memory; and paired-associate word learning (word-word and word-nonword pairs). The results showed that almost all measures were significantly correlated with one another. The strongest predictor for the discrimination and word-nonword learning results was nonword (r=+0.62) and digit span (r=+0.51), respectively. When the identification test results were partialed out, only nonword span significantly correlated with discrimination. The results show a strong influence of short-term memory capacity on the encoding of phonetic detail within phonetic categories and suggest that long-term memory representations regulate the capacity of short-term memory to preserve information for subsequent encoding. The results of this study will also be discussed with regards to resolving the tension between episodic and abstract models of phonetic category structure.

Spherical harmonics and rigged Hilbert spaces

NASA Astrophysics Data System (ADS)

Celeghini, E.; Gadella, M.; del Olmo, M. A.

2018-05-01

This paper is devoted to study discrete and continuous bases for spaces supporting representations of SO(3) and SO(3, 2) where the spherical harmonics are involved. We show how discrete and continuous bases coexist on appropriate choices of rigged Hilbert spaces. We prove the continuity of relevant operators and the operators in the algebras spanned by them using appropriate topologies on our spaces. Finally, we discuss the properties of the functionals that form the continuous basis.

Global climate change will increase the abundance of symbiotic nitrogen-fixing trees in much of North America.

PubMed

Liao, Wenying; Menge, Duncan N L; Lichstein, Jeremy W; Ángeles-Pérez, Gregorio

2017-11-01

Symbiotic nitrogen (N)-fixing trees can drive N and carbon cycling and thus are critical components of future climate projections. Despite detailed understanding of how climate influences N-fixation enzyme activity and physiology, comparatively little is known about how climate influences N-fixing tree abundance. Here, we used forest inventory data from the USA and Mexico (>125,000 plots) along with climate data to address two questions: (1) How does the abundance distribution of N-fixing trees (rhizobial, actinorhizal, and both types together) vary with mean annual temperature (MAT) and precipitation (MAP)? (2) How will changing climate shift the abundance distribution of N-fixing trees? We found that rhizobial N-fixing trees were nearly absent below 15°C MAT, but above 15°C MAT, they increased in abundance as temperature rose. We found no evidence for a hump-shaped response to temperature throughout the range of our data. Rhizobial trees were more abundant in dry than in wet ecosystems. By contrast, actinorhizal trees peaked in abundance at 5-10°C MAT and were least abundant in areas with intermediate precipitation. Next, we used a climate-envelope approach to project how N-fixing tree relative abundance might change in the future. The climate-envelope projection showed that rhizobial N-fixing trees will likely become more abundant in many areas by 2080, particularly in the southern USA and western Mexico, due primarily to rising temperatures. Projections for actinorhizal N-fixing trees were more nuanced due to their nonmonotonic dependence on temperature and precipitation. Overall, the dominant trend is that warming will increase N-fixing tree abundance in much of the USA and Mexico, with large increases up to 40° North latitude. The quantitative link we provide between climate and N-fixing tree abundance can help improve the representation of symbiotic N fixation in Earth System Models. © 2017 John Wiley & Sons Ltd.

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.

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.

Smoke and Mirrors: U.K. Newspaper Representations of Intimate Partner Domestic Violence.

PubMed

Lloyd, Michele; Ramon, Shula

2017-01-01

News media are in a position to project certain perspectives on domestic violence while marginalizing others, which has implications for public understanding and policy development. This study applies discourse analysis to articles on domestic violence in two U.K. national daily newspapers published in 2001-2002 and 2011-2012 to evaluate evidence of change over a 10-year time span. The research examines how discourses of domestic violence are constructed through newspaper representations of victims, predominantly women, and perpetrators, predominantly men. Although one of the newspapers adopts a respectful position toward women, the textual and visual techniques adopted by the other reveal a tendency for blaming the victim and sexualizing violence related to perceptions of "deserving" or "undeserving" women victims. © The Author(s) 2016.

Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

PubMed

Goloboff, Pablo A

2014-10-01

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner trees and for moving around plateaus can be useful when analyzing phylogenomic data sets formed by concatenation of genes with uneven taxon representation ("sparse" supermatrices), which are likely to present a tree landscape with extensive plateaus. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Sensitivity Analysis of Flutter Response of a Wing Incorporating Finite-Span Corrections

NASA Technical Reports Server (NTRS)

Issac, Jason Cherian; Kapania, Rakesh K.; Barthelemy, Jean-Francois M.

1994-01-01

Flutter analysis of a wing is performed in compressible flow using state-space representation of the unsteady aerodynamic behavior. Three different expressions are used to incorporate corrections due to the finite-span effects of the wing in estimating the lift-curve slope. The structural formulation is based on a Rayleigh-Pitz technique with Chebyshev polynomials used for the wing deflections. The aeroelastic equations are solved as an eigen-value problem to determine the flutter speed of the wing. The flutter speeds are found to be higher in these cases, when compared to that obtained without accounting for the finite-span effects. The derivatives of the flutter speed with respect to the shape parameters, namely: aspect ratio, area, taper ratio and sweep angle, are calculated analytically. The shape sensitivity derivatives give a linear approximation to the flutter speed curves over a range of values of the shape parameter which is perturbed. Flutter and sensitivity calculations are performed on a wing using a lifting-surface unsteady aerodynamic theory using modules from a system of programs called FAST.

Interference between maintenance and processing in working memory: the effect of item-distractor similarity in complex span.

PubMed

Oberauer, Klaus; Farrell, Simon; Jarrold, Christopher; Pasiecznik, Kazimir; Greaves, Martin

2012-05-01

Four experiments examined the effect of phonological similarity between items and distractors on complex span performance. Item-distractor similarity benefited serial recall when distractors followed the items they were similar to, but not when distractors preceded the items they were similar to. These findings are predicted by C-SOB (contextual serial order in a box), a computational model of complex span. The model assumes that distractors are involuntarily encoded into memory, being associated to the preceding item's list position. Distractors interfere with items by superposition of distributed representations that are associated to the same position. Superposition distorts item memory; this distortion is less severe when the distractor is similar to the item. Further support for the assumption that distractors are encoded at the position of the preceding item comes from the finding that intrusions of distractors at recall tended to come from the position of the target item. In addition, intruding distractors tend to replace items to which they are similar, showing that lack of distinctiveness also contributes to interference. (c) 2012 APA, all rights reserved.

Machine learning reveals orbital interaction in materials

NASA Astrophysics Data System (ADS)

Lam Pham, Tien; Kino, Hiori; Terakura, Kiyoyuki; Miyake, Takashi; Tsuda, Koji; Takigawa, Ichigaku; Chi Dam, Hieu

2017-12-01

We propose a novel representation of materials named an 'orbital-field matrix (OFM)', which is based on the distribution of valence shell electrons. We demonstrate that this new representation can be highly useful in mining material data. Experimental investigation shows that the formation energies of crystalline materials, atomization energies of molecular materials, and local magnetic moments of the constituent atoms in bimetal alloys of lanthanide metal and transition-metal can be predicted with high accuracy using the OFM. Knowledge regarding the role of the coordination numbers of the transition-metal and lanthanide elements in determining the local magnetic moments of the transition-metal sites can be acquired directly from decision tree regression analyses using the OFM.

View of the shuttle Discovery on the launch pad just prior to STS 51-D launch

NASA Image and Video Library

1985-04-12

Just below center of this scene is a distant representation of a large ignition as the Shuttle Discovery lifts off from a Kennedy Space Center (KSC) launch pad. The ignition can be seen through the fronds of the trees. Birds in flight frame the light spot representing the orbiter as it launches.

Positivity of Curvature-Squared Corrections in Gravity

NASA Astrophysics Data System (ADS)

Cheung, Clifford; Remmen, Grant N.

2017-02-01

We study the Gauss-Bonnet (GB) term as the leading higher-curvature correction to pure Einstein gravity. Assuming a tree-level ultraviolet completion free of ghosts or tachyons, we prove that the GB term has a nonnegative coefficient in dimensions greater than 4. Our result follows from unitarity of the spectral representation for a general ultraviolet completion of the GB term.

Prescribed burning for oak savanna restoration in central Minnesota.

Treesearch

Alan S. White

1986-01-01

Low intensity, spring prescribed burns have been used since 1964 at the Cedar Creek Natural History Area in Minnesota in an attempt to restore the area to an oak savanna. Burned areas are now more savanna like (having greater grass and forb and lower shrub and lower tree representation) than unburned areas but still have higher overstory densities than apparently...

An Integrated Textbook, Video, and Software Environment for Novice and Expert Prolog Programmers. Technical Report No. 23.

ERIC Educational Resources Information Center

Eisenstadt, Marc; Brayshaw, Mike

This paper describes a Prolog execution model which serves as the uniform basis of textbook material, video-based teaching material, and an advanced graphical user interface for Prolog programmers. The model, based upon an augmented AND/OR tree representation of Prolog programs, uses an enriched "status box" in place of the traditional…

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

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.

Conceptual and linguistic representations of kinds and classes

PubMed Central

Prasada, Sandeep; Hennefield, Laura; Otap, Daniel

2013-01-01

We investigate the hypothesis that our conceptual systems provide two formally distinct ways of representing categories by investigating the manner in which lexical nominals (e.g., tree, picnic table) and phrasal nominals (e.g., black bird, birds that like rice) are interpreted. Four experiments found that lexical nominals may be mapped onto kind representations whereas phrasal nominals map onto class representations but not kind representations. Experiment 1 found that phrasal nominals, unlike lexical nominals, are mapped onto categories whose members need not be of a single kind. Experiments 2 and 3 found that categories named by lexical nominals enter into both class inclusion and kind hierarchies and thus support both class inclusion (is a) and kind specification (kind of) relations, whereas phrasal nominals map onto class representations which support only class inclusion relations. Experiment 4 showed that the two types of nominals represent hierarchical relations in different ways. Phrasal nominals (e.g., white bear) are mapped onto classes that have criteria of membership in addition to those specified by the class picked out by the head noun of the phrase (e.g., bear). In contrast, lexical nominals (e.g., polar bear) specify one way to meet the criteria specified by the more general kind concept (e.g., bear). Implications for the language-conceptual system interface, representation of hierarchical relations, lexicalization, and theories of conceptual combination are discussed. PMID:22671567

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

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.

Tree-, stand- and site-specific controls on landscape-scale patterns of transpiration

NASA Astrophysics Data System (ADS)

Hassler, Sibylle; Markus, Weiler; Theresa, Blume

2017-04-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions as well as for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. For individual trees, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status control sap flow amounts of individual trees. Within forest stands, properties such as species composition, basal area or stand density additionally affect sap flow, for example via competition mechanisms. Finally, sap flow patterns might also be influenced by landscape-scale characteristics such as geology, slope position or aspect because they affect water and energy availability; however, little is known about the dynamic interplay of these controls. We studied the relative importance of various tree-, stand- and site-specific characteristics with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km2-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we modelled the daily sap velocities of these 61 trees and determined the importance of the different predictors. Results indicate that a combination of tree-, stand- and site-specific factors controls sap velocity patterns in the landscape, namely tree species, tree diameter, the stand density, geology and aspect. Compared to these predictors, spatial variability of atmospheric demand and soil moisture explains only a small fraction of the variability in the daily datasets. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, are correlated to the temporal dynamics of potential evaporation. Thus, transpiration estimates at the landscape scale would benefit from not only considering hydro-meteorological drivers, but also including tree, stand and site characteristics in order to improve the spatial representation of transpiration for hydrological and soil-vegetation-atmosphere transfer models.

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 .

Testing for Independence between Evolutionary Processes.

PubMed

Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

2016-09-01

Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

Topological Analysis and Gaussian Decision Tree: Effective Representation and Classification of Biosignals of Small Sample Size.

PubMed

Zhang, Zhifei; Song, Yang; Cui, Haochen; Wu, Jayne; Schwartz, Fernando; Qi, Hairong

2017-09-01

Bucking the trend of big data, in microdevice engineering, small sample size is common, especially when the device is still at the proof-of-concept stage. The small sample size, small interclass variation, and large intraclass variation, have brought biosignal analysis new challenges. Novel representation and classification approaches need to be developed to effectively recognize targets of interests with the absence of a large training set. Moving away from the traditional signal analysis in the spatiotemporal domain, we exploit the biosignal representation in the topological domain that would reveal the intrinsic structure of point clouds generated from the biosignal. Additionally, we propose a Gaussian-based decision tree (GDT), which can efficiently classify the biosignals even when the sample size is extremely small. This study is motivated by the application of mastitis detection using low-voltage alternating current electrokinetics (ACEK) where five categories of bisignals need to be recognized with only two samples in each class. Experimental results demonstrate the robustness of the topological features as well as the advantage of GDT over some conventional classifiers in handling small dataset. Our method reduces the voltage of ACEK to a safe level and still yields high-fidelity results with a short assay time. This paper makes two distinctive contributions to the field of biosignal analysis, including performing signal processing in the topological domain and handling extremely small dataset. Currently, there have been no related works that can efficiently tackle the dilemma between avoiding electrochemical reaction and accelerating assay process using ACEK.

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.

Constraining Centennial-Scale Ecosystem-Climate Interactions with a Pre-colonial Forest Reconstruction across the Upper Midwest and Northeastern United States

NASA Astrophysics Data System (ADS)

Matthes, J. H.; Dietze, M.; Fox, A. M.; Goring, S. J.; McLachlan, J. S.; Moore, D. J.; Poulter, B.; Quaife, T. L.; Schaefer, K. M.; Steinkamp, J.; Williams, J. W.

2014-12-01

Interactions between ecological systems and the atmosphere are the result of dynamic processes with system memories that persist from seconds to centuries. Adequately capturing long-term biosphere-atmosphere exchange within earth system models (ESMs) requires an accurate representation of changes in plant functional types (PFTs) through time and space, particularly at timescales associated with ecological succession. However, most model parameterization and development has occurred using datasets than span less than a decade. We tested the ability of ESMs to capture the ecological dynamics observed in paleoecological and historical data spanning the last millennium. Focusing on an area from the Upper Midwest to New England, we examined differences in the magnitude and spatial pattern of PFT distributions and ecotones between historic datasets and the CMIP5 inter-comparison project's large-scale ESMs. We then conducted a 1000-year model inter-comparison using six state-of-the-art biosphere models at sites that bridged regional temperature and precipitation gradients. The distribution of ecosystem characteristics in modeled climate space reveals widely disparate relationships between modeled climate and vegetation that led to large differences in long-term biosphere-atmosphere fluxes for this region. Model simulations revealed that both the interaction between climate and vegetation and the representation of ecosystem dynamics within models were important controls on biosphere-atmosphere exchange.

HD-MTL: Hierarchical Deep Multi-Task Learning for Large-Scale Visual Recognition.

PubMed

Fan, Jianping; Zhao, Tianyi; Kuang, Zhenzhong; Zheng, Yu; Zhang, Ji; Yu, Jun; Peng, Jinye

2017-02-09

In this paper, a hierarchical deep multi-task learning (HD-MTL) algorithm is developed to support large-scale visual recognition (e.g., recognizing thousands or even tens of thousands of atomic object classes automatically). First, multiple sets of multi-level deep features are extracted from different layers of deep convolutional neural networks (deep CNNs), and they are used to achieve more effective accomplishment of the coarseto- fine tasks for hierarchical visual recognition. A visual tree is then learned by assigning the visually-similar atomic object classes with similar learning complexities into the same group, which can provide a good environment for determining the interrelated learning tasks automatically. By leveraging the inter-task relatedness (inter-class similarities) to learn more discriminative group-specific deep representations, our deep multi-task learning algorithm can train more discriminative node classifiers for distinguishing the visually-similar atomic object classes effectively. Our hierarchical deep multi-task learning (HD-MTL) algorithm can integrate two discriminative regularization terms to control the inter-level error propagation effectively, and it can provide an end-to-end approach for jointly learning more representative deep CNNs (for image representation) and more discriminative tree classifier (for large-scale visual recognition) and updating them simultaneously. Our incremental deep learning algorithms can effectively adapt both the deep CNNs and the tree classifier to the new training images and the new object classes. Our experimental results have demonstrated that our HD-MTL algorithm can achieve very competitive results on improving the accuracy rates for large-scale visual recognition.

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.

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.

Brain reflections: A circuit-based framework for understanding information processing and cognitive control.

PubMed

Gratton, Gabriele

2018-03-01

Here, I propose a view of the architecture of the human information processing system, and of how it can be adapted to changing task demands (which is the hallmark of cognitive control). This view is informed by an interpretation of brain activity as reflecting the excitability level of neural representations, encoding not only stimuli and temporal contexts, but also action plans and task goals. The proposed cognitive architecture includes three types of circuits: open circuits, involved in feed-forward processing such as that connecting stimuli with responses and characterized by brief, transient brain activity; and two types of closed circuits, positive feedback circuits (characterized by sustained, high-frequency oscillatory activity), which help select and maintain representations, and negative feedback circuits (characterized by brief, low-frequency oscillatory bursts), which are instead associated with changes in representations. Feed-forward activity is primarily responsible for the spread of activation along the information processing system. Oscillatory activity, instead, controls this spread. Sustained oscillatory activity due to both local cortical circuits (gamma) and longer corticothalamic circuits (alpha and beta) allows for the selection of individuated representations. Through the interaction of these circuits, it also allows for the preservation of representations across different temporal spans (sensory and working memory) and their spread across the brain. In contrast, brief bursts of oscillatory activity, generated by novel and/or conflicting information, lead to the interruption of sustained oscillatory activity and promote the generation of new representations. I discuss how this framework can account for a number of psychological and behavioral phenomena. © 2017 Society for Psychophysiological Research.

Mapping Topographic Structure in White Matter Pathways with Level Set Trees

PubMed Central

Kent, Brian P.; Rinaldo, Alessandro; Yeh, Fang-Cheng; Verstynen, Timothy

2014-01-01

Fiber tractography on diffusion imaging data offers rich potential for describing white matter pathways in the human brain, but characterizing the spatial organization in these large and complex data sets remains a challenge. We show that level set trees–which provide a concise representation of the hierarchical mode structure of probability density functions–offer a statistically-principled framework for visualizing and analyzing topography in fiber streamlines. Using diffusion spectrum imaging data collected on neurologically healthy controls (N = 30), we mapped white matter pathways from the cortex into the striatum using a deterministic tractography algorithm that estimates fiber bundles as dimensionless streamlines. Level set trees were used for interactive exploration of patterns in the endpoint distributions of the mapped fiber pathways and an efficient segmentation of the pathways that had empirical accuracy comparable to standard nonparametric clustering techniques. We show that level set trees can also be generalized to model pseudo-density functions in order to analyze a broader array of data types, including entire fiber streamlines. Finally, resampling methods show the reliability of the level set tree as a descriptive measure of topographic structure, illustrating its potential as a statistical descriptor in brain imaging analysis. These results highlight the broad applicability of level set trees for visualizing and analyzing high-dimensional data like fiber tractography output. PMID:24714673

Computing all hybridization networks for multiple binary phylogenetic input trees.

PubMed

Albrecht, Benjamin

2015-07-30

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

Bayesian Networks for Modeling Dredging Decisions

DTIC Science & Technology

2011-10-01

change scenarios. Arctic Expert elicitation Netica Bacon et al . 2002 Identify factors that might lead to a change in land use from farming to...tree) algorithms developed by Lauritzen and Spiegelhalter (1988) and Jensen et al . (1990). Statistical inference is simply the process of...causality when constructing a Bayesian network (Kjaerulff and Madsen 2008, Darwiche 2009, Marcot et al . 2006). A knowledge representation approach is the

Querying Proofs

NASA Technical Reports Server (NTRS)

Aspinall, David; Denney, Ewen; Lueth, Christoph

2012-01-01

We motivate and introduce a query language PrQL designed for inspecting machine representations of proofs. PrQL natively supports hiproofs which express proof structure using hierarchical nested labelled trees. The core language presented in this paper is locally structured (first-order), with queries built using recursion and patterns over proof structure and rule names. We define the syntax and semantics of locally structured queries, demonstrate their power, and sketch some implementation experiments.

Learning object-to-class kernels for scene classification.

PubMed

Zhang, Lei; Zhen, Xiantong; Shao, Ling

2014-08-01

High-level image representations have drawn increasing attention in visual recognition, e.g., scene classification, since the invention of the object bank. The object bank represents an image as a response map of a large number of pretrained object detectors and has achieved superior performance for visual recognition. In this paper, based on the object bank representation, we propose the object-to-class (O2C) distances to model scene images. In particular, four variants of O2C distances are presented, and with the O2C distances, we can represent the images using the object bank by lower-dimensional but more discriminative spaces, called distance spaces, which are spanned by the O2C distances. Due to the explicit computation of O2C distances based on the object bank, the obtained representations can possess more semantic meanings. To combine the discriminant ability of the O2C distances to all scene classes, we further propose to kernalize the distance representation for the final classification. We have conducted extensive experiments on four benchmark data sets, UIUC-Sports, Scene-15, MIT Indoor, and Caltech-101, which demonstrate that the proposed approaches can significantly improve the original object bank approach and achieve the state-of-the-art performance.

Patterns of thinking about phylogenetic trees: A study of student learning and the potential of tree thinking to improve comprehension of biological concepts

NASA Astrophysics Data System (ADS)

Naegle, Erin

Evolution education is a critical yet challenging component of teaching and learning biology. There is frequently an emphasis on natural selection when teaching about evolution and conducting educational research. A full understanding of evolution, however, integrates evolutionary processes, such as natural selection, with the resulting evolutionary patterns, such as species divergence. Phylogenetic trees are models of evolutionary patterns. The perspective gained from understanding biology through phylogenetic analyses is referred to as tree thinking. Due to the increasing prevalence of tree thinking in biology, understanding how to read phylogenetic trees is an important skill for students to learn. Interpreting graphics is not an intuitive process, as graphical representations are semiotic objects. This is certainly true concerning phylogenetic tree interpretation. Previous research and anecdotal evidence report that students struggle to correctly interpret trees. The objective of this research was to describe and investigate the rationale underpinning the prior knowledge of introductory biology students' tree thinking Understanding prior knowledge is valuable as prior knowledge influences future learning. In Chapter 1, qualitative methods such as semi-structured interviews were used to explore patterns of student rationale in regard to tree thinking. Seven common tree thinking misconceptions are described: (1) Equating the degree of trait similarity with the extent of relatedness, (2) Environmental change is a necessary prerequisite to evolution, (3) Essentialism of species, (4) Evolution is inherently progressive, (5) Evolution is a linear process, (6) Not all species are related, and (7) Trees portray evolution through the hybridization of species. These misconceptions are based in students' incomplete or incorrect understanding of evolution. These misconceptions are often reinforced by the misapplication of cultural conventions to make sense of trees. Chapter 2 explores the construction, validity, and reliability of a tree thinking concept inventory. Concept inventories are research based instruments that diagnose faulty reasoning among students. Such inventories are tools for improving teaching and learning of concepts. Test scores indicate that tree thinking misconceptions are held by novice and intermediate biology students. Finally, Chapter 3 presents a tree thinking rubric. The rubric aids teachers in selecting and improving introductory tree thinking learning exercises that address students' tree thinking misconceptions.

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...

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.

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

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.

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.

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.

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.

Adaptive compressive ghost imaging based on wavelet trees and sparse representation.

PubMed

Yu, Wen-Kai; Li, Ming-Fei; Yao, Xu-Ri; Liu, Xue-Feng; Wu, Ling-An; Zhai, Guang-Jie

2014-03-24

Compressed sensing is a theory which can reconstruct an image almost perfectly with only a few measurements by finding its sparsest representation. However, the computation time consumed for large images may be a few hours or more. In this work, we both theoretically and experimentally demonstrate a method that combines the advantages of both adaptive computational ghost imaging and compressed sensing, which we call adaptive compressive ghost imaging, whereby both the reconstruction time and measurements required for any image size can be significantly reduced. The technique can be used to improve the performance of all computational ghost imaging protocols, especially when measuring ultra-weak or noisy signals, and can be extended to imaging applications at any wavelength.