Science.gov

Sample records for honeylocust trees

  1. Trees

    ERIC Educational Resources Information Center

    Al-Khaja, Nawal

    2007-01-01

    This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

  2. Alcohol co-production from tree crops

    SciTech Connect

    Seibert, M.; Folger, G.; Milne, T.

    1982-06-01

    A concept for the sustainable production of alcohol from fermentable substrates produced on an annual basis by the reproductive organs (pods, fruits, nuts, berries, etc.) of tree crops is presented. The advantages of tree-crop systems include suitability for use on marginal land, potential productivity equivalent to row crops, minimal maintenance and energy-input requirements, environmental compatibility, and the possibility of co-product production. Honeylocust, mesquite, and persimmon are examined as potential US tree-crop species. Other species not previously considered, including osage orange and breadfruit, are suggested as tree-crop candidates for North America and the tropical developing world, respectively. Fermentation of tree-crop organs and the economics of tree-crop systems are also discussed. Currently the greatest area of uncertainty lies in actual pod or fruit yields one can expect from large tree farms under real life conditions. However, ballpark ethanol yield estimates of from 880 to 3470 l hectare/sup -1/ (94 to 400 gal acre/sup -1/) justify further consideration of tree crop systems.

  3. Tree Scanning

    PubMed Central

    Templeton, Alan R.; Maxwell, Taylor; Posada, David; Stengård, Jari H.; Boerwinkle, Eric; Sing, Charles F.

    2005-01-01

    We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci. PMID:15371364

  4. Tree Lifecycle.

    ERIC Educational Resources Information Center

    Nature Study, 1998

    1998-01-01

    Presents a Project Learning Tree (PLT) activity that has students investigate and compare the lifecycle of a tree to other living things and the tree's role in the ecosystem. Includes background material as well as step-by-step instructions, variation and enrichment ideas, assessment opportunities, and student worksheets. (SJR)

  5. Talking Trees

    ERIC Educational Resources Information Center

    Tolman, Marvin

    2005-01-01

    Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

  6. Tree Amigos.

    ERIC Educational Resources Information Center

    Center for Environmental Study, Grand Rapids, MI.

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

  7. Greenhouse trees

    SciTech Connect

    Hanover, J.W.; Hart, J.W.

    1980-05-09

    Michigan State University has been conducting research on growth control of woody plants with emphasis on commercial plantations. The objective was to develop the optimum levels for the major factors that affect tree seedling growth and development so that high quality plants can be produced for a specific use. This article describes the accelerated-optimal-growth (AOG) concept, describes precautions to take in its application, and shows ways to maximize the potential of AOG for producing ornamental trees. Factors considered were container growing system; protective culture including light, temperature, mineral nutrients, water, carbon dioxide, growth regulators, mycorrhizae, growing media, competition, and pests; size of seedlings; and acclamation. 1 table. (DP)

  8. Audubon Tree Study Program.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    Included are an illustrated student reader, "The Story of Trees," a leaders' guide, and a large tree chart with 37 colored pictures. The student reader reviews several aspects of trees: a definition of a tree; where and how trees grow; flowers, pollination and seed production; how trees make their food; how to recognize trees; seasonal changes;…

  9. Visualizing phylogenetic trees using TreeView.

    PubMed

    Page, Roderic D M

    2002-08-01

    TreeView provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE-PUZZLE, and ClustalX. While some phylogenetic programs (such as the Macintosh version of PAUP*) have excellent tree printing facilities, many programs do not have the ability to generate publication quality trees. TreeView addresses this need. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*. PMID:18792942

  10. Technical Tree Climbing.

    ERIC Educational Resources Information Center

    Jenkins, Peter

    Tree climbing offers a safe, inexpensive adventure sport that can be performed almost anywhere. Using standard procedures practiced in tree surgery or rock climbing, almost any tree can be climbed. Tree climbing provides challenge and adventure as well as a vigorous upper-body workout. Tree Climbers International classifies trees using a system…

  11. The Tree Worker's Manual.

    ERIC Educational Resources Information Center

    Smithyman, S. J.

    This manual is designed to prepare students for entry-level positions as tree care professionals. Addressed in the individual chapters of the guide are the following topics: the tree service industry; clothing, eqiupment, and tools; tree workers; basic tree anatomy; techniques of pruning; procedures for climbing and working in the tree; aerial…

  12. Tree Tectonics

    NASA Astrophysics Data System (ADS)

    Vogt, Peter R.

    2004-09-01

    Nature often replicates her processes at different scales of space and time in differing media. Here a tree-trunk cross section I am preparing for a dendrochronological display at the Battle Creek Cypress Swamp Nature Sanctuary (Calvert County, Maryland) dried and cracked in a way that replicates practically all the planform features found along the Mid-Oceanic Ridge (see Figure 1). The left-lateral offset of saw marks, contrasting with the right-lateral ``rift'' offset, even illustrates the distinction between transcurrent (strike-slip) and transform faults, the latter only recognized as a geologic feature, by J. Tuzo Wilson, in 1965. However, wood cracking is but one of many examples of natural processes that replicate one or several elements of lithospheric plate tectonics. Many of these examples occur in everyday venues and thus make great teaching aids, ``teachable'' from primary school to university levels. Plate tectonics, the dominant process of Earth geology, also occurs in miniature on the surface of some lava lakes, and as ``ice plate tectonics'' on our frozen seas and lakes. Ice tectonics also happens at larger spatial and temporal scales on the Jovian moons Europa and perhaps Ganymede. Tabletop plate tectonics, in which a molten-paraffin ``asthenosphere'' is surfaced by a skin of congealing wax ``plates,'' first replicated Mid-Oceanic Ridge type seafloor spreading more than three decades ago. A seismologist (J. Brune, personal communication, 2004) discovered wax plate tectonics by casually and serendipitously pulling a stick across a container of molten wax his wife and daughters had used in making candles. Brune and his student D. Oldenburg followed up and mirabile dictu published the results in Science (178, 301-304).

  13. The Needs of Trees

    ERIC Educational Resources Information Center

    Boyd, Amy E.; Cooper, Jim

    2004-01-01

    Tree rings can be used not only to look at plant growth, but also to make connections between plant growth and resource availability. In this lesson, students in 2nd-4th grades use role-play to become familiar with basic requirements of trees and how availability of those resources is related to tree ring sizes and tree growth. These concepts can…

  14. Fault tree handbook

    SciTech Connect

    Haasl, D.F.; Roberts, N.H.; Vesely, W.E.; Goldberg, F.F.

    1981-01-01

    This handbook describes a methodology for reliability analysis of complex systems such as those which comprise the engineered safety features of nuclear power generating stations. After an initial overview of the available system analysis approaches, the handbook focuses on a description of the deductive method known as fault tree analysis. The following aspects of fault tree analysis are covered: basic concepts for fault tree analysis; basic elements of a fault tree; fault tree construction; probability, statistics, and Boolean algebra for the fault tree analyst; qualitative and quantitative fault tree evaluation techniques; and computer codes for fault tree evaluation. Also discussed are several example problems illustrating the basic concepts of fault tree construction and evaluation.

  15. 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

  16. Evolution of tree nutrition.

    PubMed

    Raven, John A; Andrews, Mitchell

    2010-09-01

    Using a broad definition of trees, the evolutionary origins of trees in a nutritional context is considered using data from the fossil record and molecular phylogeny. Trees are first known from the Late Devonian about 380 million years ago, originated polyphyletically at the pteridophyte grade of organization; the earliest gymnosperms were trees, and trees are polyphyletic in the angiosperms. Nutrient transporters, assimilatory pathways, homoiohydry (cuticle, intercellular gas spaces, stomata, endohydric water transport systems including xylem and phloem-like tissue) and arbuscular mycorrhizas preceded the origin of trees. Nutritional innovations that began uniquely in trees were the seed habit and, certainly (but not necessarily uniquely) in trees, ectomycorrhizas, cyanobacterial, actinorhizal and rhizobial (Parasponia, some legumes) diazotrophic symbioses and cluster roots. PMID:20581011

  17. Tree Classification Software

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1993-01-01

    This paper introduces the IND Tree Package to prospective users. IND does supervised learning using classification trees. This learning task is a basic tool used in the development of diagnosis, monitoring and expert systems. The IND Tree Package was developed as part of a NASA project to semi-automate the development of data analysis and modelling algorithms using artificial intelligence techniques. The IND Tree Package integrates features from CART and C4 with newer Bayesian and minimum encoding methods for growing classification trees and graphs. The IND Tree Package also provides an experimental control suite on top. The newer features give improved probability estimates often required in diagnostic and screening tasks. The package comes with a manual, Unix 'man' entries, and a guide to tree methods and research. The IND Tree Package is implemented in C under Unix and was beta-tested at university and commercial research laboratories in the United States.

  18. Chem-Is-Tree.

    ERIC Educational Resources Information Center

    Barry, Dana M.

    1997-01-01

    Provides details on the chemical composition of trees including a definition of wood. Also includes an activity on anthocyanins as well as a discussion of the resistance of wood to solvents and chemicals. Lists interesting products from trees. (DDR)

  19. Decision-Tree Program

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  20. Winter Birch Trees

    ERIC Educational Resources Information Center

    Sweeney, Debra; Rounds, Judy

    2011-01-01

    Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

  1. Illumination Under Trees

    SciTech Connect

    Max, N

    2002-08-19

    This paper is a survey of the author's work on illumination and shadows under trees, including the effects of sky illumination, sun penumbras, scattering in a misty atmosphere below the trees, and multiple scattering and transmission between leaves. It also describes a hierarchical image-based rendering method for trees.

  2. Minnesota's Forest Trees. Revised.

    ERIC Educational Resources Information Center

    Miles, William R.; Fuller, Bruce L.

    This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

  3. The Wish Tree Project

    ERIC Educational Resources Information Center

    Brooks, Sarah DeWitt

    2010-01-01

    This article describes the author's experience in implementing a Wish Tree project in her school in an effort to bring the school community together with a positive art-making experience during a potentially stressful time. The concept of a wish tree is simple: plant a tree; provide tags and pencils for writing wishes; and encourage everyone to…

  4. Diary of a Tree.

    ERIC Educational Resources Information Center

    Srulowitz, Frances

    1992-01-01

    Describes an activity to develop students' skills of observation and recordkeeping by studying the growth of a tree's leaves during the spring. Children monitor the growth of 11 tress over a 2-month period, draw pictures of the tree at different stages of growth, and write diaries of the tree's growth. (MDH)

  5. Distributed Contour Trees

    SciTech Connect

    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.

  6. Growth of a Pine Tree

    ERIC Educational Resources Information Center

    Rollinson, Susan Wells

    2012-01-01

    The growth of a pine tree is examined by preparing "tree cookies" (cross-sectional disks) between whorls of branches. The use of Christmas trees allows the tree cookies to be obtained with inexpensive, commonly available tools. Students use the tree cookies to investigate the annual growth of the tree and how it corresponds to the number of whorls…

  7. Tree planters notes. Volume 43, Number 3, Summer 1992. Quarterly report

    SciTech Connect

    Mangold, R.; Nisley, R.; Karrfalt, R.; Landis, T.; Lantz, C.

    1992-01-01

    Contents: survival and growth of planted alaska-cedar seedling in southeast southeast alaska; propagation of loblolly, slash, and longleaf pine from needle fascicles; moisture determination on seeds of honeylocust and mimosa; performance of himalayan blue pine in the northeastern united states; advantages of an effective weed control program for populus hybrids; pales weevil: a serious threat to longleaf pine production; costs and cost component trends of trends of hand and machine planting in the southern united states (1952 to 1990); comparison of a drill-type seeder and a vacuum-drum precision seeder in a virginia loblolly pine nursery; missoula technology and development center's nursery and reforestation programs.

  8. Species integrity in trees.

    PubMed

    Ortiz-Barrientos, Daniel; Baack, Eric J

    2014-09-01

    From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space. PMID:25155715

  9. Trees Are Terrific!

    ERIC Educational Resources Information Center

    Braus, Judy, Ed.

    1992-01-01

    Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. Contents are organized into the following sections: (1) "What Makes a Tree a Tree?," including information…

  10. The Flame Tree

    ERIC Educational Resources Information Center

    Lewis, Richard

    2004-01-01

    Lewis's own experiences living in Indonesia are fertile ground for telling "a ripping good story," one found in "The Flame Tree." He hopes people will enjoy the tale and appreciate the differences of an unfamiliar culture. The excerpt from "The Flame Tree" will reel readers in quickly.

  11. Trees for Mother Earth.

    ERIC Educational Resources Information Center

    Greer, Sandy

    1993-01-01

    Describes Trees for Mother Earth, a program in which secondary students raise funds to buy fruit trees to plant during visits to the Navajo Reservation. Benefits include developing feelings of self-worth among participants, promoting cultural exchange and understanding, and encouraging self-sufficiency among the Navajo. (LP)

  12. Tree Topology Estimation.

    PubMed

    Estrada, Rolando; Tomasi, Carlo; Schmidler, Scott C; Farsiu, Sina

    2015-08-01

    Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree - what connects to what - from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar graph, and the inverse problem of reconstructing the topology of the tree from that of the graph is ill-posed. We regularize this problem with a generative, parametric tree-growth model. Under this model, reconstruction is possible in linear time if one knows the direction of each edge in the graph - which edge endpoint is closer to the root of the tree - but becomes NP-hard if the directions are not known. For the latter case, we present a heuristic search algorithm to estimate the most likely topology of a rooted, three-dimensional tree from a single two-dimensional image. Experimental results on retinal vessel, plant root, and synthetic tree data sets show that our methodology is both accurate and efficient. PMID:26353004

  13. Structural Equation Model Trees

    ERIC Educational Resources Information Center

    Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

    2013-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

  14. CSI for Trees

    ERIC Educational Resources Information Center

    Rubino, Darrin L.; Hanson, Deborah

    2009-01-01

    The circles and patterns in a tree's stem tell a story, but that story can be a mystery. Interpreting the story of tree rings provides a way to heighten the natural curiosity of students and help them gain insight into the interaction of elements in the environment. It also represents a wonderful opportunity to incorporate the nature of science.…

  15. Tree nut oils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The major tree nuts include almonds, Brazil nuts, cashew nuts, hazelnuts, macadamia nuts, pecans, pine nuts, pistachio nuts, and walnuts. Tree nut oils are appreciated in food applications because of their flavors and are generally more expensive than other gourmet oils. Research during the last de...

  16. From Family Trees to Decision Trees.

    ERIC Educational Resources Information Center

    Trobian, Helen R.

    This paper is a preliminary inquiry by a non-mathematician into graphic methods of sequential planning and ways in which hierarchical analysis and tree structures can be helpful in developing interest in the use of mathematical modeling in the search for creative solutions to real-life problems. Highlights include a discussion of hierarchical…

  17. Phylogenetic trees in bioinformatics

    SciTech Connect

    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 the 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.

  18. Lazy decision trees

    SciTech Connect

    Friedman, J.H.; Yun, Yeogirl; Kohavi, R.

    1996-12-31

    Lazy learning algorithms, exemplified by nearest-neighbor algorithms, do not induce a concise hypothesis from a given training set; the inductive process is delayed until a test instance is given. Algorithms for constructing decision trees, such as C4.5, ID3, and CART create a single {open_quotes}best{close_quotes} decision tree during the training phase, and this tree is then used to classify test instances. The tests at the nodes of the constructed tree are good on average, but there may be better tests for classifying a specific instance. We propose a lazy decision tree algorithm-LazyDT-that conceptually constructs the {open_quotes}best{close_quote} decision tree for each test instance. In practice, only a path needs to be constructed, and a caching scheme makes the algorithm fast. The algorithm is robust with respect to missing values without resorting to the complicated methods usually seen in induction of decision trees. Experiments on real and artificial problems are presented.

  19. Learning classification trees

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1991-01-01

    Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

  20. Evolutionary tree reconstruction

    NASA Technical Reports Server (NTRS)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

  1. 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.

  2. Loops and trees

    NASA Astrophysics Data System (ADS)

    Caron-Huot, S.

    2011-05-01

    We investigate relations between loop and tree amplitudes in quantum field theory that involve putting on-shell some loop propagators. This generalizes the so-called Feynman tree theorem which is satisfied at 1-loop. Exploiting retarded boundary conditions, we give a generalization to ℓ-loop expressing the loops as integrals over the on-shell phase space of exactly ℓ particles. We argue that the corresponding integrand for ℓ > 2 does not involve the forward limit of any physical tree amplitude, except in planar gauge theories. In that case we explicitly construct the relevant physical amplitude. Beyond the planar limit, abandoning direct integral representations, we propose that loops continue to be determined implicitly by the forward limit of physical connected trees, and we formulate a precise conjecture along this line. Finally, we set up technology to compute forward amplitudes in supersymmetric theories, in which specific simplifications occur.

  3. Structural Equation Model Trees

    PubMed Central

    Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

    2015-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree structures that separate a data set recursively into subsets with significantly different parameter estimates in a SEM. SEM Trees provide means for finding covariates and covariate interactions that predict differences in structural parameters in observed as well as in latent space and facilitate theory-guided exploration of empirical data. We describe the methodology, discuss theoretical and practical implications, and demonstrate applications to a factor model and a linear growth curve model. PMID:22984789

  4. Tree Nut Allergies

    MedlinePlus

    ... tree nut used on the label. Read all product labels carefully before purchasing and consuming any item. Ingredients ... Getting Started Newly Diagnosed Emergency Care Plan Food Labels Mislabeled Products Tips for Managing Food Allergies Resources For... Most ...

  5. The tree BVOC index.

    PubMed

    Simpson, J R; McPherson, E G

    2011-01-01

    Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes in BVOC emissions are calculated as the result of transitioning to a lower-emitting species mix in future planting. A simplified method for calculating the emissions reduction and a Tree BVOC index based on the calculated reduction is described. An example illustrates the use of the index as a tool for implementation and monitoring of a tree program designed to reduce BVOC emissions as a control measure being developed as part of the State Implementation Plan (SIP) for the Sacramento Federal Nonattainment Area. PMID:21435760

  6. Generalized constructive tree weights

    SciTech Connect

    Rivasseau, Vincent E-mail: adrian.tanasa@ens-lyon.org; Tanasa, Adrian E-mail: adrian.tanasa@ens-lyon.org

    2014-04-15

    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 to 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.

  7. Tea tree oil.

    PubMed

    Larson, David; Jacob, Sharon E

    2012-01-01

    Tea tree oil is an increasingly popular ingredient in a variety of household and cosmetic products, including shampoos, massage oils, skin and nail creams, and laundry detergents. Known for its potential antiseptic properties, it has been shown to be active against a variety of bacteria, fungi, viruses, and mites. The oil is extracted from the leaves of the tea tree via steam distillation. This essential oil possesses a sharp camphoraceous odor followed by a menthol-like cooling sensation. Most commonly an ingredient in topical products, it is used at a concentration of 5% to 10%. Even at this concentration, it has been reported to induce contact sensitization and allergic contact dermatitis reactions. In 1999, tea tree oil was added to the North American Contact Dermatitis Group screening panel. The latest prevalence rates suggest that 1.4% of patients referred for patch testing had a positive reaction to tea tree oil. PMID:22653070

  8. Tree-bank grammars

    SciTech Connect

    Charniak, E.

    1996-12-31

    By a {open_quotes}tree-bank grammar{close_quotes} we mean a context-free grammar created by reading the production rules directly from hand-parsed sentences in a tree bank. Common wisdom has it that such grammars do not perform well, though we know of no published data on the issue. The primary purpose of this paper is to show that the common wisdom is wrong. In particular, we present results on a tree-bank grammar based on the Penn Wall Street Journal tree bank. To the best of our knowledge, this grammar outperforms all other non-word-based statistical parsers/grammars on this corpus. That is, it outperforms parsers that consider the input as a string of tags and ignore the actual words of the corpus.

  9. Leonardo's Tree Theory.

    ERIC Educational Resources Information Center

    Werner, Suzanne K.

    2003-01-01

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

  10. Trees for reclamation

    SciTech Connect

    Not Available

    1980-01-01

    Land reclamation programs sponsored by several state forestry organizations are summarized in these presentations. The use of trees as a preferred specie for revegetation of surface mined lands is addressed. Modern methods of forestry can be used to make land economically and aesthetically acceptable. Tree planting techniques are presented and the role of Mycorrhizae is discussed. There are 30 papers included in this proceedings. States represented include: Alabama, Arkansas, Georgia, Illinois, Kansas, Kentucky, Maryland, Virginia, Iowa, Ohio, Pennsylvania, and West Virginia.

  11. Tree Topology Estimation

    PubMed Central

    Estrada, Rolando; Tomasi, Carlo; Schmidler, Scott C.; Farsiu, Sina

    2015-01-01

    Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree—what connects to what—from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar graph, and the inverse problem of reconstructing the topology of the tree from that of the graph is ill-posed. We regularize this problem with a generative, parametric tree-growth model. Under this model, reconstruction is possible in linear time if one knows the direction of each edge in the graph—which edge endpoint is closer to the root of the tree—but becomes NP-hard if the directions are not known. For the latter case, we present a heuristic search algorithm to estimate the most likely topology of a rooted, three-dimensional tree from a single two-dimensional image. Experimental results on retinal vessel, plant root, and synthetic tree datasets show that our methodology is both accurate and efficient. PMID:26353004

  12. How Trees Can Save Energy.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1991-01-01

    This document might easily have been called "How To Use Trees To Save Energy". It presents the energy saving advantages of landscaping the home and community with trees. The discussion includes: (1) landscaping advice to obtain the benefits of tree shade; (2) the heat island phenomenon in cities; (3) how and where to properly plant trees for…

  13. Aging on Parisi's Tree

    NASA Astrophysics Data System (ADS)

    Bouchaud, J.-P.; Dean, D. S.

    1995-03-01

    We present a detailed study of simple “tree" models for off equilibrium dynamics and aging in glassy systems. The simplest tree describes the landscape of a random energy model, whereas multifurcating trees occur in the solution of the Sherrington-Kirkpatrick model. An important ingredient taken from these models is the exponential distribution of deep free-energies, which translate into a power-law distribution of the residence time within metastable “valleys". These power law distributions have infinite mean in the spin-glass phase and this leads to the aging phenomenon. To each level of the tree is associated an overlap and the exponent of the time distribution. We solve these models for a finite (but arbitrary) number of levels and show that a two-level tree accounts very well for many experimental observations (thermoremanent magnetization, a.c. susceptibility, second noise spectrum....). We introduce the idea that the deepest levels of the tree correspond to equilibrium dynamics whereas the upper levels correspond to aging. Temperature cycling experiments suggest that the borderline between the two is temperature dependent. The spin-glass transition corresponds to the temperature at which the uppermost level is put out of equilibrium but is subsequently followed by a sequence of (dynamical) phase transitions corresponding to non equilibrium dynamics within deeper and deeper levels. We tentatively try to relate this “tree" picture to the real space “droplet" model, and speculate on how the final description of spin-glasses might look like.

  14. Reinforcement Learning Trees

    PubMed Central

    Zhu, Ruoqing; Zeng, Donglin; Kosorok, Michael R.

    2015-01-01

    In this paper, we introduce a new type of tree-based method, reinforcement learning trees (RLT), which exhibits significantly improved performance over traditional methods such as random forests (Breiman, 2001) under high-dimensional settings. The innovations are three-fold. First, the new method implements reinforcement learning at each selection of a splitting variable during the tree construction processes. By splitting on the variable that brings the greatest future improvement in later splits, rather than choosing the one with largest marginal effect from the immediate split, the constructed tree utilizes the available samples in a more efficient way. Moreover, such an approach enables linear combination cuts at little extra computational cost. Second, we propose a variable muting procedure that progressively eliminates noise variables during the construction of each individual tree. The muting procedure also takes advantage of reinforcement learning and prevents noise variables from being considered in the search for splitting rules, so that towards terminal nodes, where the sample size is small, the splitting rules are still constructed from only strong variables. Last, we investigate asymptotic properties of the proposed method under basic assumptions and discuss rationale in general settings. PMID:26903687

  15. Tree nut allergens.

    PubMed

    Roux, Kenneth H; Teuber, Suzanne S; Sathe, Shridhar K

    2003-08-01

    Allergic reactions to tree nuts can be serious and life threatening. Considerable research has been conducted in recent years in an attempt to characterize those allergens that are most responsible for allergy sensitization and triggering. Both native and recombinant nut allergens have been identified and characterized and, for some, the IgE-reactive epitopes described. Some allergens, such as lipid transfer proteins, profilins, and members of the Bet v 1-related family, represent minor constituents in tree nuts. These allergens are frequently cross-reactive with other food and pollen homologues, and are considered panallergens. Others, such as legumins, vicilins, and 2S albumins, represent major seed storage protein constituents of the nuts. The allergenic tree nuts discussed in this review include those most commonly responsible for allergic reactions such as hazelnut, walnut, cashew, and almond as well as those less frequently associated with allergies including pecan, chestnut, Brazil nut, pine nut, macadamia nut, pistachio, coconut, Nangai nut, and acorn. PMID:12915766

  16. Predictive Classification Trees

    NASA Astrophysics Data System (ADS)

    Dlugosz, Stephan; Müller-Funk, Ulrich

    CART (Breiman et al., Classification and Regression Trees, Chapman and Hall, New York, 1984) and (exhaustive) CHAID (Kass, Appl Stat 29:119-127, 1980) figure prominently among the procedures actually used in data based management, etc. CART is a well-established procedure that produces binary trees. CHAID, in contrast, admits multiple splittings, a feature that allows to exploit the splitting variable more extensively. On the other hand, that procedure depends on premises that are questionable in practical applications. This can be put down to the fact that CHAID relies on simultaneous Chi-Square- resp. F-tests. The null-distribution of the second test statistic, for instance, relies on the normality assumption that is not plausible in a data mining context. Moreover, none of these procedures - as implemented in SPSS, for instance - take ordinal dependent variables into account. In the paper we suggest an alternative tree-algorithm that: Requires explanatory categorical variables

  17. The gene tree delusion.

    PubMed

    Springer, Mark S; Gatesy, John

    2016-01-01

    Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are

  18. 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

  19. Tree-Ties.

    ERIC Educational Resources Information Center

    Gresczyk, Rick

    Created to help students understand how plants were used for food, for medicine, and for arts and crafts among the Ojibwe (Chippewa) Indians, the game Tree-Ties combines earth and social sciences within a specific culture. The game requires mutual respect, understanding, and agreement to succeed. Sounding like the word "treaties", the title is a…

  20. Christmas Tree Category Manual.

    ERIC Educational Resources Information Center

    Bowman, James S.; Turmel, Jon P.

    This manual provides information needed to meet the standards for pesticide applicator certification. Pests and diseases of christmas tree plantations are identified and discussed. Section one deals with weeds and woody plants and the application, formulation and effects of herbicides in controlling them. Section two discusses specific diseases…

  1. Tree theorem for inflation

    SciTech Connect

    Weinberg, Steven

    2008-09-15

    It is shown that the generating function for tree graphs in the ''in-in'' formalism may be calculated by solving the classical equations of motion subject to certain constraints. This theorem is illustrated by application to the evolution of a single inflaton field in a Robertson-Walker background.

  2. A Universal Phylogenetic Tree.

    ERIC Educational Resources Information Center

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  3. MPI File Tree Walk

    Energy Science and Technology Software Center (ESTSC)

    2007-04-30

    MPI-FTW is a scalable MPI based software application that navigates a directory tree by dynamically allocating processes to navigate sub-directories found. Upon completion, MPI-FTW provides statistics on the number of directories found, files found, and time to complete. Inaddition, commands can be executed at each directory level.

  4. Starting Trees from Cuttings.

    ERIC Educational Resources Information Center

    Kramer, David C.

    1983-01-01

    Describes a procedure for starting tree cuttings from woody plants, explaining "lag time," recommending materials, and giving step-by-step instructions for rooting and planting. Points out species which are likely candidates for cuttings and provides tips for teachers for developing a unit. (JM)

  5. The Medicine Tree.

    ERIC Educational Resources Information Center

    Brokenleg, Martin

    2000-01-01

    Demographic changes in population continue to bring children of different cultural backgrounds to classrooms. This article provides suggestions teachers and counselors can use to bridge cultures. Using the parable of a medicine tree, it explains how no society can endure without caring for its young. (Author/JDM)

  6. Phylogenics & Tree-Thinking

    ERIC Educational Resources Information Center

    Baum, David A.; Offner, Susan

    2008-01-01

    Phylogenetic trees, which are depictions of the inferred evolutionary relationships among a set of species, now permeate almost all branches of biology and are appearing in increasing numbers in biology textbooks. While few state standards explicitly require knowledge of phylogenetics, most require some knowledge of evolutionary biology, and many…

  7. Trees at the Center.

    ERIC Educational Resources Information Center

    Flannery, Maura

    1998-01-01

    Recommends introducing students to biology using a topical focus that can offer intriguing perspectives on the discipline. Describes a biology course that uses trees as a topical focus. Presents a list of literary resources and reviews student interactions. Contains 50 references. (DDR)

  8. Arbutus unedo, Strawberry Tree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Encylopedia of Fruit and Nuts is designed as a research reference source on temperate and tropical fruit and nut crops. Strawberry tree or madrone is native to the Mediterranean region of southern Europe (Arbutus unedo L., Ericaceae) with a relict population in Ireland, as well as in North Ameri...

  9. The Sacred Tree.

    ERIC Educational Resources Information Center

    Lethbridge Univ. (Alberta).

    Designed as a text for high school students and adults, this illustrated book presents ethical concepts and teachings of Native societies throughout North America concerning the nature and possibilities of human existence. The final component of a course in self-discovery and development, the book begins with the legend of the "Sacred Tree"…

  10. Digging Deeper with Trees.

    ERIC Educational Resources Information Center

    Growing Ideas, 2001

    2001-01-01

    Describes hands-on science areas that focus on trees. A project on leaf pigmentation involves putting crushed leaves in a test tube with solvent acetone to dissolve pigment. In another project, students learn taxonomy by sorting and classifying leaves based on observable characteristics. Includes a language arts connection. (PVD)

  11. Hug a Tree!

    ERIC Educational Resources Information Center

    Rockwell, Robert E.; And Others

    1983-01-01

    Methods for teaching pupils to use their senses to explore colors, shapes, textures, and sounds of the great outdoors are described. Ideas include: (1) having children hug their own special tree; (2) looking for geometric shapes in nature; (3) taking nocturnal nature walks; (4) building a track for racing insects; and (5) collecting objects with…

  12. Building Your Own Abseil Tree.

    ERIC Educational Resources Information Center

    Barnett, Des

    2002-01-01

    The foot and mouth crisis forced many British outdoor education providers to develop new options. The construction of an abseiling tree is described, which requires a living, healthy, straight tree with a trunk thick enough to remain stable under load and with few branches in the lower 15-20 meters. An abseil tree code of practice is presented.…

  13. The Re-Think Tree.

    ERIC Educational Resources Information Center

    Gear, Jim

    1993-01-01

    The Re-Think Tree is a simple framework to help individuals assess and improve their behaviors related to environmental issues. The branches of the tree in order of priority are refuse, reduce, re-use, and recycle. Roots of the tree include such things as public opinion, education, and watchdog groups. (KS)

  14. Our Air: Unfit for Trees.

    ERIC Educational Resources Information Center

    Dochinger, Leon S.

    To help urban, suburban, and rural tree owners know about air pollution's effects on trees and their tolerance and intolerance to pollutants, the USDA Forest Service has prepared this booklet. It answers the following questions about atmospheric pollution: Where does it come from? What can it do to trees? and What can we do about it? In addition,…

  15. The Tree Worker's Manual. [Revised.

    ERIC Educational Resources Information Center

    Lilly, S. J.

    This manual acquaints readers with the general operations of the tree care industry. The manual covers subjects important to a tree worker and serves as a training aid for workers at the entry level as tree care professionals. Each chapter begins with a set of objectives and may include figures, tables, and photographs. Ten chapters are included:…

  16. The Hopi Fruit Tree Book.

    ERIC Educational Resources Information Center

    Nyhuis, Jane

    Referring as often as possible to traditional Hopi practices and to materials readily available on the reservation, the illustrated booklet provides information on the care and maintenance of young fruit trees. An introduction to fruit trees explains the special characteristics of new trees, e.g., grafting, planting pits, and watering. The…

  17. Building up rhetorical structure trees

    SciTech Connect

    Marcu, D.

    1996-12-31

    I use the distinction between the nuclei and the satellites that pertain to discourse relations to introduce a compositionality criterion for discourse trees. I provide a first-order formalization of rhetorical structure trees and, on its basis, I derive an algorithm that constructs all the valid rhetorical trees that can be associated with a given discourse.

  18. New Life From Dead Trees

    ERIC Educational Resources Information Center

    DeGraaf, Richard M.

    1978-01-01

    There are numerous bird species that will nest only in dead or dying trees. Current forestry practices include clearing forests of these snags, or dead trees. This practice is driving many species out of the forests. An illustrated example of bird succession in and on a tree is given. (MA)

  19. PoInTree: a polar and interactive phylogenetic tree.

    PubMed

    Carreras, Marco; Marco, Cerreras; Gianti, Eleonora; Eleonora, Gianti; Sartori, Luca; Luca, Sartori; Plyte, Simon Edward; Edward, Plyte Simon; Isacchi, Antonella; Antonella, Isacchi; Bosotti, Roberta; Roberta, Bosotti

    2005-02-01

    PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize and customize phylogenetic trees in a polar interactive and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software). PMID:16144524

  20. Tree Colors: Color Schemes for Tree-Structured Data.

    PubMed

    Tennekes, Martijn; de Jonge, Edwin

    2014-12-01

    We present a method to map tree structures to colors from the Hue-Chroma-Luminance color model, which is known for its well balanced perceptual properties. The Tree Colors method can be tuned with several parameters, whose effect on the resulting color schemes is discussed in detail. We provide a free and open source implementation with sensible parameter defaults. Categorical data are very common in statistical graphics, and often these categories form a classification tree. We evaluate applying Tree Colors to tree structured data with a survey on a large group of users from a national statistical institute. Our user study suggests that Tree Colors are useful, not only for improving node-link diagrams, but also for unveiling tree structure in non-hierarchical visualizations. PMID:26356921

  1. Rate of tree carbon accumulation increases continuously with tree size.

    PubMed

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

    2014-03-01

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence. PMID:24429523

  2. Rate of tree carbon accumulation increases continuously with tree size

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  3. Women, land, and trees.

    PubMed

    1999-07-01

    This article discusses women's land rights in the context of the findings of the paper, "Women's Land Rights in the Transition to Individualized Ownership: Implications for Tree Resource Management in Western Ghana." The study showed that customary land tenure institutions have evolved toward individualized systems, which provide incentives to invest in tree planting. In effect, individualization of land tenure had strengthened women's land rights through inter vivos gifts. However, transferring of land ownership to women is unlikely to raise productivity if access to and use of other inputs remains unequal. This suggests that attempts to equalize land rights of men and women are unlikely to lead to gender equity and improved efficiency and productivity of women farmers unless other constraints faced by women are also addressed. The article also documents comments, suggestions, and recommendations in response to the summary of the paper. In addition, the different practices of guaranteeing land ownership for women in some countries of Africa are presented. PMID:12295514

  4. Global value trees.

    PubMed

    Zhu, Zhen; Puliga, Michelangelo; Cerina, Federica; Chessa, Alessandro; Riccaboni, Massimo

    2015-01-01

    The fragmentation of production across countries has become an important feature of the globalization in recent decades and is often conceptualized by the term "global value chains" (GVCs). When empirically investigating the GVCs, previous studies are mainly interested in knowing how global the GVCs are rather than how the GVCs look like. From a complex networks perspective, we use the World Input-Output Database (WIOD) to study the evolution of the global production system. We find that the industry-level GVCs are indeed not chain-like but are better characterized by the tree topology. Hence, we compute the global value trees (GVTs) for all the industries available in the WIOD. Moreover, we compute an industry importance measure based on the GVTs and compare it with other network centrality measures. Finally, we discuss some future applications of the GVTs. PMID:25978067

  5. Doubly robust survival trees.

    PubMed

    Steingrimsson, Jon Arni; Diao, Liqun; Molinaro, Annette M; Strawderman, Robert L

    2016-09-10

    Estimating a patient's mortality risk is important in making treatment decisions. Survival trees are a useful tool and employ recursive partitioning to separate patients into different risk groups. Existing 'loss based' recursive partitioning procedures that would be used in the absence of censoring have previously been extended to the setting of right censored outcomes using inverse probability censoring weighted estimators of loss functions. In this paper, we propose new 'doubly robust' extensions of these loss estimators motivated by semiparametric efficiency theory for missing data that better utilize available data. Simulations and a data analysis demonstrate strong performance of the doubly robust survival trees compared with previously used methods. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27037609

  6. Global Value Trees

    PubMed Central

    Zhu, Zhen; Puliga, Michelangelo; Cerina, Federica; Chessa, Alessandro; Riccaboni, Massimo

    2015-01-01

    The fragmentation of production across countries has become an important feature of the globalization in recent decades and is often conceptualized by the term “global value chains” (GVCs). When empirically investigating the GVCs, previous studies are mainly interested in knowing how global the GVCs are rather than how the GVCs look like. From a complex networks perspective, we use the World Input-Output Database (WIOD) to study the evolution of the global production system. We find that the industry-level GVCs are indeed not chain-like but are better characterized by the tree topology. Hence, we compute the global value trees (GVTs) for all the industries available in the WIOD. Moreover, we compute an industry importance measure based on the GVTs and compare it with other network centrality measures. Finally, we discuss some future applications of the GVTs. PMID:25978067

  7. Ensemble of Causal Trees

    NASA Astrophysics Data System (ADS)

    Bialas, Piotr

    2003-10-01

    We discuss the geometry of trees endowed with a causal structure using the conventional framework of equilibrium statistical mechanics. We show how this ensemble is related to popular growing network models. In particular we demonstrate that on a class of afine attachment kernels the two models are identical but they can differ substantially for other choice of weights. We show that causal trees exhibit condensation even for asymptotically linear kernels. We derive general formulae describing the degree distribution, the ancestor--descendant correlation and the probability that a randomly chosen node lives at a given geodesic distance from the root. It is shown that the Hausdorff dimension dH of the causal networks is generically infinite.

  8. Insert tree completion system

    SciTech Connect

    Brands, K.W.; Ball, I.G.; Cegielski, E.J.; Gresham, J.S.; Saunders, D.N.

    1982-09-01

    This paper outlines the overall project for development and installation of a low-profile, caisson-installed subsea Christmas tree. After various design studies and laboratory and field tests of key components, a system for installation inside a 30-in. conductor was ordered in July 1978 from Cameron Iron Works Inc. The system is designed to have all critical-pressure-containing components below the mudline and, with the reduced profile (height) above seabed, provides for improved safety of satellite underwater wells from damage by anchors, trawl boards, and even icebergs. In addition to the innovative nature of the tree design, the completion includes improved 3 1/2-in. through flowline (TFL) pumpdown completion equipment with deep set safety valves and a dual detachable packer head for simplified workover capability. The all-hydraulic control system incorporates a new design of sequencing valve for both Christmas tree control and remote flowline connection. A semisubmersible drilling rig was used to initiate the first end flowline connection at the wellhead for subsequent tie-in to the prelaid, surface-towed, all-welded subsea pipeline bundle.

  9. Tree Rings: Timekeepers of the Past.

    ERIC Educational Resources Information Center

    Phipps, R. L.; McGowan, J.

    One of a series of general interest publications on science issues, this booklet describes the uses of tree rings in historical and biological recordkeeping. Separate sections cover the following topics: dating of tree rings, dating with tree rings, tree ring formation, tree ring identification, sample collections, tree ring cross dating, tree…

  10. How To Write a Municipal Tree Ordinance.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1990-01-01

    At the heart of the Tree City USA program are four basic requirements: The community must have the following: (1) a tree board or department; (2) an annual community forestry program with financial provisions for trees and tree care; (3) an annual Arbor Day proclamation and observance; and (4) a tree ordinance. Sections of a model tree ordinance…

  11. Exact solutions for species tree inference from discordant gene trees.

    PubMed

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

    2013-10-01

    Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions. PMID:24131054

  12. Rate of tree carbon accumulation increases continuously with tree size

    USGS Publications Warehouse

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

    2014-01-01

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

  13. On Determining if Tree-based Networks Contain Fixed Trees.

    PubMed

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

    2016-05-01

    We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable. PMID:27125655

  14. The fault-tree compiler

    NASA Technical Reports Server (NTRS)

    Martensen, Anna L.; Butler, Ricky W.

    1987-01-01

    The Fault Tree Compiler Program is a new reliability tool used to predict the top event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N gates. The high level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Corporation VAX with the VMS operation system.

  15. Barking up the Right Tree

    ERIC Educational Resources Information Center

    Houston, Paul D.

    2006-01-01

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

  16. Distributed Merge Trees

    SciTech Connect

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

    Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions. As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization. We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.

  17. Tree Modeling and Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Tian-shuang, Fu; Yi-bing, Li; Dong-xu, Shen

    This paper introduces the theory about tree modeling and dynamic movements simulation in computer graphics. By comparing many methods we choose Geometry-based rendering as our method. The tree is decomposed into branches and leaves, under the rotation and quaternion methods we realize the tree animation and avoid the Gimbals Lock in Euler rotation. We take Orge 3D as render engine, which has good graphics programming ability. By the end we realize the tree modeling and dynamic movements simulation, achieve realistic visual quality with little computation cost.

  18. Human decision error (HUMDEE) trees

    SciTech Connect

    Ostrom, L.T.

    1993-08-01

    Graphical presentations of human actions in incident and accident sequences have been used for many years. However, for the most part, human decision making has been underrepresented in these trees. This paper presents a method of incorporating the human decision process into graphical presentations of incident/accident sequences. This presentation is in the form of logic trees. These trees are called Human Decision Error Trees or HUMDEE for short. The primary benefit of HUMDEE trees is that they graphically illustrate what else the individuals involved in the event could have done to prevent either the initiation or continuation of the event. HUMDEE trees also present the alternate paths available at the operator decision points in the incident/accident sequence. This is different from the Technique for Human Error Rate Prediction (THERP) event trees. There are many uses of these trees. They can be used for incident/accident investigations to show what other courses of actions were available and for training operators. The trees also have a consequence component so that not only the decision can be explored, also the consequence of that decision.

  19. Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

    PubMed

    Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

    2013-11-01

    Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology. PMID:24037268

  20. DIF Trees: Using Classification Trees to Detect Differential Item Functioning

    ERIC Educational Resources Information Center

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

    A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

  1. Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

    NASA Technical Reports Server (NTRS)

    Lee, Charles; Alena, Richard L.; Robinson, Peter

    2004-01-01

    We started from ISS fault trees example to migrate to decision trees, presented a method to convert fault trees to decision trees. The method shows that the visualizations of root cause of fault are easier and the tree manipulating becomes more programmatic via available decision tree programs. The visualization of decision trees for the diagnostic shows a format of straight forward and easy understands. For ISS real time fault diagnostic, the status of the systems could be shown by mining the signals through the trees and see where it stops at. The other advantage to use decision trees is that the trees can learn the fault patterns and predict the future fault from the historic data. The learning is not only on the static data sets but also can be online, through accumulating the real time data sets, the decision trees can gain and store faults patterns in the trees and recognize them when they come.

  2. The Group Tree of Experience.

    ERIC Educational Resources Information Center

    Ping, Ki

    1994-01-01

    Describes a group activity that uses a tree as a metaphor to reflect both group and personal growth during adventure activities. The tree's roots represent the group's formation, the branches and leaves represent the group's diversity and capabilities, and the seeds represent the personal learning and growth that took place within the group.…

  3. Studying Evergreen Trees in December.

    ERIC Educational Resources Information Center

    Platt, Dorothy K.

    1991-01-01

    This lesson plan uses evergreen trees on sale in cities and villages during the Christmas season to teach identification techniques. Background information, activities, and recommended references guides deal with historical, symbolic and current uses of evergreen trees, physical characteristics, selection, care, and suggestions for post-Christmas…

  4. Fractions, trees and unfinished business

    NASA Astrophysics Data System (ADS)

    Shraiman, Boris

    In this talk, mourning the loss of a teacher and a dear friend, I would like to share some unfinished thoughts loosely connecting - via Farey fraction trees - Kadanoff's study of universality of quasi-periodic route to chaos with the effort to understand universal features of genealogical trees.

  5. Tree Hydraulics: How Sap Rises

    ERIC Educational Resources Information Center

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown--a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by…

  6. Hydrocarbons from plants and trees

    SciTech Connect

    Calvin, M.

    1982-07-01

    The way energy was used in the US in 1980 was examined. A diagram shows the development of energy from its source to its end use. The following are described: the carbon dioxide problem - the greenhouse effect, sugar cane as an energy source, hydrocarbon-producing plants and trees, and isoprenoids from plants and trees. (MHR)

  7. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees...

  8. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees...

  9. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees...

  10. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees...

  11. Subsea tree cap well choke system

    SciTech Connect

    Bednar, J.M.

    1991-04-30

    This patent describes an apparatus useful in subsea well completions requiring a subsea choke. It comprises: a wellhead connector; a tree flow passage; a tree annulus passage; a tree cap; a choke; and a production line.

  12. A Cost Benefit Analysis of Urban Trees

    SciTech Connect

    Akbari, Hashem

    1997-09-01

    Urban shade trees offer significant benefits in reducing building air- conditioning and improving urban air quality by reducing smog. The savings associated with these benefits varies by climate regions and can be up to $200 per tree. The cost of planting trees and maintaining them can vary from $10 to $500 per tree. Tree planting programs can be designed offer savings to communities that plant trees.

  13. Are There Infinite Irrigation Trees?

    NASA Astrophysics Data System (ADS)

    Bernot, M.; Caselles, V.; Morel, J. M.

    2006-08-01

    In many natural or artificial flow systems, a fluid flow network succeeds in irrigating every point of a volume from a source. Examples are the blood vessels, the bronchial tree and many irrigation and draining systems. Such systems have raised recently a lot of interest and some attempts have been made to formalize their description, as a finite tree of tubes, and their scaling laws [25], [26]. In contrast, several mathematical models [5], [22], [10], propose an idealization of these irrigation trees, where a countable set of tubes irrigates any point of a volume with positive Lebesgue measure. There is no geometric obstruction to this infinitesimal model and general existence and structure theorems have been proved. As we show, there may instead be an energetic obstruction. Under Poiseuille law R(s) = s -2 for the resistance of tubes with section s, the dissipated power of a volume irrigating tree cannot be finite. In other terms, infinite irrigation trees seem to be impossible from the fluid mechanics viewpoint. This also implies that the usual principle analysis performed for the biological models needs not to impose a minimal size for the tubes of an irrigating tree; the existence of the minimal size can be proven from the only two obvious conditions for such irrigation trees, namely the Kirchhoff and Poiseuille laws.

  14. Terrestrial apes and phylogenetic trees

    PubMed Central

    Arsuaga, Juan Luis

    2010-01-01

    The image that best expresses Darwin’s thinking is the tree of life. However, Darwin’s human evolutionary tree lacked almost everything because only the Neanderthals were known at the time and they were considered one extreme expression of our own species. Darwin believed that the root of the human tree was very deep and in Africa. It was not until 1962 that the root was shown to be much more recent in time and definitively in Africa. On the other hand, some neo-Darwinians believed that our family tree was not a tree, because there were no branches, but, rather, a straight stem. The recent years have witnessed spectacular discoveries in Africa that take us close to the origin of the human tree and in Spain at Atapuerca that help us better understand the origin of the Neanderthals as well as our own species. The final form of the tree, and the number of branches, remains an object of passionate debate. PMID:20445090

  15. Implementing municipal tree planting: Los Angeles million-tree initiative.

    PubMed

    Pincetl, Stephanie

    2010-02-01

    Urban forests are increasingly being seen as an important infrastructure that can help cities remediate their environmental impacts. This work reports on the first steps in implementing a million tree program in Los Angeles and the ways such a biogenic-living-infrastructure has been approached. Numbers of studies have been done to quantify the benefits of urban forests, but little has been written on the process of implementing urban tree planting programs. The investigative methods were primarily qualitative, involving interviews, attending meetings and conducting literature reviews. Results indicate that multiple nonprofit and city agency programs are involved in planting and maintaining trees and this has required coordination among groups that here-to-fore were unaccustomed to having to collaborate. The main finding that emerge from this research is that the implementation of such a program in Los Angeles is more complicated than it may seem due to several interacting factors: the need to rely on multiple public and private organizations to put trees into the ground and to maintain them; coordination of these multiple efforts must be centralized, but requires a great deal of time and effort and maybe resisted by some of the partners; funding for planting and long term maintenance must be pieced together from multiple sources; acceptance of trees by residents varies by neighborhood as does tree canopy cover; appropriate nursery supply can be limited; the location of the program within the city administration is determined by who initiates the program. PMID:20016982

  16. Implementing Municipal Tree Planting: Los Angeles Million-Tree Initiative

    NASA Astrophysics Data System (ADS)

    Pincetl, Stephanie

    2010-02-01

    Urban forests are increasingly being seen as an important infrastructure that can help cities remediate their environmental impacts. This work reports on the first steps in implementing a million tree program in Los Angeles and the ways such a biogenic—living—infrastructure has been approached. Numbers of studies have been done to quantify the benefits of urban forests, but little has been written on the process of implementing urban tree planting programs. The investigative methods were primarily qualitative, involving interviews, attending meetings and conducting literature reviews. Results indicate that multiple nonprofit and city agency programs are involved in planting and maintaining trees and this has required coordination among groups that here-to-fore were unaccustomed to having to collaborate. The main finding that emerge from this research is that the implementation of such a program in Los Angeles is more complicated than it may seem due to several interacting factors: the need to rely on multiple public and private organizations to put trees into the ground and to maintain them; coordination of these multiple efforts must be centralized, but requires a great deal of time and effort and maybe resisted by some of the partners; funding for planting and long term maintenance must be pieced together from multiple sources; acceptance of trees by residents varies by neighborhood as does tree canopy cover; appropriate nursery supply can be limited; the location of the program within the city administration is determined by who initiates the program.

  17. STRAW: Species TRee Analysis Web server

    PubMed Central

    Shaw, Timothy I.; Ruan, Zheng; Glenn, Travis C.; Liu, Liang

    2013-01-01

    The coalescent methods for species tree reconstruction are increasingly popular because they can accommodate coalescence and multilocus data sets. Herein, we present STRAW, a web server that offers workflows for reconstruction of phylogenies of species using three species tree methods—MP-EST, STAR and NJst. The input data are a collection of rooted gene trees (for STAR and MP-EST methods) or unrooted gene trees (for NJst). The output includes the estimated species tree, modified Robinson-Foulds distances between gene trees and the estimated species tree and visualization of trees to compare gene trees with the estimated species tree. The web sever is available at http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/. PMID:23661681

  18. Decision tree modeling using R

    PubMed Central

    2016-01-01

    In machine learning field, decision tree learner is powerful and easy to interpret. It employs recursive binary partitioning algorithm that splits the sample in partitioning variable with the strongest association with the response variable. The process continues until some stopping criteria are met. In the example I focus on conditional inference tree, which incorporates tree-structured regression models into conditional inference procedures. While growing a single tree is subject to small changes in the training data, random forests procedure is introduced to address this problem. The sources of diversity for random forests come from the random sampling and restricted set of input variables to be selected. Finally, I introduce R functions to perform model based recursive partitioning. This method incorporates recursive partitioning into conventional parametric model building. PMID:27570769

  19. Decision tree modeling using R.

    PubMed

    Zhang, Zhongheng

    2016-08-01

    In machine learning field, decision tree learner is powerful and easy to interpret. It employs recursive binary partitioning algorithm that splits the sample in partitioning variable with the strongest association with the response variable. The process continues until some stopping criteria are met. In the example I focus on conditional inference tree, which incorporates tree-structured regression models into conditional inference procedures. While growing a single tree is subject to small changes in the training data, random forests procedure is introduced to address this problem. The sources of diversity for random forests come from the random sampling and restricted set of input variables to be selected. Finally, I introduce R functions to perform model based recursive partitioning. This method incorporates recursive partitioning into conventional parametric model building. PMID:27570769

  20. Fault Tree Analysis: A Bibliography

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Fault tree analysis is a top-down approach to the identification of process hazards. It is as one of the best methods for systematically identifying an graphically displaying the many ways some things can go wrong. This bibliography references 266 documents in the NASA STI Database that contain the major concepts. fault tree analysis, risk an probability theory, in the basic index or major subject terms. An abstract is included with most citations, followed by the applicable subject terms.

  1. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

    PubMed

    Leaché, Adam D; Banbury, Barbara L; Felsenstein, Joseph; de Oca, Adrián Nieto-Montes; Stamatakis, Alexandros

    2015-11-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the

  2. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

    PubMed Central

    Leaché, Adam D.; Banbury, Barbara L.; Felsenstein, Joseph; de Oca, Adrián nieto-Montes; Stamatakis, Alexandros

    2015-01-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the

  3. Multipolar consensus for phylogenetic trees.

    PubMed

    Bonnard, Cécile; Berry, Vincent; Lartillot, Nicolas

    2006-10-01

    Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html PMID:17060203

  4. Generic physical protection logic trees

    SciTech Connect

    Paulus, W.K.

    1981-10-01

    Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle.

  5. Microwave sensing of tree trunks

    NASA Astrophysics Data System (ADS)

    Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

    2015-04-01

    The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

  6. Growing a Forest for the Trees.

    ERIC Educational Resources Information Center

    Growing Ideas, 2001

    2001-01-01

    Describes a tree studies program in a fourth-grade classroom. Students collected local tree seeds and seeds from supermarket fruits, researched growing conditions, and grew seeds under various conditions. Students kept journals on local trees, observing seed dispersal mechanisms and examining rings on trunk slices. Inquiry-based tree studies…

  7. How To Select and Plant a Tree.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1991-01-01

    This bulletin furnishes information about selecting and planting trees. The tree selection process includes being aware of the physical characteristics of bare root seedlings, containerized seedlings, balled and burlapped, or potted trees and determining the proper size and root ball proportions. The section on tree planting discusses how to: (1)…

  8. TreeGenes: A Forest Tree Genome Database

    PubMed Central

    Wegrzyn, Jill L.; Lee, Jennifer M.; Tearse, Brandon R.; Neale, David B.

    2008-01-01

    The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange. PMID:18725987

  9. Sussing Merger Trees: The Merger Trees Comparison Project

    NASA Astrophysics Data System (ADS)

    Srisawat, Chaichalit; Knebe, Alexander; Pearce, Frazer R.; Schneider, Aurel; Thomas, Peter A.; Behroozi, Peter; Dolag, Klaus; Elahi, Pascal J.; Han, Jiaxin; Helly, John; Jing, Yipeng; Jung, Intae; Lee, Jaehyun; Mao, Yao-Yuan; Onions, Julian; Rodriguez-Gomez, Vicente; Tweed, Dylan; Yi, Sukyoung K.

    2013-11-01

    Merger trees follow the growth and merger of dark-matter haloes over cosmic history. As well as giving important insights into the growth of cosmic structure in their own right, they provide an essential backbone to semi-analytic models of galaxy formation. This paper is the first in a series to arise from the Sussing Merger Trees Workshop in which 10 different tree-building algorithms were applied to the same set of halo catalogues and their results compared. Although many of these codes were similar in nature, all algorithms produced distinct results. Our main conclusions are that a useful merger-tree code should possess the following features: (i) the use of particle IDs to match haloes between snapshots; (ii) the ability to skip at least one, and preferably more, snapshots in order to recover subhaloes that are temporarily lost during merging; (iii) the ability to cope with (and ideally smooth out) large, temporary fluctuations in halo mass. Finally, to enable different groups to communicate effectively, we defined a common terminology that we used when discussing merger trees and we encourage others to adopt the same language. We also specified a minimal output format to record the results.

  10. Genealogical trees from genetic distances

    NASA Astrophysics Data System (ADS)

    Prignano, L.; Serva, M.

    2009-06-01

    In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to exactly reconstruct their genealogical tree. Unfortunately, in most cases, genealogical distances are unknown and only genetic distances are available. The genetic distance between two individuals is measurable from differences in mtDNA (mitochondrial DNA) since in the case of humans or other complex organisms mtDNA is transmitted in a haploid manner. An analogous distance can be also computed for languages where it may be measured from lexical differences, in this case, nevertheless, haploid reproduction is only a raw approximation. Assuming a constant rate of mutation, these genetic distances are random and proportional only on average to genealogical ones. The reconstruction of the genealogical tree from the available genetic distances is forceful imprecise. In this paper we try to quantify the error one may commit in the reconstruction of the tree for different degrees of randomness. The errors may concern both topology of the tree (the branching hierarchy) and, in case of correct topology, the proportions of the tree (length of various branches).

  11. New program controls tree management

    SciTech Connect

    Beaty, W.

    1995-02-01

    Senior management of TransAlta Utilities Corp. (TAU) Calgary, Alberta, Canada, was highly dissatisfied with the fact that even though the distribution line clearance budget had been increased an average 35 percent a year between 1978 and 1984, there were few if any discernible positive results. Tree-related power outages kept increasing and budget requests from the field kept increasing. In searching for a solution TAU had to deal with the concept that the right level of funding can only be determined through an inventory of tree work. This inventory is comprised of two factors, the number of trees in proximity to the power lines and the local growth rates. Based on the inventory of a hired consultant, a 12-year budget projection was established. The period covered entailed a six-year, first-cycle or catch up phase, and a six-year, second-cycle maintenance phase. In implementing the new vegetation management program in 1986, TAU decided to contact each landowner directly to obtain consent to undertake the tree work. The intent was to reduce the risk of claims while maximizing tree removals. Complaints and claims were dramatically reduced and currently run at about one per 1,000 landowners and budgets have dropped back to the 1985 levels as predicted for the maintenance phase.

  12. Tree Growth Stage and Environment after Pathogen Inoculation Alters Susceptibility of Pear Trees to Phytophthora Canker

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated whether growth stage of pear (Pyrus communis) tree rootstock and environment after inoculation with Phytophthora syringae influences tree susceptibility to infection. Trees at different stages of dormancy development were inoculated with the pathogen and maintained in different condi...

  13. Measurement of tree canopy architecture

    NASA Technical Reports Server (NTRS)

    Martens, S. N.; Ustin, S. L.; Norman, J. M.

    1991-01-01

    The lack of accurate extensive geometric data on tree canopies has retarded development and validation of radiative transfer models. A stratified sampling method was devised to measure the three-dimensional geometry of 16 walnut trees which had received irrigation treatments of either 100 or 33 per cent of evapotranspirational (ET) demand for the previous two years. Graphic reconstructions of the three-dimensional geometry were verified by 58 independent measurements. The distributions of stem- and leaf-size classes, lengths, and angle classes were determined and used to calculate leaf area index (LAI), stem area, and biomass. Reduced irrigation trees have lower biomass of stems, leaves and fruit, lower LAI, steeper leaf angles and altered biomass allocation to large stems. These data can be used in ecological models that link canopy processes with remotely sensed measurements.

  14. Mapping tree density at a global scale

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  15. Mapping tree density at a global scale.

    PubMed

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

    2015-09-10

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization. PMID:26331545

  16. Coalescent Histories for Lodgepole Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2015-10-01

    Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the lodgepole species trees (λn)n ≥ 0, in which tree λn has m = 2n+1 taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with m!! in the number of taxa m. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with m taxa, increasing a previous bound of [Formula: see text] to [Formula: see text]. We discuss the implications of our enumerative results for phylogenetic computations. PMID:25973633

  17. Attention trees and semantic paths

    NASA Astrophysics Data System (ADS)

    Giusti, Christian; Pieroni, Goffredo G.; Pieroni, Laura

    2007-02-01

    In the last few decades several techniques for image content extraction, often based on segmentation, have been proposed. It has been suggested that under the assumption of very general image content, segmentation becomes unstable and classification becomes unreliable. According to recent psychological theories, certain image regions attract the attention of human observers more than others and, generally, the image main meaning appears concentrated in those regions. Initially, regions attracting our attention are perceived as a whole and hypotheses on their content are formulated; successively the components of those regions are carefully analyzed and a more precise interpretation is reached. It is interesting to observe that an image decomposition process performed according to these psychological visual attention theories might present advantages with respect to a traditional segmentation approach. In this paper we propose an automatic procedure generating image decomposition based on the detection of visual attention regions. A new clustering algorithm taking advantage of the Delaunay- Voronoi diagrams for achieving the decomposition target is proposed. By applying that algorithm recursively, starting from the whole image, a transformation of the image into a tree of related meaningful regions is obtained (Attention Tree). Successively, a semantic interpretation of the leaf nodes is carried out by using a structure of Neural Networks (Neural Tree) assisted by a knowledge base (Ontology Net). Starting from leaf nodes, paths toward the root node across the Attention Tree are attempted. The task of the path consists in relating the semantics of each child-parent node pair and, consequently, in merging the corresponding image regions. The relationship detected in this way between two tree nodes generates, as a result, the extension of the interpreted image area through each step of the path. The construction of several Attention Trees has been performed and partial

  18. Trees, soils, and food security

    PubMed Central

    Sanchez, P. A.; Buresh, R. J.; Leakey, R. R. B.

    1997-01-01

    Trees have a different impact on soil properties than annual crops, because of their longer residence time, larger biomass accumulation, and longer-lasting, more extensive root systems. In natural forests nutrients are efficiently cycled with very small inputs and outputs from the system. In most agricultural systems the opposite happens. Agroforestry encompasses the continuum between these extremes, and emerging hard data is showing that successful agroforestry systems increase nutrient inputs, enhance internal flows, decrease nutrient losses and provide environmental benefits: when the competition for growth resources between the tree and the crop component is well managed. The three main determinants for overcoming rural poverty in Africa are (i) reversing soil fertility depletion, (ii) intensifying and diversifying land use with high-value products, and (iii) providing an enabling policy environment for the smallholder farming sector. Agroforestry practices can improve food production in a sustainable way through their contribution to soil fertility replenishment. The use of organic inputs as a source of biologically-fixed nitrogen, together with deep nitrate that is captured by trees, plays a major role in nitrogen replenishment. The combination of commercial phosphorus fertilizers with available organic resources may be the key to increasing and sustaining phosphorus capital. High-value trees, 'Cinderella' species, can fit in specific niches on farms, thereby making the system ecologically stable and more rewarding economically, in addition to diversifying and increasing rural incomes and improving food security. In the most heavily populated areas of East Africa, where farm size is extremely small, the number of trees on farms is increasing as farmers seek to reduce labour demands, compatible with the drift of some members of the family into the towns to earn off-farm income. Contrary to the concept that population pressure promotes deforestation, there is

  19. Transport of Methane in Trees

    NASA Astrophysics Data System (ADS)

    Kutschera, E.; Khalil, A. K.; Shearer, M. J.; Rosenstiel, T.; Rice, A. L.

    2011-12-01

    Although overall methane (CH4) emissions for croplands, wetlands, and forests have been measured, the exact dynamics of CH4 transport through trees is not well understood. What roles transport mechanisms play in emission rates has been thoroughly investigated for rice, but is fairly unknown for trees. Better defined plant transport mechanisms yield more accurate determination of greenhouse gas flux and its variations, contributing to a comprehensive theory quantifying greenhouse gas emissions globally. CH4 emissions from the common wetland tree species black cottonwood (Populus trichocarpa) native to the Pacific Northwest have been measured under hydroponic conditions in order to separate plant transport processes from the influence of soil processes. Canopy emissions of CH4 have been measured via canopy enclosure. Measurements of CH4 flux from each of 16 trees have indicated that emissions are normally constant over the half-hour sampling period. Samples for stable carbon isotope composition have been taken during these experiments and measured on a mass spectrometer. Compared to the isotopic composition of root water CH4, canopy CH4 is depleted in 13C; this indicates that CH4 moving through the tree is not following a bulk flow pathway (where no depletion would occur), but instead moves either diffusively or through other cell or tissue barriers. No correlation was found to exist between leaf area and CH4 emission; this is vital to upscaling tree-level emissions to the global scale since leaf area index (LAI) cannot be treated as an appropriate parameter to upscale flux. Correctly informing global-scale CH4 fluxes from plants requires an association between the role plant physiology plays in the production and transport of CH4 and magnitudes of flux. This research was supported by the Office of Science (BER), U. S. Department of Energy, Grant No. DE-FG02-08ER64515. Supported in part through NASA / Oregon Space Grant Consortium, grant NNG05GJ85H.

  20. Tree hydraulics: how sap rises

    NASA Astrophysics Data System (ADS)

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown—a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by transpiration or capillary action; we investigate the effectiveness of both these forces for the two conduit architectures considered. The level of analysis is appropriate for undergraduates. The subject is of broad interest because it provides a naturally-occurring example of an unusual metastable state of matter: liquid under tension.

  1. 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.

  2. Interpreting the universal phylogenetic tree

    PubMed Central

    Woese, Carl 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. PMID:10900003

  3. Water Transport in Trees--An Artificial Laboratory Tree

    ERIC Educational Resources Information Center

    Susman, K.; Razpet, N.; Cepic, M.

    2011-01-01

    Water transport in tall trees is an everyday phenomenon, seldom noticed and not completely understood even by scientists. As a topic of current research in plant physiology it has several advantages for presentation within school physics lectures: it is interdisciplinary and clearly shows the connection between physics and biology; the…

  4. Tree Height Calculator: An Android App for Estimating Tree Height

    NASA Astrophysics Data System (ADS)

    Burca, V. S.; Htet, N. M.; Huang, X.; de Lanerolle, T. R.; Morelli, R.; Gourley, J. R.

    2011-12-01

    Conventionally, measuring tree height requires a collection of different tools - clinometer, transit, pencil, paper, laptop computer. Results are recorded manually and entered into a spreadsheet or database for future calculation and analysis. Tree Height Calculator is a mobile Android app the integrates the various steps in this process thereby improving the accuracy and dramatically reducing the time required to go from taking measurements to analyzing data. Given the user's height and the distance from the base of the tree (which can be downloaded into the app from a server), the app uses the phone's orientation sensor to calculate the angle of elevation. A simple trigonometric formula is then used to calculate and record the tree's height in the phone's database. When the phone has a WiFi connection, the data are transmitted to a server, from where they can be downloaded directly into a spreadsheet. The application was first tested in an Environmental Science laboratory at Trinity College. On the first trial, 103 data samples were collected, stored, and uploaded to the online database with only couple of dropped data points. On the second trial, 98 data samples were gathered with no loss of data. The app combined the individual measurements taken by the students in the lab, reducing the time required to produce a graph of the class's results from days to hours.

  5. On Tree-Based Phylogenetic Networks.

    PubMed

    Zhang, Louxin

    2016-07-01

    A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model. PMID:27228397

  6. AncesTrees: ancestry estimation with randomized decision trees.

    PubMed

    Navega, David; Coelho, Catarina; Vicente, Ricardo; Ferreira, Maria Teresa; Wasterlain, Sofia; Cunha, Eugénia

    2015-09-01

    In forensic anthropology, ancestry estimation is essential in establishing the individual biological profile. The aim of this study is to present a new program--AncesTrees--developed for assessing ancestry based on metric analysis. AncesTrees relies on a machine learning ensemble algorithm, random forest, to classify the human skull. In the ensemble learning paradigm, several models are generated and co-jointly used to arrive at the final decision. The random forest algorithm creates ensembles of decision trees classifiers, a non-linear and non-parametric classification technique. The database used in AncesTrees is composed by 23 craniometric variables from 1,734 individuals, representative of six major ancestral groups and selected from the Howells' craniometric series. The program was tested in 128 adult crania from the following collections: the African slaves' skeletal collection of Valle da Gafaria; the Medical School Skull Collection and the Identified Skeletal Collection of 21st Century, both curated at the University of Coimbra. The first step of the test analysis was to perform ancestry estimation including all the ancestral groups of the database. The second stage of our test analysis was to conduct ancestry estimation including only the European and the African ancestral groups. In the first test analysis, 75% of the individuals of African ancestry and 79.2% of the individuals of European ancestry were correctly identified. The model involving only African and European ancestral groups had a better performance: 93.8% of all individuals were correctly classified. The obtained results show that AncesTrees can be a valuable tool in forensic anthropology. PMID:25053239

  7. Electric Trees and Pond Creatures.

    ERIC Educational Resources Information Center

    Weaver, Helen; Hounshell, Paul B.

    1978-01-01

    Two learning activities are presented to develop observation and classification skills at the elementary level. The first is an electric box that associates tree names with leaf and bark specimens, and the second is a pond water observation and slide preparation activity. (BB)

  8. The Tree of Animal Life

    ERIC Educational Resources Information Center

    Braude, Stan

    2007-01-01

    In this article, the author describes a short activity which introduces third- to fifth-grade students to animal classification. The Tree of Animal Life activity is a simple, sorting exercise that can help them see a bigger picture. The activity sets the stage for learning about animal taxonomy and introduces the characteristics of various animal…

  9. Not Just a Fall Tree

    ERIC Educational Resources Information Center

    Miller-Hewes, Kathy A.

    2004-01-01

    Trees burst with color in the northern states. Autumn leaves dust the ground. Painting the fall landscape is nothing new. Teachers have been doing it in classrooms for decades. The approach, however, can make the difference between whether the fall landscape is simply painting for fun, or a real learning experience. Students learn best when they…

  10. 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 aged 7-11…

  11. Trees of Our National Forests.

    ERIC Educational Resources Information Center

    Forest Service (USDA), Washington, DC.

    Presented is a description of the creation of the National Forests system, how trees grow, managing the National Forests, types of management systems, and managing for multiple use, including wildlife, water, recreation and other uses. Included are: (1) photographs; (2) line drawings of typical leaves, cones, flowers, and seeds; and (3)…

  12. Statistical Methods for Evolutionary Trees

    PubMed Central

    Edwards, A. W. F.

    2009-01-01

    In 1963 and 1964, L. L. Cavalli-Sforza and A. W. F. Edwards introduced novel methods for computing evolutionary trees from genetical data, initially for human populations from blood-group gene frequencies. The most important development was their introduction of statistical methods of estimation applied to stochastic models of evolution. PMID:19797062

  13. Key for Trees of Iowa.

    ERIC Educational Resources Information Center

    Coder, Kim D.; Wray, Paul H.

    This key is designed to help identify the most common trees found in Iowa. It is based on vegetative characteristics such as leaves, fruits, and bark and is illustrated with black and white line drawings. Since vegetative characteristics vary due to climate, age, soil fertility, and other conditions, the numerical sizes listed, such as length and…

  14. The Gift of the Tree

    ERIC Educational Resources Information Center

    Jones, Marla Wagner

    2009-01-01

    A piece of children's literature can be a powerful tool for teaching and learning science; however, it takes more than reading about a topic to qualify as "doing science." Inspired by the book, "The Gift of the Tree", the author developed an in-depth interdisciplinary lesson for her sixth-grade students without diluting the science. Through this…

  15. Chopping Down the Cherry Tree.

    ERIC Educational Resources Information Center

    Griswold, Jerry

    1995-01-01

    Attempts once again to put to rest the infamous "I cannot tell a lie" episode involving George Washington and a downed cherry tree. Appends an editor's note that states that William Bennett's "The Children's Book of Virtues" which perpetuates this infamous piece of "fakelore." (RS)

  16. The Tree of Life Project

    ERIC Educational Resources Information Center

    Milbrath, Sherry

    2009-01-01

    Middle-school students are just beginning to recognize their place in the world. That is why this author believes it is important to incorporate their world into their art. In this article, the author discusses the "Tree of Life" project, which she developed for her students in order to make them aware of various environmental issues, and how to…

  17. The Education of Little Tree.

    ERIC Educational Resources Information Center

    Carter, Forrest

    First published in 1976, this autobiography contains Forrest Carter's--Little Tree's--remembrances of life with his Eastern Cherokee Hill country grandparents in the 1930s. There are 21 chapters, recounting humorous and serious episodes from a 5-year period and dealing with the themes of growing up, Indian life and values, family relationships,…

  18. MYCOTOXINS IN EDIBLE TREE NUTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tree nuts (almonds, pistachios, and walnuts) are an exceptionally valuable crop, especially in California, with an aggregate value approaching $3.5 billion. Much of this economic value comes from overseas markets, with up to 60% of the crop being exported. The product can be contaminated with aflat...

  19. The Trees that surround us

    NASA Astrophysics Data System (ADS)

    Costa, M. E. G.; Rodrigues, M. A. S.

    2012-04-01

    In our school the activities linked with sciences are developed in a partnership with other school subjects. Interdisciplinary projects are always valued from beginning to end of a project. It is common for teachers of different areas to work together in a Science project. Research of English written articles is very important not only for the development of our students' scientific literacy but also as a way of widening knowledge and a view on different perspectives of life instead of being limited to research of any articles in Portuguese language. In this study we are going to collect data about the predominant tree species in the region, especially the invasive trees from the acacia species, the native tree species and the commercial species. We are going to study the reasons for the appearance of each species and draw a chart of soil occupation in the council. This chart will also allow the study of the distribution and use of land for each tree species. This research work is the first stage for a contribution to warn the town council of the dangers of the invasive species to the future economy of the council.

  20. Compartmentalization of Decay in Trees.

    ERIC Educational Resources Information Center

    Shigo, Alex L.

    1985-01-01

    Unlike animals, which heal, trees compartmentalize by setting boundaries that resist the spread of invading microorganisms. Discusses the creation of new walls by anatomical and chemical means in response to death of a branch or pruning. Points out that genetic control of compartmentalization has resulted from evolution of resistant species. (DH)

  1. Isoprene emission from Indian trees

    NASA Astrophysics Data System (ADS)

    Varshney, C. K.; Singh, Abhai Pratap

    2003-12-01

    Isoprene is the most dominant non-methane volatile organic compound (NMVOC) emitted by plants. NMVOCs play an important role in regulating the composition of atmospheric trace gases including global concentration of tropospheric ozone. Our present knowledge about NMVOCs emission is mainly from studies on temperate tree species. So far information on biogenic NMVOCs emission from tropical tree species is limited. In this study, isoprene emission rates from 40 tropical Indian tree species belonging to 33 genera and 17 families were measured for the first time using a dynamic flow through enclosure chamber technique. The isoprene emission rate from plants (30°C and PAR 1000 μmolm-2s-1) ranged from undetectable to 81.5 μg g-1 h-1 and values were found to be comparable with other studies on tropical tree species. Tree species screened for isoprene emission in the present study may be grouped into the four categories, proposed by [2001], namely, 18 species were negligible or BDL isoprene emitting (<1 μg g-1 h-1), 6 species were low emitting (1 ≤ to <10 μg g-1 h-1), 5 species were moderate emitting (10≤ to <25 μg g-1 h-1), and 11 species were high isoprene emitting (≥25 μg g-1 h-1). Maximum isoprene emission rate (81.5 μg g-1 h-1) was observed in the case of Dalbergia sissoo Linn. It was interesting to find that Citrus limon Linn., Citrus reticulata Linn., Citrus sinensis Linn., Grevillea robusta A. Cunn., and Morus alba Linn., which were earlier reported as BDL or non isoprene emitters in US [, 1998; , 2001] were found to be appreciably high isoprene emitters (0.61-21.60 μg g-1 h-1) in the present study.

  2. Bayesian Evidence Framework for Decision Tree Learning

    NASA Astrophysics Data System (ADS)

    Chatpatanasiri, Ratthachat; Kijsirikul, Boonserm

    2005-11-01

    This work is primary interested in the problem of, given the observed data, selecting a single decision (or classification) tree. Although a single decision tree has a high risk to be overfitted, the induced tree is easily interpreted. Researchers have invented various methods such as tree pruning or tree averaging for preventing the induced tree from overfitting (and from underfitting) the data. In this paper, instead of using those conventional approaches, we apply the Bayesian evidence framework of Gull, Skilling and Mackay to a process of selecting a decision tree. We derive a formal function to measure `the fitness' for each decision tree given a set of observed data. Our method, in fact, is analogous to a well-known Bayesian model selection method for interpolating noisy continuous-value data. As in regression problems, given reasonable assumptions, this derived score function automatically quantifies the principle of Ockham's razor, and hence reasonably deals with the issue of underfitting-overfitting tradeoff.

  3. Genomics of Tropical Fruit Tree Crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

  4. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions §...

  5. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions §...

  6. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions §...

  7. Totally Tree-mendous Activities: Projects To Discover the Beauty and Benefits of Trees.

    ERIC Educational Resources Information Center

    Hollister, Sarah

    This teacher's guide supplies information and hands-on activities to teach about trees from several disciplines. Activities are grouped into six areas that cover botany, social studies, arts and literature (aesthetics), and trees as a resource. Sections include: (1) Tree Identification, which defines trees and leaves and presents activities that…

  8. Using tree diversity to compare phylogenetic heuristics

    PubMed Central

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-01-01

    Background Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Results Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Conclusion Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees—especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest. PMID:19426451

  9. Sleeping tree choice by Bwindi chimpanzees.

    PubMed

    Stanford, Craig B; O'Malley, Robert C

    2008-07-01

    Unlike nearly all other nonhuman primates, great apes build sleeping nests. In Bwindi Impenetrable National Park, Uganda, chimpanzees build nests nightly and also build day nests. We investigated patterns of nest tree use by Bwindi chimpanzees to understand ecological influences on nest tree selection. We analyzed data on 3,414 chimpanzee nests located from 2000 to 2004. Chimpanzees at Bwindi were selective in their use of nest trees. Of at least 163 tree species known to occur in Bwindi [Butynski, Ecological survey of the Impenetrable (Bwindi) Forest, Uganda, and recommendations for its conservation and management. Report to the Government of Uganda, 1984], chimpanzees utilized only 38 species for nesting. Of these, four tree species (Cassipourea sp., Chrysophyllum gorungosanum, Drypetes gerrardii, and Teclea nobilis) accounted for 72.1% of all nest trees. There was considerable variation in nesting frequencies among the top four species between and within years. However, these species were used significantly more often for nesting than other species in 70.9% (39 of 55) of the months of this study. A Spearman rank correlation found no significant relationship between tree abundance and tree species preference. Ninety-three percent of all nests were constructed in food tree species, although not necessarily at the same time the trees bore food items used by chimpanzees. The results indicate that nesting tree species preferences exist. Bwindi chimpanzees' choice of nesting tree species does not appear to be dependent on tree species density or use of the tree for food. We discuss possible reasons for the selectivity in nest trees by the Bwindi population. PMID:18381629

  10. Trees Outside Forest In Poland

    NASA Astrophysics Data System (ADS)

    Zajączkowski, Jacek; Zajączkowski, Kazimierz

    2015-01-01

    Increasing environmental threats to agricultural production and the stability of ecosystems have been observed on the Polish lowlands since the 1970s. Several hundred million trees and shrubs have been planted on farmland, mostly along roads and with the involvement of public agencies, with a view to timber being produced, and soil erosion and the water deficit mitigated. On the basis of over 50 years of practical observations and scientific experiments, recommendations have been drawn up as regards the structural and spatial features of new tree planting outside forests that maximize environmental, production-related and social benefits. This paper gives a brief description of the history of the active establishment of woody vegetation across agricultural landscapes in Poland, along with best practices elaborated for this at several scientific centres.

  11. Extremal properties of random trees

    NASA Astrophysics Data System (ADS)

    Ben-Naim, E.; Krapivsky, P. L.; Majumdar, Satya N.

    2001-09-01

    We investigate extremal statistical properties such as the maximal and the minimal heights of randomly generated binary trees. By analyzing the master evolution equations we show that the cumulative distribution of extremal heights approaches a traveling wave form. The wave front in the minimal case is governed by the small-extremal-height tail of the distribution, and conversely, the front in the maximal case is governed by the large-extremal-height tail of the distribution. We determine several statistical characteristics of the extremal height distribution analytically. In particular, the expected minimal and maximal heights grow logarithmically with the tree size, N, hmin~vmin ln N, and hmax~vmax ln N, with vmin=0.373365... and vmax=4.31107..., respectively. Corrections to this asymptotic behavior are of order O(ln ln N).

  12. Real Trees in the Classroom

    ERIC Educational Resources Information Center

    Fernandes, Francisca Maria; de Carvalho, Luis Mendonca; Silveira, Margarida

    2006-01-01

    At home, children often have pets that they take care of and play with; even in the classroom it is not uncommon to find a wormery, an aquarium or an ant farm. However, children rarely have the opportunity to own and care for a plant over a lengthy period of time, let alone a tree. The authors describe a project in Portugal aimed at improving…

  13. Polychlorinated biphenyls in tree bark

    SciTech Connect

    Hermanson, M.H.; Hites, R.A. )

    1990-05-01

    Polychlorinated biphenyl (PCB) concentrations in tree bark vary with proximity to a source. Higher total PCB bark/air ratios in areas near contamination show that bark may retain PCB from prior periods of high atmospheric concentrations. Bark is enriched in the more chlorinated PCB homologues relative to air. Congener-specific analyses show that, when compared with air, bark favorably accumulates the less volatile congeners. Lipophilicity is not a good indicator of bark PCB concentrations, but vapor pressure is.

  14. 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.

  15. On finding minimum-diameter clique trees

    SciTech Connect

    Blair, J.R.S. . Dept. of Computer Science); Peyton, B.W. )

    1991-08-01

    It is well-known that any chordal graph can be represented as a clique tree (acyclic hypergraph, join tree). Since some chordal graphs have many distinct clique tree representations, it is interesting to consider which one is most desirable under various circumstances. A clique tree of minimum diameter (or height) is sometimes a natural candidate when choosing clique trees to be processed in a parallel computing environment. This paper introduces a linear time algorithm for computing a minimum-diameter clique tree. The new algorithm is an analogue of the natural greedy algorithm for rooting an ordinary tree in order to minimize its height. It has potential application in the development of parallel algorithms for both knowledge-based systems and the solution of sparse linear systems of equations. 31 refs., 7 figs.

  16. Colloquium paper: terrestrial apes and phylogenetic trees.

    PubMed

    Arsuaga, Juan Luis

    2010-05-11

    The image that best expresses Darwin's thinking is the tree of life. However, Darwin's human evolutionary tree lacked almost everything because only the Neanderthals were known at the time and they were considered one extreme expression of our own species. Darwin believed that the root of the human tree was very deep and in Africa. It was not until 1962 that the root was shown to be much more recent in time and definitively in Africa. On the other hand, some neo-Darwinians believed that our family tree was not a tree, because there were no branches, but, rather, a straight stem. The recent years have witnessed spectacular discoveries in Africa that take us close to the origin of the human tree and in Spain at Atapuerca that help us better understand the origin of the Neanderthals as well as our own species. The final form of the tree, and the number of branches, remains an object of passionate debate. PMID:20445090

  17. Inference of fitness from genealogical trees

    NASA Astrophysics Data System (ADS)

    Vucelja, Marija; Dayarian, Adel; Shraiman, Boris

    2013-03-01

    Natural populations are fitness diverse and can have numerous genes under selection. The genealogical trees, that one obtains by sampling, often bear hallmarks of selection, such multiple mergers, asymmetric tree branches and long terminal branches (the trees are squished towards the root). These are qualitative differences compared to trees in the absence of selection. We propose a theoretical model that links the morphology of a tree with the fitness of the leaves. We obtain multipoint correlation functions of the fitness along the tree. In this way we are able extract some quantitative information about the strength of selection from data-reconstructed trees. The extensions of this approach can potentially be useful for inferring relative fitness of sequenced genomes of tumors and for predicting viral outbreaks.

  18. Effect of Antioxidants on DC Tree and Grounded DC Tree in XLPE

    NASA Astrophysics Data System (ADS)

    Kawanami, Hiroshi; Komatsu, Isao; Sekii, Yasuo; Saito, Mitsugu; Sugi, Kazuyuki

    To study the effects of antioxidants on the initiation of the DC tree and the grounded DC tree, experiments were conducted using XLPE specimens containing phenolic and sulfur type antioxidants. Experimental results showed that sulfur type antioxidants in XLPE have the effect of increasing inception voltages of both the DC tree and the grounded DC tree. Based on results of those experiments, the mechanism of increase in the inception voltage of the DC tree and the grounded DC tree by antioxidants was examined along with the mechanism of polarity effects on those trees. Results showed a promotional effect of charge injection from a needle electrode by antioxidants, which are responsible for the increased inception voltages of the DC tree. Charge trapping by antioxidants explains the increase of inception voltages of the grounded DC tree.

  19. Liana competition with tropical trees varies seasonally but not with tree species identity.

    PubMed

    Leonor, Alvarez-Cansino; Schnitzer, Stefan A; Reid, Joseph P; Powers, Jennifer S

    2015-01-01

    Lianas in tropical forests compete intensely with trees for above- and belowground resources and limit tree growth and regeneration. Liana competition with adult canopy trees may be particularly strong, and, if lianas compete more intensely with some tree species than others, they may influence tree species composition. We performed the first systematic, large-scale liana removal experiment to assess the competitive effects of lianas on multiple tropical tree species by measuring sap velocity and growth in a lowland tropical forest in Panama. Tree sap velocity increased 60% soon after liana removal compared to control trees, and tree diameter growth increased 25% after one year. Although tree species varied in their response to lianas, this variation was not significant, suggesting that lianas competed similarly with all tree species examined. The effect of lianas on tree sap velocity was particularly strong during the dry season, when soil moisture was low, suggesting that lianas compete intensely with trees for water. Under the predicted global change scenario of increased temperature and drought intensity, competition from lianas may become more prevalent in seasonal tropical forests, which, according to our data, should have a negative effect on most tropical tree species. PMID:26236888

  20. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    PubMed

    Chen, Shu-Chuan; Ogata, Aaron

    2015-01-01

    The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process. PMID:25826378

  1. Assessment of student conceptions of evolutionary trees

    NASA Astrophysics Data System (ADS)

    Blacquiere, Luke

    Biologists use evolutionary trees to depict hypotheses about the relationships among taxa. Trees possess lines that represent lineages, internal nodes that represent where lineages become evolutionarily isolated from one another and terminal nodes that represent the taxa under consideration. Interpreting a tree (i.e., "tree-thinking") is an important skill for biologists yet many students struggle when reading evolutionary trees. Common documented misconceptions include using morphological similarity, internal node counting or terminal node proximity, instead of identifying the internal node that represents a most recent common ancestor (MRCA), to determine relationships among taxa. I developed an instrument to assess whether students were using common ancestry or another, non-scientific, strategy to determine relationships among taxa. The study is the first to explicitly test hypotheses about how students approach reading evolutionary trees. To test the hypotheses an instrument was developed. The instrument is the first reliable and valid assessment testing student understanding of how to use most recent common ancestor to interpret evolutionary relationships in tree diagrams. Instructors can use the instrument as a diagnostic tool enabling them to help students learn this challenging concept. This study shows that, contrary to the assertion that students hold misconceptions about evolutionary trees made in the literature, students do not consistently use erroneous strategies when interpreting trees. This study suggests that a constructivist perspective of cognitive structure describes students' conception of evolutionary trees more closely than a misconception perspective.

  2. Breakpoint Distance and PQ-Trees

    NASA Astrophysics Data System (ADS)

    Jiang, Haitao; Chauve, Cedric; Zhu, Binhai

    The PQ-tree is a fundamental data structure that can encode large sets of permutations. It has recently been used in comparative genomics to model ancestral genomes with some uncertainty: given a phylogeny for some species, extant genomes are represented by permutations on the leaves of the tree, and each internal node in the phylogenetic tree represents an extinct ancestral genome, represented by a PQ-tree. An open problem related to this approach is then to quantify the evolution between genomes represented by PQ-trees. In this paper we present results for two problems of PQ-tree comparison motivated by this application. First, we show that the problem of comparing two PQ-trees by computing the minimum breakpoint distance among all pairs of permutations generated respectively by the two considered PQ-trees is NP-complete for unsigned permutations. Next, we consider a generalization of the classical Breakpoint Median problem, where an ancestral genome is represented by a PQ-tree and p permutations are given, with p ≥ 1, and we want to compute a permutation generated by the PQ-tree that minimizes the sum of the breakpoint distances to the p permutations. We show that this problem is Fixed-Parameter Tractable with respect to the breakpoint distance value. This last result applies both on signed and unsigned permutations, and to uni-chromosomal and multi-chromosomal permutations.

  3. 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. PMID:21869062

  4. Fault Tree, Event Tree, and Piping and Instrumentation Diagram (FEP) editors, Version 4. 0

    SciTech Connect

    McKay, M.K.; Skinner, N.L.; Wood, S.T. )

    1992-05-01

    The Fault Tree, Event Tree, and Piping Instrumentation Diagram (FEP) editors allow the user to graphically build and edit fault trees, event trees, and piping instrumentation diagrams (P IDs). The software is designed to enable the use of graphical-based editors found in the Integrated Reliability and Risk Assessment System (IRRAS). FEP is made up of three separate editors (Fault Tree, Event Tree, and Piping Instrumentation Diagram) and a utility module. This reference manual provides a screen-by-screen walkthrough of the entire FEP System.

  5. Tree canopy radiance measurement system

    NASA Technical Reports Server (NTRS)

    Caldwell, William; Vanderbilt, V. C.

    1989-01-01

    A system is described for obtaining both an estimate of the spatial mean bidirectional reflectance factor (BRF) for a tree canopy (displaying a horizontally heterogeneous foliage distribution) and the statistical significance of that estimate. The system includes a manlift supporting a horizontal beam 7 m long on which are mounted four radiometers. These radiometers may be pointed, and radiance data acquired, in any of 11 view directions in the principal plane of the sun. A total of 80 data points, acquired in 3 min, were used to estimate the BRF of a walnut orchard 5 m tall and detect true differences of 12 percent of the mean approximately 90 percent of the time.

  6. Phytoremediation of trichloroethene (TCE) using cottonwood trees

    USGS Publications Warehouse

    Jones, S.A.; Lee, R.W.; Kuniansky, E.L.

    1999-01-01

    The ability of cottonwood trees for phytoremediation was studied on aerobic shallow groundwater containing TCE. Cottonwood trees were planted over a 0.2-ha area at the Naval Air Station at Fort Worth, TX, in April 1996. Two years later, groundwater chemistry in the terrace alluvial aquifer was changing locally. Dissolved oxygen (DO) concentrations declined at the southern end of the whip plantings while total iron concentration increased. Groundwater chemistry near a mature cottonwood tree ~ 60 m from the caliper trees was different from that observed elsewhere. Anaerobic conditions near the mature cottonwood tree were evident. Reductive dechlorination of TCE occurred in the aquifer near the mature tree, as demonstrated by very small concentration of TCE in groundwater, a small median ratio of TCE to the degradation product cis-1,2-DCE and the presence of vinyl chloride.

  7. Local Frame Junction Trees in SLAM

    NASA Astrophysics Data System (ADS)

    Kuehnel, Frank O.

    2005-11-01

    Junction trees (JT) is a general purpose tool for exact inference on graphical models. Many of the existing algorithms for building junction trees require a fixed static graphical model. The construction process is not unique, finding the one with the best computational structure (smallest clique size) is also a hard problem. For large scale inference problems, such as Geo-referencing using triangular geodetic networks or equivalent, the simultaneous localization and mapping (SLAM) problem in robotics pose some challenges to junction tree applications. Incremental junction tree techniques for dynamic graphical models prescribe heuristic methods for growing the tree structure, and are applicable to large scale graphical models. Of concern are the proliferative widening of the tree, which makes message passing expensive. In the context of SLAM we present a new apporach that exploits the local frame dependence of novel observation variables.

  8. Reconciliation with Non-Binary Species Trees

    PubMed Central

    Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton

    2008-01-01

    Abstract Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|VG| · (kS + hS)) time, where |VG| is the number of nodes in the gene tree, hS is the height of the species tree and kS is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in Notung, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets. PMID:18808330

  9. Phillips goes subsea trees in Ivory Coast

    SciTech Connect

    Bryngelson, R.H.

    1982-11-15

    Describes installation of 3 wet, diver-assist trees, in the Espoir field offshore Ivory Coast, as part of Phillips Petroleum's plans to use 5 satellite wells with downhole completion equipment and subsea production trees. Simplicity in design and attention to training has resulted in an installation time of about 3 weeks for one of the largest subsea trees in the industry. Presents diagram showing the converted jackup, Dan Duke drilling unit, which supports equipment to handle production from subsea wells.

  10. Tutorial: Advanced fault tree applications using HARP

    NASA Technical Reports Server (NTRS)

    Dugan, Joanne Bechta; Bavuso, Salvatore J.; Boyd, Mark A.

    1993-01-01

    Reliability analysis of fault tolerant computer systems for critical applications is complicated by several factors. These modeling difficulties are discussed and dynamic fault tree modeling techniques for handling them are described and demonstrated. Several advanced fault tolerant computer systems are described, and fault tree models for their analysis are presented. HARP (Hybrid Automated Reliability Predictor) is a software package developed at Duke University and NASA Langley Research Center that is capable of solving the fault tree models presented.

  11. Sulfur nutrition of deciduous trees

    NASA Astrophysics Data System (ADS)

    Herschbach, Cornelia; Rennenberg, Heinz

    2001-01-01

    Sulfur in its reduced form (-II) is an essential nutrient for growth and development, but is mainly available to plants in its oxidised form as sulfate. Deciduous trees take up sulfate by the roots from the soil solution and reduce sulfate to sulfide via assimilatory sulfate reduction in both roots and leaves. For reduction in the leaves, sulfate is loaded into the xylem and transported to the shoot. The surplus of sulfate not reduced in the chloroplast or stored in the vacuole and the surplus of reduced S not used for protein synthesis in the leaves is loaded into the phloem and transported back to the roots. Along the transport path, sulfate and glutathione (GSH) is unloaded from the phloem for storage in xylem and phloem parenchyma as well as in pit and ray cells. Re-mobilised S from storage tissues is loaded into the xylem during spring, but a phloem to xylem exchange does not appear to exist later in the season. As a consequence, a cycling pool of S was only found during the change of the seasons. The sulfate:glutathione ratio in the phloem seems to be involved in the regulation of S nutrition. This picture of S nutrition is discussed in relation to the different growth patterns of deciduous trees from the temperate climate zone, i.e. (1) terminated, (2) periodic and (3) indeterminate growth patterns, and in relation to environmental changes.

  12. Fruit load governs transpiration of olive trees.

    PubMed

    Bustan, Amnon; Dag, Arnon; Yermiyahu, Uri; Erel, Ran; Presnov, Eugene; Agam, Nurit; Kool, Dilia; Iwema, Joost; Zipori, Isaac; Ben-Gal, Alon

    2016-03-01

    We tested the hypothesis that whole-tree water consumption of olives (Olea europaea L.) is fruit load-dependent and investigated the driving physiological mechanisms. Fruit load was manipulated in mature olives grown in weighing-drainage lysimeters. Fruit was thinned or entirely removed from trees at three separate stages of growth: early, mid and late in the season. Tree-scale transpiration, calculated from lysimeter water balance, was found to be a function of fruit load, canopy size and weather conditions. Fruit removal caused an immediate decline in water consumption, measured as whole-plant transpiration normalized to tree size, which persisted until the end of the season. The later the execution of fruit removal, the greater was the response. The amount of water transpired by a fruit-loaded tree was found to be roughly 30% greater than that of an equivalent low- or nonyielding tree. The tree-scale response to fruit was reflected in stem water potential but was not mirrored in leaf-scale physiological measurements of stomatal conductance or photosynthesis. Trees with low or no fruit load had higher vegetative growth rates. However, no significant difference was observed in the overall aboveground dry biomass among groups, when fruit was included. This case, where carbon sources and sinks were both not limiting, suggests that the role of fruit on water consumption involves signaling and alterations in hydraulic properties of vascular tissues and tree organs. PMID:26802540

  13. Why are so many trees hollow?

    PubMed

    Ruxton, Graeme D

    2014-11-01

    In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically. PMID:25392312

  14. Multispectral sensing of citrus young tree decline

    NASA Technical Reports Server (NTRS)

    Edwards, G. J.; Ducharme, E. P.; Schehl, T.

    1975-01-01

    Computer processing of MSS data to identify and map citrus trees affected by young tree decline is analyzed. The data were obtained at 1500-feet altitude in six discrete spectral bands covering regions from 0.53 to 1.3 millimicrons as well as from instrumental ground truths of tree crowns. Measurable spectral reflectance intensity differences are observed in the leaves of healthy and diseased trees, especially at wavelengths of 500 to 600 nm and 700 to 800 nm. The overall accuracy of the method is found to be 89%.

  15. The space of ultrametric phylogenetic trees.

    PubMed

    Gavryushkin, Alex; Drummond, Alexei J

    2016-08-21

    The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. PMID:27188249

  16. Horizontal subsea trees allow frequent deepwater workovers

    SciTech Connect

    Krenek, M.; Hall, G.; Sheng, W.Z.

    1995-05-01

    Horizontal subsea wellheads have found application in the Liuhua oil field in the South China Sea. These trees allow installation and retrieval of downhole equipment through the tree without having to disturb the tree or its external connections to flow lines, service lines, or control umbilicals. This access to the well is important because the Liuhua wells will be produced with electrical submersible pumps (ESPs), which may have relatively short intervals between maintenance, leading to frequent well work. The wells will be completed subsea in about 300 m of water. The large bore, horizontal trees allow all downhole equipment to be pulled without removal of the subsea tree. This wellhead configuration also provides well control and vertical access to downhole equipment through a conventional marine drilling riser and subsea blowout preventer (BOP), eliminating the need for costly specialized completion risers. Another benefit of the horizontal tree is its extremely compact profile with a low number of valves for well control. Valve size and spacing are decoupled from the size and bore spacing of the tubing hanger. The tree`s low profile geometry reduces costs of manufacturing the tree and framework and optimize load transfer to the wellhead.

  17. Creating ensembles of decision trees through sampling

    DOEpatents

    Kamath, Chandrika; Cantu-Paz, Erick

    2005-08-30

    A system for decision tree ensembles that includes a module to read the data, a module to sort the data, a module to evaluate a potential split of the data according to some criterion using a random sample of the data, a module to split the data, and a module to combine multiple decision trees in ensembles. The decision tree method is based on statistical sampling techniques and includes the steps of reading the data; sorting the data; evaluating a potential split according to some criterion using a random sample of the data, splitting the data, and combining multiple decision trees in ensembles.

  18. Belowground carbon trade among tall forest trees

    NASA Astrophysics Data System (ADS)

    Klein, Tamir; Siegwolf, Rolf; Koerner, Christian

    2016-04-01

    Just imagine one tree could hand over large quantities of carbon to another tree. How would that change our thinking about carbon relations of forests, the single biggest biological C reservoir on earth? If such a tree-to-tree C shuttle would exist, it required a demand-supply gradient and a pipeline. Here we show that exactly this unthinkable does occur in overlapping root spheres of tall trees in a mixed temperate forest. Using canopy scale stable carbon isotope labelling applied from a construction crane, we demonstrate that carbon assimilated by spruce is traded over to neighbouring beech, larch, and pine in amounts so large that fine roots almost equilibrate the carbon source signature. The isotope mixing ratio indicated that the interspecific transfer accounted for 40% of the fine root carbon, which is ca. 280 kg ha-1 a-1. This is the first forest scale evidence of a large flux of carbon among mature trees from evolutionary distant taxa. Carbon transfer most likely occurred through common ectomycorrhiza networks, which also exhibited the labelled carbon signal. These observations indicate that while competition for resources (e.g. light, water, nutrients) is often considered the dominant tree-tree interaction in a forest, trees actually interact in more complex pathways including a massive carbon exchange.

  19. Combinatorics of distance-based tree inference.

    PubMed

    Pardi, Fabio; Gascuel, Olivier

    2012-10-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206-13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  20. Combinatorics of distance-based tree inference

    PubMed Central

    Pardi, Fabio; Gascuel, Olivier

    2012-01-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206–13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  1. Understory plant communities and the functional distinction between savanna trees, forest trees, and pines.

    SciTech Connect

    Veldman, Joseph, W., Mattingly, Brett, W., Brudvig, Lars, A.

    2013-04-01

    Abstract. Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in fire frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are more fire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity.

  2. Tree-space statistics and approximations for large-scale analysis of anatomical trees.

    PubMed

    Feragen, Aasa; Owen, Megan; Petersen, Jens; Wille, Mathilde M W; Thomsen, Laura H; Dirksen, Asger; de Bruijne, Marleen

    2013-01-01

    Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than healthy ones. Software is available from http://image.diku.dk/aasa/software.php. PMID:24683959

  3. Understory plant communities and the functional distinction between savanna trees, forest trees, and pines.

    PubMed

    Veldman, Joseph W; Mattingly, W Brett; Brudvig, Lars A

    2013-02-01

    Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in fire frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are morefire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity. PMID:23691661

  4. The probability of topological concordance of gene trees and species trees.

    PubMed

    Rosenberg, Noah A

    2002-03-01

    The concordance of gene trees and species trees is reconsidered in detail, allowing for samples of arbitrary size to be taken from the species. A sense of concordance for gene tree and species tree topologies is clarified, such that if the "collapsed gene tree" produced by a gene tree has the same topology as the species tree, the gene tree is said to be topologically concordant with the species tree. The term speciodendric is introduced to refer to genes whose trees are topologically concordant with species trees. For a given three-species topology, probabilities of each of the three possible collapsed gene tree topologies are given, as are probabilities of monophyletic concordance and concordance in the sense of N. Takahata (1989), Genetics 122, 957-966. Increasing the sample size is found to increase the probability of topological concordance, but a limit exists on how much the topological concordance probability can be increased. Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation. PMID:11969392

  5. Atlas of United States Trees, Volume 2: Alaska Trees and Common Shrubs.

    ERIC Educational Resources Information Center

    Viereck, Leslie A.; Little, Elbert L., Jr.

    This volume is the second in a series of atlases describing the natural distribution or range of native tree species in the United States. The 82 species maps include 32 of trees in Alaska, 6 of shrubs rarely reaching tree size, and 44 more of common shrubs. More than 20 additional maps summarize environmental factors and furnish general…

  6. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE SALE AND DISPOSAL OF NATIONAL FOREST SYSTEM TIMBER General Provisions § 223.4 Exchange of trees...

  7. THE ENDICOTT PEAR TREE - OLDEST LIVING FRUIT TREE IN NORTH AMERICA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This brief article summarizes the history and present condition of a historic pear tree that is very likely to be the oldest fruit tree in North America. The Endicott Pear Tree was planted about 1630 in Danvers, Massachusetts by the Colonial Governor John Endicott. It has survived various hardships...

  8. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

    Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic

  9. The universal tree of life: an update

    PubMed Central

    Forterre, Patrick

    2015-01-01

    Biologists used to draw schematic “universal” trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution. PMID:26257711

  10. The universal tree of life: an update.

    PubMed

    Forterre, Patrick

    2015-01-01

    Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution. PMID:26257711

  11. Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

    SciTech Connect

    N. Price, Morgan; S. Dehal, Paramvir; P. Arkin, Adam

    2009-07-31

    Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

  12. Fault trees and imperfect coverage

    NASA Technical Reports Server (NTRS)

    Dugan, Joanne B.

    1989-01-01

    A new algorithm is presented for solving the fault tree. The algorithm includes the dynamic behavior of the fault/error handling model but obviates the need for the Markov chain solution. As the state space is expanded in a breadth-first search (the same is done in the conversion to a Markov chain), the state's contribution to each future state is calculated exactly. A dynamic state truncation technique is also presented; it produces bounds on the unreliability of the system by considering only part of the state space. Since the model is solved as the state space is generated, the process can be stopped as soon as the desired accuracy is reached.

  13. Robins gather in a tree

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In a wooded area of Kennedy Space Center, robins gather on a tree branch just beginning to show new Spring growth. A member of the thrush family, robins inhabit towns, gardens, open woodlands and agricultural lands. They range through most of North America, spending winters in large roosts mostly in the United States but also Newfoundland, southern Ontario and British Columbia. The Center shares a boundary with the Merritt Island National Wildlife Refuge, a haven and habitat for more than 331 species of birds. The Refuge encompasses 92,000 acres that are also a habitat for 31 mammals, 117 fishes, and 65 amphibians and reptiles. The marshes and open water of the refuge provide wintering areas for 23 species of migratory waterfowl, as well as a year-round home for great blue herons, great egrets, wood storks, cormorants, brown pelicans and other species of marsh and shore birds, as well as a variety of insects.

  14. Genealogical Trees of Scientific Papers

    PubMed Central

    Waumans, Michaël Charles; Bersini, Hugues

    2016-01-01

    Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a “dying” paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing “offspring”. Practically, this might be used to trace the successive published milestones of a research field. PMID:26954677

  15. A-3 First Tree Cutting

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Tree clearing for the site of the new A-3 Test Stand at Stennis Space center began June 13. NASA's first new large rocket engine test stand to be built since the site's inception, A-3 construction begins a historic era for America's largest rocket engine test complex. The 300-foot-tall structure is scheduled for completion in August 2010. A-3 will perform altitude tests on the Constellation's J-2X engine that will power the upper stage of the Ares I crew launch vehicle and earth departure stage of the Ares V cargo launch vehicle. The Constellation Program, NASA's plan for carrying out the nation's Vision for Space Exploration, will return humans to the moon and eventually carry them to Mars and beyond.

  16. Language distance and tree reconstruction

    NASA Astrophysics Data System (ADS)

    Petroni, Filippo; Serva, Maurizio

    2008-08-01

    Languages evolve over time according to a process in which reproduction, mutation and extinction are all possible. This is very similar to haploid evolution for asexual organisms and for the mitochondrial DNA of complex ones. Exploiting this similarity, it is possible, in principle, to verify hypotheses concerning the relationship among languages and to reconstruct their family tree. The key point is the definition of the distances among pairs of languages in analogy with the genetic distances among pairs of organisms. Distances can be evaluated by comparing grammar and/or vocabulary, but while it is difficult, if not impossible, to quantify grammar distance, it is possible to measure a distance from vocabulary differences. The method used by glottochronology computes distances from the percentage of shared 'cognates', which are words with a common historical origin. The weak point of this method is that subjective judgment plays a significant role. Here we define the distance of two languages by considering a renormalized edit distance among words with the same meaning and averaging over the two hundred words contained in a Swadesh list. In our approach the vocabulary of a language is the analogue of DNA for organisms. The advantage is that we avoid subjectivity and, furthermore, reproducibility of results is guaranteed. We apply our method to the Indo-European and the Austronesian groups, considering, in both cases, fifty different languages. The two trees obtained are, in many respects, similar to those found by glottochronologists, with some important differences as regards the positions of a few languages. In order to support these different results we separately analyze the structure of the distances of these languages with respect to all the others.

  17. The "Ride for Russia" Tree Lichen Survey

    ERIC Educational Resources Information Center

    Young, Simon

    2013-01-01

    The prevalence of nine indicator lichens found on trees in Northern Europe and Western Russia was used for monitoring air quality. The 4200 mile route of the survey went through eight countries. Surveys were carried out in cities, towns, countryside and forests, and along motorways. The author has conducted tree lichen surveys with pupils from…

  18. CRITIQUE OF CARBON BASED TREE GROWTH MODELS

    EPA Science Inventory

    Simulation models of the processes that control carbohydrate balance in coniferous trees are reviewed, and their appropriateness for assessing pollution effects is considered. Currently such models are at the forefront of attempts to simulate the growth process of trees, but they...

  19. Tree-hugging behavior beats the heat.

    PubMed

    Briscoe, Natalie J

    2015-01-01

    Animals can exploit spatial and temporal variation in microclimates to avoid stressful conditions, behavior that is likely to become increasingly important in a warming world. Recent research shows that during hot weather cool tree trunk surfaces can provide an important heat-loss avenue for arboreal mammals and other tree-dwelling animals. PMID:27226989

  20. Molecular basis of angiosperm tree architecture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The shoot architecture of trees greatly impacts orchard and forest management methods. Amassing greater knowledge of the molecular genetics behind tree form can benefit these industries as well as contribute to basic knowledge of plant developmental biology. This review covers basic components of ...

  1. Genetic interactions underlying tree branch orientation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Expanding our understanding of the molecular and genetic mechanisms behind branch orientation in trees both addresses a fundamental developmental phenomenon and can lead to significant impacts on tree crop agriculture and forestry. Using the p-nome (pooled genome) sequencing-based mapping approac...

  2. Tree-hugging behavior beats the heat

    PubMed Central

    Briscoe, Natalie J

    2014-01-01

    Animals can exploit spatial and temporal variation in microclimates to avoid stressful conditions, behavior that is likely to become increasingly important in a warming world. Recent research shows that during hot weather cool tree trunk surfaces can provide an important heat-loss avenue for arboreal mammals and other tree-dwelling animals. PMID:27227044

  3. The Tree Man: Robert Mazibuko's Story.

    ERIC Educational Resources Information Center

    Bloch, Joanne, Ed.

    This book for beginning readers highlights Robert Mazibuko, the "Tree Man," who spent his life teaching people how to enrich the soil and plant vegetables and trees. Born in South Africa in 1904, he lived on a farm, learning to work with livestock, raise crops, and share with the community. In college, his professor of agriculture provided a…

  4. Sussing merger trees: stability and convergence

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Pearce, Frazer R.; Knebe, Alexander; Schneider, Aurel; Srisawat, Chaichalit; Tweed, Dylan; Jung, Intae; Han, Jiaxin; Helly, John; Onions, Julian; Elahi, Pascal J.; Thomas, Peter A.; Behroozi, Peter; Yi, Sukyoung K.; Rodriguez-Gomez, Vicente; Mao, Yao-Yuan; Jing, Yipeng; Lin, Weipeng

    2016-06-01

    Merger trees are routinely used to follow the growth and merging history of dark matter haloes and subhaloes in simulations of cosmic structure formation. Srisawat et al. compared a wide range of merger-tree-building codes. Here we test the influence of output strategies and mass resolution on tree-building. We find that, somewhat surprisingly, building the tree from more snapshots does not generally produce more complete trees; instead, it tends to shorten them. Significant improvements are seen for patching schemes that attempt to bridge over occasional dropouts in the underlying halo catalogues or schemes that combine the halo-finding and tree-building steps seamlessly. The adopted output strategy does not affect the average number of branches (bushiness) of the resultant merger trees. However, mass resolution has an influence on both main branch length and the bushiness. As the resolution increases, a halo with the same mass can be traced back further in time and will encounter more small progenitors during its evolutionary history. Given these results, we recommend that, for simulations intended as precursors for galaxy formation models where of the order of 100 or more snapshots are analysed, the tree-building routine should be integrated with the halo finder, or at the very least be able to patch over multiple adjacent snapshots.

  5. Reliability computation using fault tree analysis

    NASA Technical Reports Server (NTRS)

    Chelson, P. O.

    1971-01-01

    A method is presented for calculating event probabilities from an arbitrary fault tree. The method includes an analytical derivation of the system equation and is not a simulation program. The method can handle systems that incorporate standby redundancy and it uses conditional probabilities for computing fault trees where the same basic failure appears in more than one fault path.

  6. How Trees Help the Power Company!

    ERIC Educational Resources Information Center

    King, Rik

    1992-01-01

    Proposes the utilization of graph theory to solve optimization problems. Defines the notion of spanning trees and presents two algorithms to determine optimization of a spanning tree. Discusses an example to connect towns by power transmission lines at minimum cost. (MDH)

  7. Algorithmic height compression of unordered trees.

    PubMed

    Ben-Naoum, Farah; Godin, Christophe

    2016-01-21

    By nature, tree structures frequently present similarities between their sub-parts. Making use of this redundancy, different types of tree compression techniques have been designed in the literature to reduce the complexity of tree structures. A popular and efficient way to compress a tree consists of merging its isomorphic subtrees, which produces a directed acyclic graph (DAG) equivalent to the original tree. An important property of this method is that the compressed structure (i.e. the DAG) has the same height as the original tree, thus limiting partially the possibility of compression. In this paper we address the problem of further compressing this DAG in height. The difficulty is that compression must be carried out on substructures that are not exactly isomorphic as they are strictly nested within each-other. We thus introduced a notion of quasi-isomorphism between subtrees that makes it possible to define similar patterns along any given path in a tree. We then proposed an algorithm to detect these patterns and to merge them, thus leading to compressed structures corresponding to DAGs augmented with return edges. In this way, redundant information is removed from the original tree in both width and height, thus achieving minimal structural compression. The complete compression algorithm is then illustrated on the compression of various plant-like structures. PMID:26551155

  8. Steiner trees and spanning trees in six-pin soap films

    NASA Astrophysics Data System (ADS)

    Dutta, Prasun; Khastgir, S. Pratik; Roy, Anushree

    2010-02-01

    The problem of finding minimum (local as well as absolute) path lengths joining given points (or terminals) on a plane is known as the Steiner problem. The Steiner problem arises in finding the minimum total road length joining several towns and cities. We study the Steiner tree problem using six-pin soap films. Experimentally, we observe spanning trees as well as Steiner trees partly by varying the pin diameter. We propose a possibly exact expression for the length of a spanning tree or a Steiner tree, which fails mysteriously in certain cases.

  9. Node degree distribution in spanning trees

    NASA Astrophysics Data System (ADS)

    Pozrikidis, C.

    2016-03-01

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

  10. Practical application of fault tree analysis

    SciTech Connect

    Prugh, R.W.

    1980-01-01

    A detailed survey of standard and novel approaches to Fault Tree construction, based on recent developments at Du Pont, covers the effect-to-cause procedure for control systems as in process plants; the effect-to-cause procedure for processes; source-of-hazard analysis, as in pressure vessel rupture; use of the ''fire triangle'' in a Fault Tree; critical combinations of safeguard failures; action points for automatic or operator control of a process; situations involving hazardous reactant ratios; failure-initiating and failure-enabling events and intervention by the operator; ''daisy-chain'' hazards, e.g., in batch processes and ship accidents; combining batch and continuous operations in a Fault Tree; possible future structure-development procedures for fault-tree construction; and the use of quantitative results (calculated frequencies of Top-Event occurrence) to restructure the Fault Tree after improving the process to any acceptable risk level.

  11. Efficient tree codes on SIMD computer architectures

    NASA Astrophysics Data System (ADS)

    Olson, Kevin M.

    1996-11-01

    This paper describes changes made to a previous implementation of an N -body tree code developed for a fine-grained, SIMD computer architecture. These changes include (1) switching from a balanced binary tree to a balanced oct tree, (2) addition of quadrupole corrections, and (3) having the particles search the tree in groups rather than individually. An algorithm for limiting errors is also discussed. In aggregate, these changes have led to a performance increase of over a factor of 10 compared to the previous code. For problems several times larger than the processor array, the code now achieves performance levels of ~ 1 Gflop on the Maspar MP-2 or roughly 20% of the quoted peak performance of this machine. This percentage is competitive with other parallel implementations of tree codes on MIMD architectures. This is significant, considering the low relative cost of SIMD architectures.

  12. Tree diversity, tree height and environmental harshness in eastern and western North America.

    PubMed

    Marks, Christian O; Muller-Landau, Helene C; Tilman, David

    2016-07-01

    Does variation in environmental harshness explain local and regional species diversity gradients? We hypothesise that for a given life form like trees, greater harshness leads to a smaller range of traits that are viable and thereby also to lower species diversity. On the basis of a strong dependence of maximum tree height on site productivity and other measures of site quality, we propose maximum tree height as an inverse measure of environmental harshness for trees. Our results show that tree species richness is strongly positively correlated with maximum tree height across multiple spatial scales in forests of both eastern and western North America. Maximum tree height co-varied with species richness along gradients from benign to harsh environmental conditions, which supports the hypothesis that harshness may be a general mechanism limiting local diversity and explaining diversity gradients within a biogeographic region. PMID:27146846

  13. Reconciliation of Gene and Species Trees

    PubMed Central

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

    2014-01-01

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

  14. Urban Tree Effects on Soil Organic Carbon

    PubMed Central

    Edmondson, Jill L.; O'Sullivan, Odhran S.; Inger, Richard; Potter, Jonathan; McHugh, Nicola; Gaston, Kevin J.; Leake, Jonathan R.

    2014-01-01

    Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ∼75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC) and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth) compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C∶N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered. PMID:25003872

  15. Urban tree effects on soil organic carbon.

    PubMed

    Edmondson, Jill L; O'Sullivan, Odhran S; Inger, Richard; Potter, Jonathan; McHugh, Nicola; Gaston, Kevin J; Leake, Jonathan R

    2014-01-01

    Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ∼75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC) and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth) compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C∶N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered. PMID:25003872

  16. Exploiting graph properties of game trees

    SciTech Connect

    Plaat, A.; Pijls, W.; Bruin, A. de; Schaeffer, J.

    1996-12-31

    The state space of most adversary games is a directed graph. However, due to the success of simple recursive algorithms based on alpha-beta, theoreticians and practitioners have concentrated on the traversal of trees, giving the field the name {open_quotes}game-tree search,{close_quotes} This paper shows that the focus on trees has obscured some important properties of the underlying graphs. One of the hallmarks of the field of game-tree search has been the notion of the minimal tree, the smallest tree that has to be searched by any algorithm to find the minimax value. In fact, for most games it is a directed graph. As demonstrated in chess and checkers, we show that the minimal graph is significantly smaller than previously thought, proving that there is more room for improvement of current algorithms. We exploit the graph properties of the search space to reduce the size of trees built in practice by at least 25%. For over a decade, fixed-depth alpha-beta searching has been considered a closed subject, with research moving on to more application-dependent techniques. This work opens up new avenues of research for further application-independent improvements.

  17. Decision Tree Technique for Particle Identification

    SciTech Connect

    Quiller, Ryan

    2003-09-05

    Particle identification based on measurements such as the Cerenkov angle, momentum, and the rate of energy loss per unit distance (-dE/dx) is fundamental to the BaBar detector for particle physics experiments. It is particularly important to separate the charged forms of kaons and pions. Currently, the Neural Net, an algorithm based on mapping input variables to an output variable using hidden variables as intermediaries, is one of the primary tools used for identification. In this study, a decision tree classification technique implemented in the computer program, CART, was investigated and compared to the Neural Net over the range of momenta, 0.25 GeV/c to 5.0 GeV/c. For a given subinterval of momentum, three decision trees were made using different sets of input variables. The sensitivity and specificity were calculated for varying kaon acceptance thresholds. This data was used to plot Receiver Operating Characteristic curves (ROC curves) to compare the performance of the classification methods. Also, input variables used in constructing the decision trees were analyzed. It was found that the Neural Net was a significant contributor to decision trees using dE/dx and the Cerenkov angle as inputs. Furthermore, the Neural Net had poorer performance than the decision tree technique, but tended to improve decision tree performance when used as an input variable. These results suggest that the decision tree technique using Neural Net input may possibly increase accuracy of particle identification in BaBar.

  18. Binary space partitioning trees and their uses

    NASA Technical Reports Server (NTRS)

    Bell, Bradley N.

    1989-01-01

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

  19. Comprehensive Decision Tree Models in Bioinformatics

    PubMed Central

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Purpose Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. Methods This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. Results The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. Conclusions The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class

  20. Detecting Coppice Legacies from Tree Growth.

    PubMed

    Müllerová, Jana; Pejcha, Vít; Altman, Jan; Plener, Tomáš; Dörner, Petr; Doležal, Jiří

    2016-01-01

    In coppice-with-standards, once a common type of management in Central European lowland forests, selected trees (standards) were left to grow mature among the regularly harvested coppice stools to obtain construction wood. After the underwood was harvested, the forest canopy opened rapidly, giving standard trees an opportunity to benefit from reduced competition. Although this silvicultural system virtually disappeared after WWII, historical management cycles can still be traced in the tree-rings of remaining standards. Our research aims at answering the question whether tree-ring series of standard trees can be used to reconstruct past management practices. The study was carried out on 117 oak standard trees from five sites situated in formerly coppiced calcareous oak-hornbeam and acidophilous oak forests in the Bohemian Karst Protected Landscape Area, Czech Republic. The evaluation was based on the analysis of growth releases representing the response of the standards to coppicing events, and comparison to the archival records of coppice events. Our results showed that coppicing events can be successfully detected by tree-ring analysis, although there are some limitations. Altogether 241 releases were identified (49% of major releases). Large number of releases could be related to historical records, with the major ones giving better results. The overall probability of correct detection (positive predictive power) was 58%, ranging from 50 to 67%, probability for major releases was 78%, ranging from 63 to 100% for different sites. The ability of individual trees to mirror past coppice events was significantly affected by competition from neighboring trees (their number and the sum of distance-weighted basal areas). A dendro-ecological approach to the study of forest management history can serve as an input for current attempts of coppice reintroduction and for conservation purposes. PMID:26784583

  1. Detecting Coppice Legacies from Tree Growth

    PubMed Central

    Müllerová, Jana; Pejcha, Vít; Altman, Jan; Plener, Tomáš; Dörner, Petr; Doležal, Jiří

    2016-01-01

    In coppice-with-standards, once a common type of management in Central European lowland forests, selected trees (standards) were left to grow mature among the regularly harvested coppice stools to obtain construction wood. After the underwood was harvested, the forest canopy opened rapidly, giving standard trees an opportunity to benefit from reduced competition. Although this silvicultural system virtually disappeared after WWII, historical management cycles can still be traced in the tree-rings of remaining standards. Our research aims at answering the question whether tree-ring series of standard trees can be used to reconstruct past management practices. The study was carried out on 117 oak standard trees from five sites situated in formerly coppiced calcareous oak-hornbeam and acidophilous oak forests in the Bohemian Karst Protected Landscape Area, Czech Republic. The evaluation was based on the analysis of growth releases representing the response of the standards to coppicing events, and comparison to the archival records of coppice events. Our results showed that coppicing events can be successfully detected by tree-ring analysis, although there are some limitations. Altogether 241 releases were identified (49% of major releases). Large number of releases could be related to historical records, with the major ones giving better results. The overall probability of correct detection (positive predictive power) was 58%, ranging from 50 to 67%, probability for major releases was 78%, ranging from 63 to 100% for different sites. The ability of individual trees to mirror past coppice events was significantly affected by competition from neighboring trees (their number and the sum of distance-weighted basal areas). A dendro-ecological approach to the study of forest management history can serve as an input for current attempts of coppice reintroduction and for conservation purposes. PMID:26784583

  2. Tree Death Study's Climate Change Connections

    SciTech Connect

    McDowell, Nate

    2012-09-10

    What are the exact physiological mechanisms that lead to tree death during prolonged drought and rising temperatures? These are the questions that scientists are trying to answer at a Los Alamos National Laboratory research project called SUMO. SUMO stands for SUrvival/MOrtality study; it's a plot of land on the Lab's southern border that features 18 climate controlled tree study chambers and a large drought structure that limits rain and snowfall. Scientists are taking a wide variety of measurements over a long period of time to determine what happens during drought and warming, and what the connections and feedback loops might be between tree death and climate change.

  3. Physical availability of tree biomass for energy

    SciTech Connect

    Bones, J.T.; Wharton, E.H.

    1983-06-01

    The physical availability of tree biomass for energy is discussed. But first a profile of the US timberland is drawn. Land area, tree volume--by region, species group, and class of timber--and ownership of the land are calculated. Though the West clearly has the greatest volume, the North and the Southeast, with more hardwood, and considerably greater private ownership of land, are more important for wood energy. Wood manufacturing residues, logging residues, and byproducts of timber product harvesting are the major sources for tree biomass energy.

  4. Physical availability of tree biomass for energy

    SciTech Connect

    Bones, J.T.; Wharton, E.H.

    1983-06-01

    The physical availability of tree biomass for energy is discussed. But first a profile of the US timberland is drawn. Land area, tree volume--by region, species group, and class of timber--and ownership of the land are calculated. Though the west clearly has the greatest volume, the North and the Southeast, with more hardwood, and considerably greater private ownership of land, are more important for wood energy. Wood manufacturing residues, logging residues, and byproducts of timber product harvesting are the major sources for tree biomass energy.

  5. The decision tree approach to classification

    NASA Technical Reports Server (NTRS)

    Wu, C.; Landgrebe, D. A.; Swain, P. H.

    1975-01-01

    A class of multistage decision tree classifiers is proposed and studied relative to the classification of multispectral remotely sensed data. The decision tree classifiers are shown to have the potential for improving both the classification accuracy and the computation efficiency. Dimensionality in pattern recognition is discussed and two theorems on the lower bound of logic computation for multiclass classification are derived. The automatic or optimization approach is emphasized. Experimental results on real data are reported, which clearly demonstrate the usefulness of decision tree classifiers.

  6. IND - THE IND DECISION TREE PACKAGE

    NASA Technical Reports Server (NTRS)

    Buntine, W.

    1994-01-01

    A common approach to supervised classification and prediction in artificial intelligence and statistical pattern recognition is the use of decision trees. A tree is "grown" from data using a recursive partitioning algorithm to create a tree which has good prediction of classes on new data. Standard algorithms are CART (by Breiman Friedman, Olshen and Stone) and ID3 and its successor C4 (by Quinlan). As well as reimplementing parts of these algorithms and offering experimental control suites, IND also introduces Bayesian and MML methods and more sophisticated search in growing trees. These produce more accurate class probability estimates that are important in applications like diagnosis. IND is applicable to most data sets consisting of independent instances, each described by a fixed length vector of attribute values. An attribute value may be a number, one of a set of attribute specific symbols, or it may be omitted. One of the attributes is delegated the "target" and IND grows trees to predict the target. Prediction can then be done on new data or the decision tree printed out for inspection. IND provides a range of features and styles with convenience for the casual user as well as fine-tuning for the advanced user or those interested in research. IND can be operated in a CART-like mode (but without regression trees, surrogate splits or multivariate splits), and in a mode like the early version of C4. Advanced features allow more extensive search, interactive control and display of tree growing, and Bayesian and MML algorithms for tree pruning and smoothing. These often produce more accurate class probability estimates at the leaves. IND also comes with a comprehensive experimental control suite. IND consists of four basic kinds of routines: data manipulation routines, tree generation routines, tree testing routines, and tree display routines. The data manipulation routines are used to partition a single large data set into smaller training and test sets. The

  7. Algorithms for optimal dyadic decision trees

    SciTech Connect

    Hush, Don; Porter, Reid

    2009-01-01

    A new algorithm for constructing optimal dyadic decision trees was recently introduced, analyzed, and shown to be very effective for low dimensional data sets. This paper enhances and extends this algorithm by: introducing an adaptive grid search for the regularization parameter that guarantees optimal solutions for all relevant trees sizes, revising the core tree-building algorithm so that its run time is substantially smaller for most regularization parameter values on the grid, and incorporating new data structures and data pre-processing steps that provide significant run time enhancement in practice.

  8. Tree Death Study's Climate Change Connections

    ScienceCinema

    McDowell, Nate

    2014-06-25

    What are the exact physiological mechanisms that lead to tree death during prolonged drought and rising temperatures? These are the questions that scientists are trying to answer at a Los Alamos National Laboratory research project called SUMO. SUMO stands for SUrvival/MOrtality study; it's a plot of land on the Lab's southern border that features 18 climate controlled tree study chambers and a large drought structure that limits rain and snowfall. Scientists are taking a wide variety of measurements over a long period of time to determine what happens during drought and warming, and what the connections and feedback loops might be between tree death and climate change.

  9. Classification based on full decision trees

    NASA Astrophysics Data System (ADS)

    Genrikhov, I. E.; Djukova, E. V.

    2012-04-01

    The ideas underlying a series of the authors' studies dealing with the design of classification algorithms based on full decision trees are further developed. It is shown that the decision tree construction under consideration takes into account all the features satisfying a branching criterion. Full decision trees with an entropy branching criterion are studied as applied to precedent-based pattern recognition problems with real-valued data. Recognition procedures are constructed for solving problems with incomplete data (gaps in the feature descriptions of the objects) in the case when the learning objects are nonuniformly distributed over the classes. The authors' basic results previously obtained in this area are overviewed.

  10. Behavior Trees for Evolutionary Robotics.

    PubMed

    Scheper, Kirk Y W; Tijmons, Sjoerd; de Visser, Cornelis C; de Croon, Guido C H E

    2016-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this article we show the first application of the Behavior Tree framework on a real robotic platform using the evolutionary robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behavior over that of the traditional neural network formulation. As a result, the behavior is easier to comprehend and manually adapt when crossing the reality gap from simulation to reality. This functionality is shown by performing real-world flight tests with the 20-g DelFly Explorer flapping wing micro air vehicle equipped with a 4-g onboard stereo vision system. The experiments show that the DelFly can fully autonomously search for and fly through a window with only its onboard sensors and processing. The success rate of the optimized behavior in simulation is 88%, and the corresponding real-world performance is 54% after user adaptation. Although this leaves room for improvement, it is higher than the 46% success rate from a tuned user-defined controller. PMID:26606468

  11. Distributed game-tree searching

    SciTech Connect

    Schaeffer, J. )

    1989-02-01

    Conventional parallelizations of the alpha-beta ({alpha}{beta}) algorithm have met with limited success. Implementations suffer primarily from the synchronization and search overheads of parallelization. This paper describes a parallel {alpha}{beta} searching program that achieves high performance through the use of four different types of processes: Controllers, Searchers, Table Managers, and Scouts. Synchronization is reduced by having Controller process reassigning idle processes to help out busy ones. Search overhead is reduced by having two types of parallel table management: global Table Managers and the periodic merging and redistribution of local tables. Experiments show that nine processors can achieve 5.67-fold speedups but beyond that, additional processors provide diminishing returns. Given that additional resources are of little benefit, speculative computing is introduced as a means of extending the effective number of processors that can be utilized. Scout processes speculatively search ahead in the tree looking for interesting features and communicate this information back to the {alpha}{beta} program. In this way, the effective search depth is extended. These ideas have been tested experimentally and empirically as part of the chess program ParaPhoenix.

  12. A tree of tree frogs around the Black Sea.

    PubMed

    Irwin, Darren E

    2016-09-01

    Speciation, the process by which one species evolves into two or more, is a major focus of ongoing debate, particularly regarding the geographic context in which it occurs. Geographic models of speciation tend to fall into discrete categories, typically referred to as allopatric, parapatric and sympatric speciation, according to whether two groups evolve reproductive isolation while geographically isolated, differentiated but connected by gene flow, or completely co-occurring. Yet molecular studies indicate that full development of reproductive isolation can take very long compared with the timescale at which climatic oscillations occur, such that the geographic context of differentiating forms might change often during the long process to full species. Studies of genetic relationships across the ranges of organisms with low-dispersal distances have the potential to reveal these complex histories. In a particularly elegant example in this issue, Dufresnes et al. () use genetic variation and ecological niche modelling to show that a ring of populations of the eastern tree frog (Hyla orientalis) surrounding the Black Sea had a complex history of geographic differentiation. Alternating phases of geographic fragmentation and phases of gene flow between neighbouring populations have produced a pattern of gradual genetic change connecting the western, southern and eastern sides of the ring, with the northwestern and northeastern forms being most differentiated. In the north, a population in Crimea appears to have been produced through mixture of the two extreme forms. The overall genetic relationships are reminiscent of those found in ring species, which have been used as prime demonstrations of the process of speciation. The difference, however, is that the terminal forms appear to have mixed rather than be reproductively isolated, although more research is needed to infer whether there might be some reproductive isolation on the northern side of the ring. PMID

  13. Controls on tree water uptake and information storage in tree rings

    NASA Astrophysics Data System (ADS)

    Blume, Theresa; Simard, Sonia; Heidbüchel, Ingo; Güntner, Andreas; Heinrich, Ingo

    2016-04-01

    Controls on tree water uptake are investigated in various forest stands in the northeastern German lowlands by a multi-method approach. This approach combines sapflow and dendrometer measurements as well as tree-ring analyses with soil moisture derived root water uptake rates. The latter method has the advantage that it provides depth distributions of root water uptake and thus additional information allowing for a more detailed analysis of the relationship between water availability and water uptake. High resolution climatic data makes it possible to investigate the site specific interplay between atmospheric demand and water availability on the one hand and tree response and adaptation on the other hand. The comparison of spatio-temporal patterns of these responses with concurrent tree growth as well as tree-ring analyses enables a first matching of actual and "archived" patterns and thus an estimate of how much of this information is stored in tree rings.

  14. Worms and Trees: An Exciting Adventure.

    ERIC Educational Resources Information Center

    El Harim, Jean Love

    1997-01-01

    Outlines procedures for using silkworms in elementary science, mathematics, history, ecology, social studies, language arts, art, and physical education. Also focuses on the silkworm's use of the mulberry tree. (DDR)

  15. Tree ring record chronicles major Mesoamerican droughts

    NASA Astrophysics Data System (ADS)

    Tretkoff, Ernie

    2011-05-01

    A new tree ring record chronicles major Mesoamerican droughts in the past millennium that may have contributed to the decline of some pre-Hispanic civilizations. Although there is other evidence of droughts during the past millennium, the paleoclimate record had gaps. Stahle et al. used core samples from Montezuma bald cypress trees found in Barranca de Amealco, Querétaro, Mexico, to develop a 1238-year tree ring chronology. They reconstructed the soil moisture record from the tree ring growth patterns. The new record provides the first dated, annually resolved climate record for Mexico and Central America spanning this time period.(Geophysical Research Letters, doi:10.1029/2010GL046472, 2011)

  16. Decision Tree Modeling for Ranking Data

    NASA Astrophysics Data System (ADS)

    Yu, Philip L. H.; Wan, Wai Ming; Lee, Paul H.

    Ranking/preference data arises from many applications in marketing, psychology, and politics. We establish a new decision tree model for the analysis of ranking data by adopting the concept of classification and regression tree. The existing splitting criteria are modified in a way that allows them to precisely measure the impurity of a set of ranking data. Two types of impurity measures for ranking data are introduced, namelyg-wise and top-k measures. Theoretical results show that the new measures exhibit properties of impurity functions. In model assessment, the area under the ROC curve (AUC) is applied to evaluate the tree performance. Experiments are carried out to investigate the predictive performance of the tree model for complete and partially ranked data and promising results are obtained. Finally, a real-world application of the proposed methodology to analyze a set of political rankings data is presented.

  17. Tree Ensembles on the Induced Discrete Space.

    PubMed

    Yildiz, Olcay Taner

    2016-05-01

    Decision trees are widely used predictive models in machine learning. Recently, K -tree is proposed, where the original discrete feature space is expanded by generating all orderings of values of k discrete attributes and these orderings are used as the new attributes in decision tree induction. Although K -tree performs significantly better than the proper one, their exponential time complexity can prohibit their use. In this brief, we propose K -forest, an extension of random forest, where a subset of features is selected randomly from the induced discrete space. Simulation results on 17 data sets show that the novel ensemble classifier has significantly lower error rate compared with the random forest based on the original feature space. PMID:26011897

  18. The mathematical information system MathTree

    NASA Astrophysics Data System (ADS)

    Ershov, Yu L.; Klimenko, O. A.; Matveeva, I. I.; Pikalov, V. V.

    2007-10-01

    This article describes the mathematical information system MathTree, created and developed in the Siberian Branch of the Russian Academy of Sciences. Its potentials, current status, and prospects for future development are discussed.

  19. Constructing event trees for volcanic crises

    USGS Publications Warehouse

    Newhall, C.; Hoblitt, R.

    2002-01-01

    Event trees are useful frameworks for discussing probabilities of possible outcomes of volcanic unrest. Each branch of the tree leads from a necessary prior event to a more specific outcome, e.g., from an eruption to a pyroclastic flow. Where volcanic processes are poorly understood, probability estimates might be purely empirical - utilizing observations of past and current activity and an assumption that the future will mimic the past or follow a present trend. If processes are better understood, probabilities might be estimated from a theoritical model, either subjectively or by numerical simulations. Use of Bayes' theorem aids in the estimation of how fresh unrest raises (or lowers) the probabilities of eruptions. Use of event trees during volcanic crises can help volcanologists to critically review their analysis of hazard, and help officials and individuals to compare volcanic risks with more familiar risks. Trees also emphasize the inherently probabilistic nature of volcano forecasts, with multiple possible outcomes.

  20. Probability tree algorithm for general diffusion processes

    NASA Astrophysics Data System (ADS)

    Ingber, Lester; Chen, Colleen; Mondescu, Radu Paul; Muzzall, David; Renedo, Marco

    2001-11-01

    Motivated by path-integral numerical solutions of diffusion processes, PATHINT, we present a tree algorithm, PATHTREE, which permits extremely fast accurate computation of probability distributions of a large class of general nonlinear diffusion processes.

  1. On some trees having partition dimension four

    NASA Astrophysics Data System (ADS)

    Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri

    2016-02-01

    In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.

  2. Locating POPs Sources with Tree Bark.

    PubMed

    Peverly, Angela A; Salamova, Amina; Hites, Ronald A

    2015-12-01

    Locating sources of persistent organic pollutants (POPs) to the atmosphere can sometimes be difficult. We suggest that tree bark makes an excellent passive atmospheric sampler and that spatial analysis of tree bark POPs concentrations can often pinpoint their sources. This is an effective strategy because tree bark is lipophilic and readily adsorbs and collects POPs from the atmosphere. As such, tree bark is an ideal sampler to find POPs sources globally, regionally, or locally. This article summarizes some work on this subject with an emphasis on kriged maps and a simple power-law model, both of which have been used to locate sources. Three of the four examples led directly to the pollutant's manufacturing plant. PMID:25629888

  3. Trees and networks before and after Darwin

    PubMed Central

    2009-01-01

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

  4. Trees and networks before and after Darwin.

    PubMed

    Ragan, Mark A

    2009-01-01

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

  5. TPM: Tree-Particle-Mesh code

    NASA Astrophysics Data System (ADS)

    Bode, Paul

    2013-05-01

    TPM carries out collisionless (dark matter) cosmological N-body simulations, evolving a system of N particles as they move under their mutual gravitational interaction. It combines aspects of both Tree and Particle-Mesh algorithms. After the global PM forces are calculated, spatially distinct regions above a given density contrast are located; the tree code calculates the gravitational interactions inside these denser objects at higher spatial and temporal resolution. The code is parallel and uses MPI for message passing.

  6. Parallel object-oriented decision tree system

    DOEpatents

    Kamath; Chandrika , Cantu-Paz; Erick

    2006-02-28

    A data mining decision tree system that uncovers patterns, associations, anomalies, and other statistically significant structures in data by reading and displaying data files, extracting relevant features for each of the objects, and using a method of recognizing patterns among the objects based upon object features through a decision tree that reads the data, sorts the data if necessary, determines the best manner to split the data into subsets according to some criterion, and splits the data.

  7. Speeding up Boosting decision trees training

    NASA Astrophysics Data System (ADS)

    Zheng, Chao; Wei, Zhenzhong

    2015-10-01

    To overcome the drawback that Boosting decision trees perform fast speed in the test time while the training process is relatively too slow to meet the requirements of applications with real-time learning, we propose a fast decision trees training method by pruning those noneffective features in advance. And basing on this method, we also design a fast Boosting decision trees training algorithm. Firstly, we analyze the structure of each decision trees node, and prove that the classification error of each node has a bound through derivation. Then, by using the error boundary to prune non-effective features in the early stage, we greatly accelerate the decision tree training process, and would not affect the training results at all. Finally, the decision tree accelerated training method is integrated into the general Boosting process forming a fast boosting decision trees training algorithm. This algorithm is not a new variant of Boosting, on the contrary, it should be used in conjunction with existing Boosting algorithms to achieve more training acceleration. To test the algorithm's speedup performance and performance combined with other accelerated algorithms, the original AdaBoost and two typical acceleration algorithms LazyBoost and StochasticBoost were respectively used in conjunction with this algorithm into three fast versions, and their classification performance was tested by using the Lsis face database which contained 12788 images. Experimental results reveal that this fast algorithm can achieve more than double training speedup without affecting the results of the trained classifier, and can be combined with other acceleration algorithms. Key words: Boosting algorithm, decision trees, classifier training, preliminary classification error, face detection

  8. GRFT - Genetic Records Family Tree Web Applet.

    PubMed

    Pimentel, Samuel; Walbot, Virginia; Fernandes, John

    2011-01-01

    Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT) applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: (1) a family tree view which displays a color-coded family tree for an individual, (2) a sequential list of crosses, and (3) a list of crosses matching user-defined search criteria. Each feature contains options to specify the number of records shown and the latter two contain an option to filter results by the owner of the cross. The family tree feature is interactive, displaying a popup box with genetic information when the user mouses over an individual and allowing the user to draw a new tree by clicking on any individual in the current tree. The applet is written in JavaScript and reads genetic records from a tab-delimited text file on the server, so it is cross-platform, can be accessed by anyone with an Internet connection, and supports almost instantaneous generation of new trees and table lists. Researchers can use the tool with their own genetic cross records for any sexually reproducing organism. No additional software is required and with only minor modifications to the script, researchers can add their own custom columns. GRFT's speed, versatility, and low overhead make it an effective and innovative visualization method for genetic records. A sample tool is available at http://stanford.edu/walbot/grft-sample.html. PMID:22303311

  9. A Conceptual Tree of Laser Propulsion

    SciTech Connect

    Pakhomov, Andrew V.; Sinko, John E.

    2008-04-28

    An original attempt to develop a conceptual tree for laser propulsion is offered. The tree provides a systematic view for practically all possible laser propulsion concepts and all inter-conceptual links, based on propellant phases and phase transfers. It also helps to see which fields of laser propulsion have been already thoroughly explored, where the next effort must be applied, and which paths should be taken with proper care or avoided entirely.

  10. Whatever happened to whole-tree chipping

    SciTech Connect

    Hills, C.F.

    1980-09-01

    There has been a dramatic increase in the utilization of chipper units since 1975. Continuing and increased demand for fiber indicates harvesting the maximum fiber per acre. Overall the increased yield is in the range of 25-40% and wood-tree chips are being put to a variety of uses. This article reviews the significant developments in both harvesting and mill site equipment which have allowed increased use of whole-tree chips while reducing grit load to the mill system.

  11. Current and Potential Tree Locations in Tree Line Ecotone of Changbai Mountains, Northeast China: The Controlling Effects of Topography

    PubMed Central

    Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

    2014-01-01

    Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone. PMID:25170918

  12. Genomics-assisted breeding in fruit trees

    PubMed Central

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

  13. Chlorinated ethenes from groundwater in tree trunks

    SciTech Connect

    Vroblesky, D.A.; Nietch, C.T.; Morris, J.T.

    1999-02-01

    The purpose of this investigation was to determine whether tree-core analysis could be used to delineate shallow groundwater contamination by chlorinated ethenes. Analysis of tree cores from bald cypress [Taxodium distichum (L.) Rich], tupelo (Nyssa aquatica L.), sweet gum (Liquidambar stryaciflua L.), oak (Quercus spp.), sycamore (Platanus occidentalis L.), and loblolly pine (Pinus taeda L.) growing over shallow groundwater contaminated with cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) showed that those compounds also were present in the trees. The cores were collected and analyzed by headspace gas chromatography. Bald cypress, tupelo, and loblolly pine contained the highest concentrations of TCE, with lesser amounts in nearby oak and sweet gum. The concentrations of cDCE and TCE in various trees appeared to reflect the configuration of the chlorinated-solvent groundwater contamination plume. Bald cypress cores collected along 18.6-m vertical transects of the same trunks showed that TCE concentrations decline by 30--70% with trunk height. The ability of the tested trees to take up cDCE and TCE make tree coring a potentially cost-effective and simple approach to optimizing well placement at this site.

  14. A global history of Australian trees.

    PubMed

    Bennett, Brett M

    2011-01-01

    Scholars studying the globalization of Australian trees have previously emphasized the rapid natural propagation of Australian trees outside of their native habitats, believing their success to be a reversal of "ecological imperialism" from the "new world" to the "old world." This article argues that the expansion of Australian trees should not be viewed as a biological phenomenon, but as the result of a long-term attempt by powerful states and state-sponsored scientists to select and breed Australian species that could grow in a variety of climates and ecological conditions. Five non-biological factors largely determined the success of these attempts to grow Australian trees: the abundance or paucity of natural forests, state power, the amount of scientific research directed to planting Australian trees, the cost of labor, and the ability to utilize hardwood timbers and bark. This paper compares the use of Australian trees in Australia, India, and South Africa to demonstrate that biology was not the determining factor in the long-term success of many Australian genera and species. PMID:20665086

  15. Transforming phylogenetic networks: Moving beyond tree space.

    PubMed

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

    2016-09-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. PMID:27224010

  16. Chlorinated ethenes from groundwater in tree trunks

    USGS Publications Warehouse

    Vroblesky, Don A.; Nietch, C.T.; Morris, J.T.

    1999-01-01

    The purpose of this investigation was to determine whether tree-core analysis could be used to delineate shallow groundwater contamination by chlorinated ethenes. Analysis of tree cores from bald cypress [Taxodium distichum (L.) Rich], tupelo (Nyssa aquatica L.), sweet gum (Liquidambar stryaciflua L.), oak (Quercus spp.), sycamore (Platanus occidentalis L.), and loblolly pine (Pinus taeda L.) growing over shallow groundwater contaminated with cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) showed that those compounds also were present in the trees. The cores were collected and analyzed by headspace gas chromatography. Bald cypress, tupelo, and loblolly pine contained the highest concentrations of TCE, with lesser amounts in nearby oak and sweet gum. The concentrations of cDCE and TCE in various trees appeared to reflect the configuration of the chlorinated-solvent groundwater contamination plume. Bald cypress cores collected along 18.6-m vertical transects of the same trunks showed that TCE concentrations decline by 30−70% with trunk height. The ability of the tested trees to take up cDCE and TCE make tree coring a potentially cost-effective and simple approach to optimizing well placement at this site. 

  17. ANTLR Tree Grammar Generator and Extensions

    NASA Technical Reports Server (NTRS)

    Craymer, Loring

    2005-01-01

    A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

  18. Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

    PubMed Central

    Stadler, Tanja; Degnan, James H.; Rosenberg, Noah A.

    2016-01-01

    Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

  19. Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

    PubMed

    Stadler, Tanja; Degnan, James H; Rosenberg, Noah A

    2016-07-01

    Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth-death and multispecies coalescent model can explain the difference in empirical trees and birth-death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

  20. Growing Greener Cities: A Tree-Planting Handbook.

    ERIC Educational Resources Information Center

    Moll, Gary; Young, Stanley

    This step-by-step guide, developed by the Global ReLeaf organization, presents tree-planting advice and simple steps to organizing a successful community tree-planting and tree-care program. The text is divided into three parts. Part 1 introduces trees and discusses the role they play as components of the living urban environment. Distinctions are…

  1. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  2. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  3. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  4. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  5. A Spring Playscape Project: Building a Tree Circle

    ERIC Educational Resources Information Center

    Keeler, Rusty

    2009-01-01

    The Tree Circle is a green gathering area for children made by planting trees in a circle. For children, the Tree Circle becomes a magical place for dramatic play, quiet retreat, or lively nature exploration. For teachers and parents it becomes a shady grove for snacks and stories. The trees create a sweet spot that changes during the seasons and…

  6. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value § 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  7. TreeRipper web application: towards a fully automated optical tree recognition software

    PubMed Central

    2011-01-01

    Background Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. Results TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3. PMID:21599881

  8. 75 FR 51507 - WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-20

    ... COMMISSION WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application August 13, 2010... materially amend subadvisory agreements without shareholder approval. Applicants: WisdomTree Asset Management, Inc (``WTAM'' or ``Adviser'') and WisdomTree Trust (``Trust''). Filing Dates: The application...

  9. Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes

    PubMed Central

    Petermann, Jana S.; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W.; Gossner, Martin M.

    2016-01-01

    Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and

  10. Headspace constituents of the tree remain of Cinnamomum camphora.

    PubMed

    Miyazawa, M; Hashimoto, Y; Taniguchi, Y; Kubota, K

    2001-01-01

    The volatile ingredients isolated from a fresh tree of Cinnamomum camphora (camphor tree) and from a tree remain of C. camphora were collected by using headspace techniques and analyzed by means of gas chromatography/mass spectrometry (GC/MS). 99.77% of the constituents consisting 23 components from the fresh tree, 98.68% of the constituents consisting 24 components from the tree remain were identified. Of these ingredients, camphor was obtained as the most abundant component. PMID:11547425

  11. Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes.

    PubMed

    Petermann, Jana S; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W; Gossner, Martin M

    2016-01-01

    Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and

  12. Radiocarbon in Tree STEM CO2 Efflux

    NASA Astrophysics Data System (ADS)

    Muhr, J.; Czimczik, C. I.; Angert, A.; Trumbore, S.

    2011-12-01

    Carbon dioxide efflux from tree stems can be a significant component of the stand-level carbon balance. Recent studies have demonstrated that tree stem CO2 efflux may reflect more than just in-situ respiration but also transport from other locations and it has been suggested that it may also include C originally respired in roots or even uptake of soil CO2. We report measurements of the radiocarbon signature of carbon emitted from a range of mature tree stems in tropical and temperate forest ecosystems. Comparison of the radiocarbon signature of respired CO2 with the observed rate of decline in atmsopheric 14C-CO2 provides a measure of the time elapsed between C fixation by the plant and its return to the atmosphere as stem CO2 efflux. In all investigated trees, we observed that stem CO2 efflux had higher radiocarbon signatures than the contemporary atmospheric 14C-CO2, and therefore was derived from C fixed one to several years earlier. In tropical forest trees, we found that the 14C signature of CO2 within the stem (~4-5 cm depth) had even higher radiocarbon signatures than the stem CO2 efflux. In one of the investigated tree species, the in-stem CO2 was derived from C sources fixed on average ~20 years previously. These results confirm observations of root-respired CO2 that also have shown contributions of C substrates older than recent photosynthetic products, and the presence of extracable C reserves in wood that reflect the presence of older C sources. Our results imply that stem CO2 efflux is not only derived from respiration of recent photosynthetic products but includes contributions from older, stored C pools. Ongoing investigations will enable us to compare CO2 efflux for trees subjected to experimental drought, and using different life strategies (deciduous versus evergreen oaks) to determine if the use of these older C stores varies with stress.

  13. Tree mineral nutrition is deteriorating in Europe.

    PubMed

    Jonard, Mathieu; Fürst, Alfred; Verstraeten, Arne; Thimonier, Anne; Timmermann, Volkmar; Potočić, Nenad; Waldner, Peter; Benham, Sue; Hansen, Karin; Merilä, Päivi; Ponette, Quentin; de la Cruz, Ana C; Roskams, Peter; Nicolas, Manuel; Croisé, Luc; Ingerslev, Morten; Matteucci, Giorgio; Decinti, Bruno; Bascietto, Marco; Rautio, Pasi

    2015-01-01

    The response of forest ecosystems to increased atmospheric CO2 is constrained by nutrient availability. It is thus crucial to account for nutrient limitation when studying the forest response to climate change. The objectives of this study were to describe the nutritional status of the main European tree species, to identify growth-limiting nutrients and to assess changes in tree nutrition during the past two decades. We analysed the foliar nutrition data collected during 1992-2009 on the intensive forest monitoring plots of the ICP Forests programme. Of the 22 significant temporal trends that were observed in foliar nutrient concentrations, 20 were decreasing and two were increasing. Some of these trends were alarming, among which the foliar P concentration in F. sylvatica, Q. Petraea and P. sylvestris that significantly deteriorated during 1992-2009. In Q. Petraea and P. sylvestris, the decrease in foliar P concentration was more pronounced on plots with low foliar P status, meaning that trees with latent P deficiency could become deficient in the near future. Increased tree productivity, possibly resulting from high N deposition and from the global increase in atmospheric CO2, has led to higher nutrient demand by trees. As the soil nutrient supply was not always sufficient to meet the demands of faster growing trees, this could partly explain the deterioration of tree mineral nutrition. The results suggest that when evaluating forest carbon storage capacity and when planning to reduce CO2 emissions by increasing use of wood biomass for bioenergy, it is crucial that nutrient limitations for forest growth are considered. PMID:24920268

  14. Temperature histories from tree rings and corals

    SciTech Connect

    Cook, E.R.

    1995-05-01

    Recent temperature trends in long tree-ring and coral proxy temperature histories are evaluated and compared in an effort to objectively determine how anomalous twentieth century temperature changes have been. These histories mostly reflect regional variations in summer warmth from the tree rings and annual warmth from the corals. In the Northern Hemisphere. the North American tree-ring temperature histories and those from the north Polar Urals, covering the past 1000 or more years, indicate that the twentieth century has been anomalously warm relative to the past. In contrast, the tree-ring history from northern Fennoscandia indicates that summer temperatures during the {open_quote}Medieval Warm Period{close_quote} were probably warmer on average than those than during this century. In the Southern Hemisphere, the tree-ring temperature histories from South America show no indication of recent warming, which is in accordance with local instrumental records. In contrast, the tree-ring, records from Tasmania and New Zealand indicate that the twentieth century has been unusually warm particularly since 1960. The coral temperature histories from the Galapagos Islands and the Great Barrier Reef are in broad agreement with the tree-ring temperature histories in those sectors, with the former showing recent cooling and the latter showing recent warming that may be unprecedented. Overall, the regional temperature histories evaluated here broadly support the larger-scale evidence for anomalous twentieth century warming based on instrumental records. However, this warming cannot be confirmed as an unprecedented event in all regions. 38 refs., 3 figs., 2 tabs.

  15. GM trees with increased resistance to herbivores: trait efficiency and their potential to promote tree growth

    PubMed Central

    Hjältén, Joakim; Axelsson, E. Petter

    2015-01-01

    Climate change, as well as a more intensive forestry, is expected to increase the risk of damage by pests and pathogens on trees, which can already be a severe problem in tree plantations. Recent development of biotechnology theoretically allows for resistance enhancement that could help reduce these risks but we still lack a comprehensive understanding of benefits and tradeoffs with pest resistant GM (genetically modified) trees. We synthesized the current knowledge on the effectiveness of GM forest trees with increased resistance to herbivores. There is ample evidence that induction of exogenous Bacillus thuringiensis genes reduce performance of target pests whereas upregulation of endogenous resistance traits e.g., phenolics, generates variable results. Our review identified very few studies estimating the realized benefits in tree growth of GM trees in the field. This is concerning as the realized benefit with insect resistant GM plants seems to be context-dependent and likely manifested only if herbivore pressure is sufficiently high. Future studies of secondary pest species and resistance evolution in pest to GM trees should be prioritized. But most importantly we need more long-term field tests to evaluate the benefits and risks with pest resistant GM trees. PMID:25983736

  16. Complementarity effects on tree growth are contingent on tree size and climatic conditions across Europe

    PubMed Central

    Madrigal-González, Jaime; Ruiz-Benito, Paloma; Ratcliffe, Sophia; Calatayud, Joaquín; Kändler, Gerald; Lehtonen, Aleksi; Dahlgren, Jonas; Wirth, Christian; Zavala, Miguel A.

    2016-01-01

    Neglecting tree size and stand structure dynamics might bias the interpretation of the diversity-productivity relationship in forests. Here we show evidence that complementarity is contingent on tree size across large-scale climatic gradients in Europe. We compiled growth data of the 14 most dominant tree species in 32,628 permanent plots covering boreal, temperate and Mediterranean forest biomes. Niche complementarity is expected to result in significant growth increments of trees surrounded by a larger proportion of functionally dissimilar neighbours. Functional dissimilarity at the tree level was assessed using four functional types: i.e. broad-leaved deciduous, broad-leaved evergreen, needle-leaved deciduous and needle-leaved evergreen. Using Linear Mixed Models we show that, complementarity effects depend on tree size along an energy availability gradient across Europe. Specifically: (i) complementarity effects at low and intermediate positions of the gradient (coldest-temperate areas) were stronger for small than for large trees; (ii) in contrast, at the upper end of the gradient (warmer regions), complementarity is more widespread in larger than smaller trees, which in turn showed negative growth responses to increased functional dissimilarity. Our findings suggest that the outcome of species mixing on stand productivity might critically depend on individual size distribution structure along gradients of environmental variation. PMID:27571971

  17. Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

    PubMed Central

    Grievink, Liat Shavit; Penny, David; Hendy, Michael D.; Holland, Barbara R.

    2010-01-01

    Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction. PMID:20525636

  18. Tree-Substrate Water Relations and Root Development in Tree Plantations Used for Mine Tailings Reclamation.

    PubMed

    Guittonny-Larchevêque, Marie; Bussière, Bruno; Pednault, Carl

    2016-05-01

    Tree water uptake relies on well-developed root systems. However, mine wastes can restrict root growth, in particular metalliferous mill tailings, which consist of the finely crushed ore that remains after valuable metals are removed. Thus, water stress could limit plantation success in reclaimed mine lands. This study evaluates the effect of substrates varying in quality (topsoil, overburden, compost and tailings mixture, and tailings alone) and quantity (50- or 20-cm-thick topsoil layer vs. 1-m plantation holes) on root development and water stress exposure of trees planted in low-sulfide mine tailings under boreal conditions. A field experiment was conducted over 2 yr with two tree species: basket willow ( L.) and hybrid poplar ( Moench × A. Henry). Trees developed roots in the tailings underlying the soil treatments despite tailings' low macroporosity. However, almost no root development occurred in tailings underlying a compost and tailings mixture. Because root development and associated water uptake was not limited to the soil, soil volume influenced neither short-term (water potential and instantaneous transpiration) nor long-term (δC) water stress exposure in trees. However, trees were larger and had greater total leaf area when grown in thicker topsoil. Despite a volumetric water content that always remained above permanent wilting point in the tailings colonized by tree roots, measured foliar water potentials at midday were lower than drought thresholds reported for both tested tree species. PMID:27136172

  19. "Trees and Things That Live in Trees": Three Children with Special Needs Experience the Project Approach

    ERIC Educational Resources Information Center

    Griebling, Susan; Elgas, Peg; Konerman, Rachel

    2015-01-01

    The authors report on research conducted during a project investigation undertaken with preschool children, ages 3-5. The report focuses on three children with special needs and the positive outcomes for each child as they engaged in the project Trees and Things That Live in Trees. Two of the children were diagnosed with developmental delays, and…

  20. Growth cessation uncouples isotopic signals in leaves and tree rings of drought-exposed oak trees.

    PubMed

    Pflug, Ellen E; Siegwolf, R; Buchmann, N; Dobbertin, M; Kuster, T M; Günthardt-Goerg, M S; Arend, M

    2015-10-01

    An increase in temperature along with a decrease in summer precipitation in Central Europe will result in an increased frequency of drought events and gradually lead to a change in species composition in forest ecosystems. In the present study, young oaks (Quercus robur L. and Quercus petraea (Matt.) Liebl.) were transplanted into large mesocosms and exposed for 3 years to experimental warming and a drought treatment with yearly increasing intensities. Carbon and oxygen isotopic (δ(13)C and δ(18)O) patterns were analysed in leaf tissue and tree-ring cellulose and linked to leaf physiological measures and tree-ring growth. Warming had no effect on the isotopic patterns in leaves and tree rings, while drought increased δ(18)O and δ(13)C. Under severe drought, an unexpected isotopic pattern, with a decrease in δ(18)O, was observed in tree rings but not in leaves. This decrease in δ(18)O could not be explained by concurrent physiological analyses and is not supported by current physiological knowledge. Analysis of intra-annual tree-ring growth revealed a drought-induced growth cessation that interfered with the record of isotopic signals imprinted on recently formed leaf carbohydrates. This missing record indicates isotopic uncoupling of leaves and tree rings, which may have serious implications for the interpretation of tree-ring isotopes, particularly from trees that experienced growth-limiting stresses. PMID:26377873

  1. Complementarity effects on tree growth are contingent on tree size and climatic conditions across Europe.

    PubMed

    Madrigal-González, Jaime; Ruiz-Benito, Paloma; Ratcliffe, Sophia; Calatayud, Joaquín; Kändler, Gerald; Lehtonen, Aleksi; Dahlgren, Jonas; Wirth, Christian; Zavala, Miguel A

    2016-01-01

    Neglecting tree size and stand structure dynamics might bias the interpretation of the diversity-productivity relationship in forests. Here we show evidence that complementarity is contingent on tree size across large-scale climatic gradients in Europe. We compiled growth data of the 14 most dominant tree species in 32,628 permanent plots covering boreal, temperate and Mediterranean forest biomes. Niche complementarity is expected to result in significant growth increments of trees surrounded by a larger proportion of functionally dissimilar neighbours. Functional dissimilarity at the tree level was assessed using four functional types: i.e. broad-leaved deciduous, broad-leaved evergreen, needle-leaved deciduous and needle-leaved evergreen. Using Linear Mixed Models we show that, complementarity effects depend on tree size along an energy availability gradient across Europe. Specifically: (i) complementarity effects at low and intermediate positions of the gradient (coldest-temperate areas) were stronger for small than for large trees; (ii) in contrast, at the upper end of the gradient (warmer regions), complementarity is more widespread in larger than smaller trees, which in turn showed negative growth responses to increased functional dissimilarity. Our findings suggest that the outcome of species mixing on stand productivity might critically depend on individual size distribution structure along gradients of environmental variation. PMID:27571971

  2. [Effects of tree height on whole-tree water use of Acacia mangium].

    PubMed

    Liu, Xiao-jing; Zhao, Ping; Wang, Quan; Cai, Xi-an; Zeng, Xiao-ping

    2009-01-01

    By using Granier's thermal dissipation probe, the sap flow of 14 sample trees in a 22-year old Acacia mangium forest in hilly land of South China was continuously measured in 2004. Environmental factors including the photosynthetically active radiation, air temperature, and air humidity above canopy and the water content in 0-30 cm soil layer were monitored simultaneously. Combining with the tree morphological features and sap flux density, the whole-tree transpiration, canopy stomatal conductance, and ratio of leaf area to sapwood area were calculated by simplified Whitehead and Jarvis equation, and the effects of tree height on these three parameters were analyzed. The results indicated that under sufficient soil water supply, the whole-tree transpiration increased in a quadratic polynomial way with tree height (P < 0.01), and the diurnal variation of canopy stomatal conductance was of one-peak pattern. Within the measured range of photosynthetically active radiation, taller A. mangium trees had higher reference canopy stomatal conductance and higher sensitivity of canopy stomatal conductance to vapor pressure deficit, compared with the shorter ones. The ratio of leaf area to sapwood area was (1.837 +/- 0.048) m2 x cm(-2), and increased in power function with tree height. A. mangium had no obvious hydraulic limitation and PMID:19449559

  3. Feedback of trees on nitrogen mineralization to restrict the advance of trees in C4 savannahs.

    PubMed

    Higgins, Steven I; Keretetse, Moagi; February, Edmund C

    2015-08-01

    Remote sensing studies suggest that savannahs are transforming into more tree-dominated states; however, progressive nitrogen limitation could potentially retard this putatively CO2-driven invasion. We analysed controls on nitrogen mineralization rates in savannah by manipulating rainfall and the cover of grass and tree elements against the backdrop of the seasonal temperature and rainfall variation. We found that the seasonal pattern of nitrogen mineralization was strongly influenced by rainfall, and that manipulative increases in rainfall could boost mineralization rates. Additionally, mineralization rates were considerably higher on plots with grasses and lower on plots with trees. Our findings suggest that shifting a savannah from a grass to a tree-dominated state can substantially reduce nitrogen mineralization rates, thereby potentially creating a negative feedback on the CO2-induced invasion of savannahs by trees. PMID:26268994

  4. Twistor-strings and gravity tree amplitudes

    NASA Astrophysics Data System (ADS)

    Adamo, Tim; Mason, Lionel

    2013-04-01

    Recently we discussed how Einstein supergravity tree amplitudes might be obtained from the original Witten and Berkovits twistor-string theory when external conformal gravitons are restricted to be Einstein gravitons. Here we obtain a more systematic understanding of the relationship between conformal and Einstein gravity amplitudes in that twistor-string theory. We show that although it does not in general yield Einstein amplitudes, we can nevertheless obtain some partial twistor-string interpretation of the remarkable formulae recently been found by Hodges and generalized to all tree amplitudes by Cachazo and Skinner. The Hodges matrix and its higher degree generalizations encode the world sheet correlators of the twistor string. These matrices control both Einstein amplitudes and those of the conformal gravity arising from the Witten and Berkovits twistor-string. Amplitudes in the latter case arise from products of the diagonal elements of the generalized Hodges matrices and reduced determinants give the former. The reduced determinants arise if the contractions in the worldsheet correlator are restricted to form connected trees at MHV. The (generalized) Hodges matrices arise as weighted Laplacian matrices for the graph of possible contractions in the correlators and the reduced determinants of these weighted Laplacian matrices give the sum of the connected tree contributions by an extension of the matrix-tree theorem.

  5. UniTree Name Server internals

    SciTech Connect

    Mecozzi, D.; Minton, J.

    1996-01-01

    The UniTree Name Server (UNS) is one of several servers which make up the UniTree storage system. The Name Server is responsible for mapping names to capabilities Names are generally human readable ASCII strings of any length. Capabilities are unique 256-bit identifiers that point to files, directories, or symbolic links. The Name Server implements a UNIX style hierarchical directory structure to facilitate name-to-capability mapping. The principal task of the Name Server is to manage the directories which make up the UniTree directory structure. The principle clients of the Name Server are the FTP Daemon, NFS and a few UniTree utility routines. However, the Name Server is a generalized server and will accept messages from any client. The purpose of this paper is to describe the internal workings of the UniTree Name Server. In cases where it seems appropriate, the motivation for a particular choice of algorithm as description of the algorithm itself will be given.

  6. How tree roots respond to drought

    PubMed Central

    Brunner, Ivano; Herzog, Claude; Dawes, Melissa A.; Arend, Matthias; Sperisen, Christoph

    2015-01-01

    The ongoing climate change is characterized by increased temperatures and altered precipitation patterns. In addition, there has been an increase in both the frequency and intensity of extreme climatic events such as drought. Episodes of drought induce a series of interconnected effects, all of which have the potential to alter the carbon balance of forest ecosystems profoundly at different scales of plant organization and ecosystem functioning. During recent years, considerable progress has been made in the understanding of how aboveground parts of trees respond to drought and how these responses affect carbon assimilation. In contrast, processes of belowground parts are relatively underrepresented in research on climate change. In this review, we describe current knowledge about responses of tree roots to drought. Tree roots are capable of responding to drought through a variety of strategies that enable them to avoid and tolerate stress. Responses include root biomass adjustments, anatomical alterations, and physiological acclimations. The molecular mechanisms underlying these responses are characterized to some extent, and involve stress signaling and the induction of numerous genes, leading to the activation of tolerance pathways. In addition, mycorrhizas seem to play important protective roles. The current knowledge compiled in this review supports the view that tree roots are well equipped to withstand drought situations and maintain morphological and physiological functions as long as possible. Further, the reviewed literature demonstrates the important role of tree roots in the functioning of forest ecosystems and highlights the need for more research in this emerging field. PMID:26284083

  7. Towards optimizing wood development in bioenergy trees.

    PubMed

    Nieminen, Kaisa; Robischon, Marcel; Immanen, Juha; Helariutta, Ykä

    2012-04-01

    To secure a sustainable energy source for the future, we need to develop an alternative to fossil fuels. Cellulose-based biofuel production has great potential for development into a sustainable and renewable energy source. The thick secondary walls of xylem cells provide a natural source of cellulose. As a result of the extensive production of wood through cambial activity, massive amounts of xylem cells can be harvested from trees. How can we obtain a maximal cellulose biomass yield from these trees? Thus far, tree breeding has been very challenging because of the long generation time. Currently, new breeding possibilities are emerging through the development of high-throughput technologies in molecular genetics. What potential does our current knowledge on the regulation of cambial activity provide for the domestication of optimal bioenergy trees? We examine the hormonal and molecular regulation of wood development with the aim of identifying the key regulatory aspects. We describe traits, including stem morphology and xylem cell dimensions, that could be modified to enhance wood production. Finally, we discuss the potential of novel marker-assisted tree breeding technologies. PMID:22474686

  8. Phillips goes subsea trees in Ivory Coast

    SciTech Connect

    Bryngelson, R.H.

    1982-11-15

    Describes installation of 3 satellite subsea trees in 500 ft of water from a semisubmersible drilling rig. These wet, diver-assist trees are part of Phillips Petroleum's early development and production program (EDPP) for the Espoir field offshore Ivory Coast, with plans calling for 5 satellite wells with downhole completion equipment and subsea production trees. Diagram shows how a converted jackup, Dan Duke, supports equipment to handle production from subsea wells. Table gives time breakdown of subsea tree installation. Before mobilizing the subsea trees, control system, and tubulars to the rig, a study of deck layout, payloads, and traffic patterns was performed. Concludes that, based on experience in this project and the cost differences between purchase and installation costs, final success is 90% dependent on informed and trained field personnel after engineering, design, and manufacturing; attention to installation procedures and training of field and operational personnel are as critical or more critical than design changes to equipment; and selection of a supplier for high technology equipment, based on a low bid alone, may not translate into lower installation costs.

  9. Urban tree influences on ultraviolet irradiance

    NASA Astrophysics Data System (ADS)

    Heisler, Gordon M.; Grant, Richard H.; Gao, Wei

    2002-01-01

    Many of the effects of ultraviolet radiation (UVR) on people and their environment--damage to various materials, survival of insects and microbial pathogens, growth of vegetation, and adverse or beneficial effects on human health--are modified by the presence of trees. Human epidemiological investigations generally consider exposure as given by indices of UVR irradiance on horizontal surfaces in the open. Though many people are exposed to UVR while reclining at a beach or swimming pool, thus experiencing irradiance on essentially horizontal surfaces in the open, exposure to UVR during daily routines in urban areas may also be important in affecting human health. Tree influences on UVR irradiance, particularly in the UVB, can differ substantially from influences on the visible portion of the solar spectrum. Trees greatly reduce UVB irradiance in their shade when they obscure both the sun and sky. Where trees obscure the sun but leave much of the sky in view, UVB irradiance will be greater than suggested by the visible shadow. In small sunny areas near trees that block much of the sky from view, UVB irradiance is reduced substantially, whereas visible irradiance may be nearly as great or slightly greater than in the open.

  10. Parallel search of strongly ordered game trees

    SciTech Connect

    Marsland, T.A.; Campbell, M.

    1982-12-01

    The alpha-beta algorithm forms the basis of many programs that search game trees. A number of methods have been designed to improve the utility of the sequential version of this algorithm, especially for use in game-playing programs. These enhancements are based on the observation that alpha beta is most effective when the best move in each position is considered early in the search. Trees that have this so-called strong ordering property are not only of practical importance but possess characteristics that can be exploited in both sequential and parallel environments. This paper draws upon experiences gained during the development of programs which search chess game trees. Over the past decade major enhancements of the alpha beta algorithm have been developed by people building game-playing programs, and many of these methods will be surveyed and compared here. The balance of the paper contains a study of contemporary methods for searching chess game trees in parallel, using an arbitrary number of independent processors. To make efficient use of these processors, one must have a clear understanding of the basic properties of the trees actually traversed when alpha-beta cutoffs occur. This paper provides such insights and concludes with a brief description of a refinement to a standard parallel search algorithm for this problem. 33 references.

  11. Fast Image Texture Classification Using Decision Trees

    NASA Technical Reports Server (NTRS)

    Thompson, David R.

    2011-01-01

    Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

  12. Hibernation by tree-roosting bats.

    PubMed

    Turbill, Christopher; Geiser, Fritz

    2008-07-01

    In summer, long-eared bats (Nyctophilus spp.) roost under bark and in tree cavities, where they appear to benefit from diurnal heating of roosts. In contrast, hibernation is thought to require a cool stable temperature, suggesting they should prefer thermally insulated tree cavities during winter. To test this prediction, we quantified the winter thermoregulatory physiology and ecology of hibernating tree-roosting bats, Nyctophilus geoffroyi and N. gouldi in the field. Surprisingly, bats in winter continued to roost under exfoliating bark (65%) on the northern, sunny side of trees and in shallow tree cavities (35%). Despite passive re-warming of torpid bats by 10-20 degrees C per day, torpor bouts lasted up to 15 days, although shorter bouts were also common. Arousals occurred more frequently and subsequent activity lasted longer on warmer nights, suggesting occasional winter foraging. We show that, because periodic arousals coincide with maximum roost temperatures, when costs of rewarming and normothermic thermoregulation are minimal, exposure to a daily temperature cycle could largely reduce energy expenditure during hibernation. Our study provides further evidence that models of torpor patterns and energy expenditure from hibernators in cold temperate climates are not directly applicable in milder climates, where prolonged torpor can be interspersed with more frequent arousals and occasional foraging. PMID:18210129

  13. Evolutionary induction of sparse neural trees

    PubMed

    Zhang; Ohm; Muhlenbein

    1997-01-01

    This paper is concerned with the automatic induction of parsimonious neural networks. In contrast to other program induction situations, network induction entails parametric learning as well as structural adaptation. We present a novel representation scheme called neural trees that allows efficient learning of both network architectures and parameters by genetic search. A hybrid evolutionary method is developed for neural tree induction that combines genetic programming and the breeder genetic algorithm under the unified framework of the minimum description length principle. The method is successfully applied to the induction of higher order neural trees while still keeping the resulting structures sparse to ensure good generalization performance. Empirical results are provided on two chaotic time series prediction problems of practical interest. PMID:10021759

  14. Scattering measurements on natural and model trees

    NASA Technical Reports Server (NTRS)

    Rogers, James C.; Lee, Sung M.

    1990-01-01

    The acoustical back scattering from a simple scale model of a tree has been experimentally measured. The model consisted of a trunk and six limbs, each with 4 branches; no foliage or twigs were included. The data from the anechoic chamber measurements were then mathematically combined to construct the effective back scattering from groups of trees. Also, initial measurements have been conducted out-of-doors on a single tree in an open field in order to characterize its acoustic scattering as a function of azimuth angle. These measurements were performed in the spring, prior to leaf development. The data support a statistical model of forest scattering; the scattered signal spectrum is highly irregular but with a remarkable general resemblance to the incident signal spectrum. Also, the scattered signal's spectra showed little dependence upon scattering angle.

  15. Creating Ensembles of Decision Trees Through Sampling

    SciTech Connect

    Kamath,C; Cantu-Paz, E

    2001-07-26

    Recent work in classification indicates that significant improvements in accuracy can be obtained by growing an ensemble of classifiers and having them vote for the most popular class. This paper focuses on ensembles of decision trees that are created with a randomized procedure based on sampling. Randomization can be introduced by using random samples of the training data (as in bagging or boosting) and running a conventional tree-building algorithm, or by randomizing the induction algorithm itself. The objective of this paper is to describe the first experiences with a novel randomized tree induction method that uses a sub-sample of instances at a node to determine the split. The empirical results show that ensembles generated using this approach yield results that are competitive in accuracy and superior in computational cost to boosting and bagging.

  16. Wind training in some prairie trees

    USGS Publications Warehouse

    Bogan, M.A.; Mollhagen, T.R.

    1969-01-01

    Asymmetry in tree crowns has been established for some time. Lawrence (Ecol. Monogr. 9:217-257, 1939) studied wind training, one cause of asymmetry, in the Columbia River Gorge. He and Boyce (Ecol. Monogr. 24: 29-67, 1954) cite the intensity and direction of wind during the growing season as the causative agents. In their study of trunk asymmetry, Potter and Green (Cology 45: 10-23, 1964) mention crown deformity in the open stands of trees. Prairie trees are typically found in open stands, and to our knowledge no quantitative studies have been done on their crown asymmetry. The present study on the nature of this asymmetry, is an attempt to fill the void.

  17. Tree attenuation at 20 GHz: Foliage effects

    NASA Astrophysics Data System (ADS)

    Vogel, Wolfhard J.; Goldhirsh, Julius

    1993-08-01

    Static tree attenuation measurements at 20 GHz (K-Band) on a 30 deg slant path through a mature Pecan tree with and without leaves showed median fades exceeding approximately 23 dB and 7 dB, respectively. The corresponding 1% probability fades were 43 dB and 25 dB. Previous 1.6 GHz (L-Band) measurements for the bare tree case showed fades larger than those at K-Band by 3.4 dB for the median and smaller by approximately 7 dB at the 1% probability. While the presence of foliage had only a small effect on fading at L-Band (approximately 1 dB additional for the median to 1% probability range), the attenuation increase was significant at K-Band, where it increased by about 17 dB over the same probability range.

  18. Tree attenuation at 20 GHz: Foliage effects

    NASA Technical Reports Server (NTRS)

    Vogel, Wolfhard J.; Goldhirsh, Julius

    1993-01-01

    Static tree attenuation measurements at 20 GHz (K-Band) on a 30 deg slant path through a mature Pecan tree with and without leaves showed median fades exceeding approximately 23 dB and 7 dB, respectively. The corresponding 1% probability fades were 43 dB and 25 dB. Previous 1.6 GHz (L-Band) measurements for the bare tree case showed fades larger than those at K-Band by 3.4 dB for the median and smaller by approximately 7 dB at the 1% probability. While the presence of foliage had only a small effect on fading at L-Band (approximately 1 dB additional for the median to 1% probability range), the attenuation increase was significant at K-Band, where it increased by about 17 dB over the same probability range.

  19. Creating ensembles of decision trees through sampling

    SciTech Connect

    Kamath, C; Cantu-Paz, E

    2001-02-02

    Recent work in classification indicates that significant improvements in accuracy can be obtained by growing an ensemble of classifiers and having them vote for the most popular class. This paper focuses on ensembles of decision trees that are created with a randomized procedure based on sampling. Randomization can be introduced by using random samples of the training data (as in bagging or arcing) and running a conventional tree-building algorithm, or by randomizing the induction algorithm itself. The objective of this paper is to describe our first experiences with a novel randomized tree induction method that uses a subset of samples at a node to determine the split. Our empirical results show that ensembles generated using this approach yield results that are competitive in accuracy and superior in computational cost.

  20. Forward estimation for game-tree search

    SciTech Connect

    Zhang, Weixiong

    1996-12-31

    It is known that bounds on the minimax values of nodes in a game tree can be used to reduce the computational complexity of minimax search for two-player games. We describe a very simple method to estimate bounds on the minimax values of interior nodes of a game tree, and use the bounds to improve minimax search. The new algorithm, called forward estimation, does not require additional domain knowledge other than a static node evaluation function, and has small constant overhead per node expansion. We also propose a variation of forward estimation, which provides a tradeoff between computational complexity and decision quality. Our experimental results show that forward estimation outperforms alpha-beta pruning on random game trees and the game of Othello.

  1. Global tree network for computing structures enabling global processing operations

    DOEpatents

    Blumrich; Matthias A.; Chen, Dong; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Steinmacher-Burow, Burkhard D.; Takken, Todd E.; Vranas, Pavlos M.

    2010-01-19

    A system and method for enabling high-speed, low-latency global tree network communications among processing nodes interconnected according to a tree network structure. The global tree network enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the tree via links to facilitate performance of low-latency global processing operations at nodes of the virtual tree and sub-tree structures. The global operations performed include one or more of: broadcast operations downstream from a root node to leaf nodes of a virtual tree, reduction operations upstream from leaf nodes to the root node in the virtual tree, and point-to-point message passing from any node to the root node. The global tree network is configurable to provide global barrier and interrupt functionality in asynchronous or synchronized manner, and, is physically and logically partitionable.

  2. Tree-based shortest-path routing algorithm

    NASA Astrophysics Data System (ADS)

    Long, Y. H.; Ho, T. K.; Rad, A. B.; Lam, S. P. S.

    1998-12-01

    A tree-based shortest path routing algorithm is introduced in this paper. With this algorithm, every network node can maintain a shortest path routing tree topology of the network with itself as the root. In this algorithm, every node constructs its own routing tree based upon its neighbors' routing trees. Initially, the routing tree at each node has the root only, the node itself. As information exchanges, every node's routing tree will evolve until a complete tree is obtained. This algorithm is a trade-off between distance vector algorithm and link state algorithm. Loops are automatically deleted, so there is no count-to- infinity effect. A simple routing tree information storage approach and a protocol data until format to transmit the tree information are given. Some special issues, such as adaptation to topology change, implementation of the algorithm on LAN, convergence and computation overhead etc., are also discussed in the paper.

  3. TSkim : A tool for skimming ROOT trees

    NASA Astrophysics Data System (ADS)

    Chamont, David

    2010-04-01

    Like many HEP researchers, the members of the Fermi collaboration have chosen to store their experiment data within ROOT trees. A frequent activity of such physicists is the tuning of selection criteria which define the events of interest, thus cutting and pruning the ROOT trees so to extract all the data linked to those specific physical events. It is rather straightforward to write a ROOT script to skim a single kind of data, for example the raw measurements of Fermi LAT detector. This proves to be trickier if one wants to process also some simulated or analysis data at the same time, because each kind of data is structured with its own rules for what concerns file names and sizes, tree names, identification of events, etc. TSkim has been designed to facilitate this task. Thanks to a user-defined configuration file which says where to find the run and event identifications in the different kind of trees, TSkim is able to collect all the tree elements which match a given ROOT cut. The tool will also help when loading the shared libraries which describe the experiment data, or when pruning the tree branches. Initially a pair of PERL and ROOT scripts, TSkim is today a fully compiled C++ application, enclosing our ROOT know-how and offering a panel of features going far beyond the original Fermi requirements. In this manuscript, we present TSkim concepts and key features, including a new kind of event list. Any collaboration using ROOT IO could profit from the use of this tool.

  4. PhyBin: binning trees by topology.

    PubMed

    Newton, Ryan R; Newton, Irene L G

    2013-01-01

    A major goal of many evolutionary analyses is to determine the true evolutionary history of an organism. Molecular methods that rely on the phylogenetic signal generated by a few to a handful of loci can be used to approximate the evolution of the entire organism but fall short of providing a global, genome-wide, perspective on evolutionary processes. Indeed, individual genes in a genome may have different evolutionary histories. Therefore, it is informative to analyze the number and kind of phylogenetic topologies found within an orthologous set of genes across a genome. Here we present PhyBin: a flexible program for clustering gene trees based on topological structure. PhyBin can generate bins of topologies corresponding to exactly identical trees or can utilize Robinson-Fould's distance matrices to generate clusters of similar trees, using a user-defined threshold. Additionally, PhyBin allows the user to adjust for potential noise in the dataset (as may be produced when comparing very closely related organisms) by pre-processing trees to collapse very short branches or those nodes not meeting a defined bootstrap threshold. As a test case, we generated individual trees based on an orthologous gene set from 10 Wolbachia species across four different supergroups (A-D) and utilized PhyBin to categorize the complete set of topologies produced from this dataset. Using this approach, we were able to show that although a single topology generally dominated the analysis, confirming the separation of the supergroups, many genes supported alternative evolutionary histories. Because PhyBin's output provides the user with lists of gene trees in each topological cluster, it can be used to explore potential reasons for discrepancies between phylogenies including homoplasies, long-branch attraction, or horizontal gene transfer events. PMID:24167782

  5. PhyBin: binning trees by topology

    PubMed Central

    Newton, Ryan R.

    2013-01-01

    A major goal of many evolutionary analyses is to determine the true evolutionary history of an organism. Molecular methods that rely on the phylogenetic signal generated by a few to a handful of loci can be used to approximate the evolution of the entire organism but fall short of providing a global, genome-wide, perspective on evolutionary processes. Indeed, individual genes in a genome may have different evolutionary histories. Therefore, it is informative to analyze the number and kind of phylogenetic topologies found within an orthologous set of genes across a genome. Here we present PhyBin: a flexible program for clustering gene trees based on topological structure. PhyBin can generate bins of topologies corresponding to exactly identical trees or can utilize Robinson-Fould’s distance matrices to generate clusters of similar trees, using a user-defined threshold. Additionally, PhyBin allows the user to adjust for potential noise in the dataset (as may be produced when comparing very closely related organisms) by pre-processing trees to collapse very short branches or those nodes not meeting a defined bootstrap threshold. As a test case, we generated individual trees based on an orthologous gene set from 10 Wolbachia species across four different supergroups (A–D) and utilized PhyBin to categorize the complete set of topologies produced from this dataset. Using this approach, we were able to show that although a single topology generally dominated the analysis, confirming the separation of the supergroups, many genes supported alternative evolutionary histories. Because PhyBin’s output provides the user with lists of gene trees in each topological cluster, it can be used to explore potential reasons for discrepancies between phylogenies including homoplasies, long-branch attraction, or horizontal gene transfer events. PMID:24167782

  6. Monitoring trees outside forests: a review.

    PubMed

    Schnell, Sebastian; Kleinn, Christoph; Ståhl, Göran

    2015-09-01

    Trees outside forests (TOFs) are an important natural resource that contributes substantially to national biomass and carbon stocks and to the livelihood of people in many regions. Over the last decades, decision makers have become increasingly aware of the importance of TOF, and as a consequence, this tree resource is nowadays often considered in forest monitoring systems. Our review shows that in many cases, TOF are included in national forest inventories, applying traditional methodologies with relatively sparse networks of field sample plots. Only in some countries, such as India, the design of the inventories has considered the special features of how TOFs occur in the landscape. Several research studies utilising remote sensing for monitoring TOF have been conducted lately, but very few studies include comparative studies to optimise sampling strategies for TOF. Our review indicates that methods combining remote sensing and field surveys appear to be very promising, especially when remote sensing techniques that assess both the horizontal and vertical structures of tree resources are applied. For example, two-phase sampling strategies with laser scanning in the first phase and a field survey in the second phase appear to be effective for assessing TOF resources. However, TOFs often exhibit different characteristics than forest trees. Thus, to improve TOF monitoring, there is often a need to develop models, e.g. for biomass assessment, that are specifically adapted to this tree resource. Alternatively, field-based remote sensing methods that provide structural information about individual trees, notably terrestrial laser scanning, could be further developed for TOF monitoring applications. This also would have a potential to reduce the problem of accessing TOF during field surveys, which is a problem, for example, in countries where TOF are present on intensively utilised private grounds like gardens and agricultural fields. PMID:26318320

  7. How do trees know it is autumn?

    NASA Astrophysics Data System (ADS)

    Jansson, Stefan

    2014-05-01

    To predict how forests will respond to climate change, it is necessary to understand how trees actually interpret environmental signals that the winter is approaching and use them to induce growth arrest, cold hardiness development, autumn leaf senescence and abscission. Autumn phenology traits and also under strong genetic control, and there exist within most tree species large variation in most phenology traits. Our model system is aspen (Populus tremula); one of the most widespread and abundant deciduous trees on earth. Growth arrest/bud set and cold hardiness in aspen is triggered by the gradual shortening of the photoperiod is the late season, and the molecular details behind have to some extent been deciphered. The molecular machinery triggering autumn leaf senescence - a trait developed to minimise nutrient loss - is in contrast, very poorly understood but bud set/growth arrest is a prerequisite for aspens to develop a competence to respond to the environmental signals triggering senescence. Once competence is developed, initiation of senescence seems to be triggered not by the daylength but some other daylight cue, and once senescence has been initiated the progression is influenced by temperature. The nitrogen, as well as carbohydrate, status interact can modify the senescence program of the tree. We are also identifying the precise genetic polymorphisms that are responsible for natural variation in autumn phenology traits in aspen, and study how different populations have different genetic makeups that provide local adaptation. Taken together, other environmental factors are more important than temperature is setting the timetable for aspens in the autumn. Although much less is know how autumn phenology traits are regulated in other tree species, the effect that increasing temperatures may have on future tree populations will also be discussed.

  8. Decision Tree Approach for Soil Liquefaction Assessment

    PubMed Central

    Gandomi, Amir H.; Fridline, Mark M.; Roke, David A.

    2013-01-01

    In the current study, the performances of some decision tree (DT) techniques are evaluated for postearthquake soil liquefaction assessment. A database containing 620 records of seismic parameters and soil properties is used in this study. Three decision tree techniques are used here in two different ways, considering statistical and engineering points of view, to develop decision rules. The DT results are compared to the logistic regression (LR) model. The results of this study indicate that the DTs not only successfully predict liquefaction but they can also outperform the LR model. The best DT models are interpreted and evaluated based on an engineering point of view. PMID:24489498

  9. Forest-fire model with immune trees

    NASA Astrophysics Data System (ADS)

    Drossel, B.; Schwabl, F.

    1993-10-01

    We present a generalization of the forest-fire model of P. Bak et al. by including the immunity g which is the probability that a tree is not ignited although one of its neighbors is burning. When g reaches a critical value gc( p), which depends on the tree growth rate p, the fire cannot survive any more, i.e. a continuous phase transition takes place from a steady state with fire to a steady state without fire. We present results of computer simulations and explain them by analytic calculations. The fire spreading at the phase transition represents a new type of percolation which is called “fluctuating site percolation”.

  10. Maximum likelihood clustering with dependent feature trees

    NASA Technical Reports Server (NTRS)

    Chittineni, C. B. (Principal Investigator)

    1981-01-01

    The decomposition of mixture density of the data into its normal component densities is considered. The densities are approximated with first order dependent feature trees using criteria of mutual information and distance measures. Expressions are presented for the criteria when the densities are Gaussian. By defining different typs of nodes in a general dependent feature tree, maximum likelihood equations are developed for the estimation of parameters using fixed point iterations. The field structure of the data is also taken into account in developing maximum likelihood equations. Experimental results from the processing of remotely sensed multispectral scanner imagery data are included.

  11. Surgical anatomy of the tracheobronchial tree

    PubMed Central

    Drevet, Gabrielle; Conti, Massimo

    2016-01-01

    Airway surgery is often indicated in the management of benign or malignant pathological processes of the tracheobronchial tree. The surgeon undertaking this type of work has, however, the responsibility of understanding the particular anatomy applicable to these structures and procedures as well as be able to correlate imaging, intraoperative findings and anatomy. These are important considerations if one wants to reduce operative morbidity and improve potential for better long-term results. This paper reviews the most important anatomic features of the tracheobronchial tree putting emphasis on those features that are important to surgeons performing surgical procedures on those organs. PMID:26981262

  12. Livermore Big Trees Park: 1998 Results

    SciTech Connect

    Mac Queen, D; Gallegos, G; Surano, K

    2002-04-18

    This report is an in-depth study of results from environmental sampling conducted in 1998 by the Lawrence Livermore National Laboratory (LLNL) at Big Trees Park in the city of Livermore. The purpose of the sampling was to determine the extent and origin of plutonium found in soil at concentrations above fallout-background levels in the park. This report describes the sampling that was conducted, the chemical and radio-chemical analyses of the samples, the quality control assessments and statistical analyses of the analytical results, and LLNL's interpretations of the results. It includes a number of data analyses not presented in LLNL's previous reports on Big Trees Park.

  13. Photoperiodic growth control in perennial trees

    PubMed Central

    Azeez, Abdul; Sane, Aniruddha P

    2015-01-01

    Plants have to cope with changing seasons and adverse environmental conditions. Being sessile, plants have developed elaborate mechanisms for their survival that allow them to sense and adapt to the environment and reproduce successfully. A major adaptive trait for the survival of trees of temperate and boreal forests is the induction of growth cessation in anticipation of winters. In the last few years enormous progress has been made to elucidate the molecular mechanisms underlying SDs induced growth cessation in model perennial tree hybrid aspen (Populus tremula × P. tremuloides). In this review we discuss the molecular mechanism underlying photoperiodic control of growth cessation and adaptive responses. PMID:26340077

  14. A survey of decision tree classifier methodology

    NASA Technical Reports Server (NTRS)

    Safavian, S. Rasoul; Landgrebe, David

    1990-01-01

    Decision Tree Classifiers (DTC's) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps, the most important feature of DTC's is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issue. After considering potential advantages of DTC's over single stage classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

  15. A survey of decision tree classifier methodology

    NASA Technical Reports Server (NTRS)

    Safavian, S. R.; Landgrebe, David

    1991-01-01

    Decision tree classifiers (DTCs) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps the most important feature of DTCs is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issues. After considering potential advantages of DTCs over single-state classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

  16. 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

  17. Equity trees and graphs via information theory

    NASA Astrophysics Data System (ADS)

    Harré, M.; Bossomaier, T.

    2010-01-01

    We investigate the similarities and differences between two measures of the relationship between equities traded in financial markets. Our measures are the correlation coefficients and the mutual information. In the context of financial markets correlation coefficients are well established whereas mutual information has not previously been as well studied despite its theoretically appealing properties. We show that asset trees which are derived from either the correlation coefficients or the mutual information have a mixture of both similarities and differences at the individual equity level and at the macroscopic level. We then extend our consideration from trees to graphs using the "genus 0" condition recently introduced in order to study the networks of equities.

  18. Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

    PubMed Central

    Burleigh, J. Gordon; Bansal, Mukul S.; Eulenstein, Oliver; Hartmann, Stefanie; Wehe, André; Vision, Todd J.

    2011-01-01

    Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life. PMID:21186249

  19. Nitrogen Isotopes in Tree Rings: A Record of Atmospheric Deposition or Tree Physiology?

    NASA Astrophysics Data System (ADS)

    Showers, W. J.; Genna, B.; Coon, M.

    2008-12-01

    Dendroisotopic analysis of nitrogen in tree rings has suggested that changes in nitrogen availability can be determined over time. These records match lake sediment and stream N flux measurements. Other studies suggest that tree ring nitrogen isotope data match foliar samples and not soil isotope data. In this study we compare the nitrogen isotope record from loblolly pine and American beech tree rings to a 10 year rainfall record and groundwater samples taken in isolated forested areas, next to a roadway and adjacent to agricultural fields. The influence of atmospheric nitrogen was determined by O17 analysis on groundwater nitrate. In areas where nutrient availability was low and O17 in groundwater nitrate was high, the tree ring nitrogen isotope record was similar to the nitrate nitrogen isotope trend. In areas where there was increased amounts of nitrate in groundwater due to local land use and O17 in groundwater nitrate was low, the nitrogen isotopic record in tree rings did not correlate to the atmospheric deposition record and probably represent internal recycling of nitrogen in the tree. These results suggest that nitrogen isotopes in tree rings can be used to monitor long term trends of atmospheric deposition of nitrogen in areas of low nutrient availability.

  20. MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees

    PubMed Central

    Taylor, Todd D.

    2016-01-01

    Metagenomic samples can contain hundreds or thousands of different species. The most common method to identify these species is to sequence the samples and then classify the reads to nodes along a phylogenic tree. Linear representations of trees with so many nodes face legibility issues. In addition, such views are not optimal for appreciating the read quantity assigned to each node. The problem is exaggerated when comparison between multiple samples is needed. MetaTreeMap adapts a visualization method that addresses these weaknesses. The tree is represented by nested rectangles that illustrate the number or percentage of assigned reads. MetaTreeMap implements various options specific to phylogenic trees that allow for quick overview and investigation of the information. More generally, the goal of this software is to provide the user with the ability to easily display phylogenic trees based on various quantities assigned to the nodes, such as read number, percentage or other values. The tool can be used online at http://metasystems.riken.jp/visualization/treemap/. PMID:27336370

  1. TreePlus: interactive exploration of networks with enhanced tree layouts.

    PubMed

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

    2006-01-01

    Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus. PMID:17073365

  2. Spatial Patterns of Trees from Airborne LiDAR Using a Simple Tree Segmentation Algorithm

    NASA Astrophysics Data System (ADS)

    Jeronimo, S.; Kane, V. R.; McGaughey, R. J.; Franklin, J. F.

    2015-12-01

    Objectives for management of forest ecosystems on public land incorporate a focus on maintenance and restoration of ecological functions through silvicultural manipulation of forest structure. The spatial pattern of residual trees - the horizontal element of structure - is a key component of ecological restoration prescriptions. We tested the ability of a simple LiDAR individual tree segmentation method - the watershed transform - to generate spatial pattern metrics similar to those obtained by the traditional method - ground-based stem mapping - on forested plots representing the structural diversity of a large wilderness area (Yosemite NP) and a large managed area (Sierra NF) in the Sierra Nevada, Calif. Most understory and intermediate-canopy trees were not detected by the LiDAR segmentation; however, LiDAR- and field-based assessments of spatial pattern in terms of tree clump size distributions largely agreed. This suggests that (1) even when individual tree segmentation is not effective for tree density estimates, it can provide a good measurement of tree spatial pattern, and (2) a simple segmentation method is adequate to measure spatial pattern of large areas with a diversity of structural characteristics. These results lay the groundwork for a LiDAR tool to assess clumping patterns across forest landscapes in support of restoration silviculture. This tool could describe spatial patterns of functionally intact reference ecosystems, measure departure from reference targets in treatment areas, and, with successive acquisitions, monitor treatment efficacy.

  3. Confirmatory Tree Sampling for Tritium in Trees at the Salmon Site, Mississippi

    SciTech Connect

    2010-06-01

    The sampling was conducted on April 20, 21, and 22, 2010. DOE acquired 36 samples for analysis, approximately 10 percent of the total number of samples the Mississippi Forestry Commission acquired. The plan was to sample trees that the Mississippi Forestry Commission also sampled, so that a tree-by-tree comparison of analysis results could be made. The Mississippi Forestry Commission provided DOE with latitude and longitude coordinates, determined by a global positioning system (GPS), for each sampled tree. The Mississippi Forestry Commission also placed a blaze-orange number on each sampled tree. DOE used a GPS unit to assist in locating trees for sampling. DOE acquired one sample from an off-site location to have a reference for comparison to on-site results if necessary. The other 35 samples were acquired on site, for a total of 36 samples. Figure 1 shows the sampling locations, the sample identifiers DOE assigned, and the corresponding tree numbers the Mississippi Forestry Commission assigned

  4. How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

    PubMed

    Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

    2014-11-01

    Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. PMID:25542897

  5. Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

    PubMed

    Lemessa, Debissa; Hambäck, Peter A; Hylander, Kristoffer

    2015-01-01

    Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests. PMID:25961306

  6. Arthropod but Not Bird Predation in Ethiopian Homegardens Is Higher in Tree-Poor than in Tree-Rich Landscapes

    PubMed Central

    Lemessa, Debissa; Hambäck, Peter A.; Hylander, Kristoffer

    2015-01-01

    Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7–9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests. PMID:25961306

  7. Surveying Dead Trees and CO2-Induced Stressed Trees Using AVIRIS in the Long Valley Caldera

    NASA Technical Reports Server (NTRS)

    deJong, Steven M.

    1996-01-01

    Since 1980 the Long Valley Caldera in the eastern Sierra Nevada (California) has shown signs of renewed volcanic activity. Frequent earthquakes, a re-inflation of the caldera, hydrothermal activity and gas emissions are the outer symptoms of this renewed activity. In 1990 and 1991 several areas of dying trees were found around Mammoth Mountain. The cause of the die off of the trees was first sought in the persistent drought in the preceding years. However, the trees died regardless of age and species. Farrar et al. (1995) started a soil-gas survey in 1994 in the dead-tree areas and found carbon dioxide concentrations ranging from 30 to 96% at soil depths between 30 and 60 cm. CO2 concentrations in the atmosphere are usually around 0.03% and in the soil profile CO2 levels do commonly not exceed 4 to 5%. Although not much is known about the effect of high levels of carbon dioxide in the soil profile on roots, it is most likely that the trees are dying due to oxygen deprivation: the CO2 drives the oxygen out of the soil. So far, four sites of dead trees have been mapped around Mammoth Mountain. The two largest dying trees sites are located near Horseshoe Lake and near Mammoth Mountain Main Lodge covering approximately an area of 10 and 8 ha respectively. Analysis of the gas composition regarding the He-3/He-4 ratio and the percentage biogenic carbon reveals the source of the gas: the magma body beneath the Long Valley Caldera. Until recently it was not known that volcanoes release abundant carbon dioxide from their flanks as diffuse soil emanations. As a result of the magma gas emission around Mammoth Mountain there is an excellent sequence of dead trees, stressed trees, healthy trees and bare soil surfaces. This research site provides excellent opportunities to: (1) Study the capabilities of imaging spectrometry to map stressed (and dead) pine and fir species; (2) Study methods to separate the vivid vegetation, stressed vegetation and dead vegetation from the soil

  8. The reality model of the plum tree based on SpeedTree

    NASA Astrophysics Data System (ADS)

    Bai, Zhi-yong; Huang, Xin-yuan

    2010-02-01

    Plum Blossom as the Chinese traditional flowers may be unique all over the world and has the first right of access to international registry of flower. In this paper, the SpeedTree software is used to quickly build reality model of the plum tree. The graphics texture mapping techniques is used, and the plum tree image maps express the geometric model of the surface material, which constitutes a visual image of the graphic objects. It is significant for non-destructive study of plum and virtual garden.

  9. TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

    SciTech Connect

    Gu, Shengyin; Anderson, Iain; Kunin, Victor; Cipriano, Michael; Minovitsky, Simon; Weber, Gunther; Amenta, Nina; Hamann, Bernd; Dubchak,Inna

    2007-05-07

    Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

  10. Effects of open-top chambers on 'Valencia' orange trees

    SciTech Connect

    Olszyk, D.M.; Takemoto, B.K.; Kats, G.; Dawson, P.J.; Morrison, C.L.

    1992-01-01

    Young 'Valencia' orange trees (Citrus sinensis(L) Osbeck) were grown for four years in large open-top chambers with ambient (nonfiltered) air or in outside air to determine any effects of the chambers on the air pollutant susceptibility of the trees. Long-term ozone average concentrations (12 hours, growing season) were 8% lower, and cumulative ozone dose (hourly values >0.1 microL/L) was 29% lower in ambient chambers compared to outside air. Fruit yields were much higher (>39%) for ambient chamber trees than for outside trees over three harvests, due at least partly to less fruit drop during the growing season for ambient chamber trees. Ambient chamber trees were much larger than outside trees and produced over twice as much leaf material over four years of study. Leaves on ambient chamber trees were larger and less dense than on outside trees. Leaves on ambient chamber trees were under more stress than leaves on outside trees during summer months; with lower stomatal conductances (14% average) and transpiration rates (12%), and more negative leaf water pressure potentials (28%). In contrast, leaves on ambient chamber trees had higher net photosynthetic rates (13%) and higher leaf starch concentrations prior to tree flowering (31%), than leaves on outside trees. While these results indicated large long-term impacts on tree growth which must be considered when using open-top chambers, they did not indicate any net effect of chambers on the air pollutant susceptibility of trees which would limit the usefulness of chamber tree data for air quality impact assessment purposes.

  11. Inferring polyploid phylogenies from multiply-labeled gene trees

    PubMed Central

    Lott, Martin; Spillner, Andreas; Huber, Katharina T; Petri, Anna; Oxelman, Bengt; Moulton, Vincent

    2009-01-01

    Background Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. Results We present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem. Conclusion We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels. PMID:19715596

  12. Fault Tree, Event Tree, and Piping and Instrumentation Diagram (FEP) editors, Version 4.0. Reference manual

    SciTech Connect

    McKay, M.K.; Skinner, N.L.; Wood, S.T.

    1992-05-01

    The Fault Tree, Event Tree, and Piping & Instrumentation Diagram (FEP) editors allow the user to graphically build and edit fault trees, event trees, and piping & instrumentation diagrams (P & IDs). The software is designed to enable the use of graphical-based editors found in the Integrated Reliability and Risk Assessment System (IRRAS). FEP is made up of three separate editors (Fault Tree, Event Tree, and Piping & Instrumentation Diagram) and a utility module. This reference manual provides a screen-by-screen walkthrough of the entire FEP System.

  13. Microwave soil moisture retrieval under trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During 2007 a field experiment was conducted with a goal of optimizing microwave soil moisture retrieval algorithms for small to medium deciduous trees. After initial field checkout in Fall 2006, the ComRAD microwave truck instrument system was deployed to a test site with several stands of deciduo...

  14. Climatic response of annual tree-rings

    NASA Astrophysics Data System (ADS)

    Ageev, Boris G.; Gruzdev, Aleksandr N.; Ponomarev, Yurii N.; Sapozhnikova, Valeria A.

    2014-11-01

    Extensive literature devoted to investigations into the influence of environmental conditions on the plant respiration and respiration rate. It is generally accepted that the respired CO2 generated in a stem completely diffuses into the atmosphere. Results obtained from explorations into the CO2 content in disc tree rings by the method proposed in this work shows that a major part of CO2 remains in tree stems and exhibits inter-annual variability. Different methods are used to describe of CO2 and H2O distributions in disc tree rings. The relation of CO2 and H2O variations in a Siberian stone pine disc to meteorological parameters are analyzed with use of wavelet, spectral and cross-spectral techniques. According to a multiple linear regression model, the time evolution of the width of Siberian stone pine rings can be partly explained by a combined influence of air temperature, precipitation, cloudiness and solar activity. Conclusions are made regarding the response of the CO2 and H2O content in coniferous tree disc rings to various climatic factors. Suggested method of CO2, (CO2+H2O) detection can be used for studying of a stem respiration in ecological risk areas.

  15. Disease and spray coverage in pecan trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan scab (Fusicladium effusum) is a destructive disease of pecan in the southeastern US. This study was conducted to investigate the vertical distribution of scab in tall pecan trees (14-16 m tall) in three experiments in 2010 and 2011. Although 2010 had average rainfall, a factor that drives scab...

  16. Improving spanning trees by upgrading nodes

    SciTech Connect

    Krumke, S.O.; Noltemeier, H.; Wirth, H.C.

    1997-01-16

    We study budget constrained optimal network upgrading problems. Such problems aim at finding optimal strategies for improving a network under some cost measure subject to certain budget constraints. A general problem in this setting is the following. We are given an edge weighted graph G = (V, E) where nodes represent processors and edges represent bidirectional communication links. The processor at a node v {element_of} V can be upgraded at a cost of c(v). Such an upgrade reduces the delay of each link emanating from v. The goal is to find a minimum cost set of nodes to be upgraded so that the resulting network has the best performance with respect to some measure. We consider the problem under two measures, namely, the weight of a minimum spanning tree and the bottleneck weight of a minimum bottleneck spanning tree. We present approximation and hardness results for the problem. Our results are tight to within constant factors. We also show that these approximation algorithms can be used to construct good approximation algorithms for the dual versions of the problems where there is a budget constraint on the upgrading cost and the objectives are minimum weight spanning tree and minimum bottleneck weight spanning tree respectively.

  17. Acoustic Detection of Insects in Palm Trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commercial-crop and ornamental palm trees serve important functions in tropical and subtropical regions of the world, and considerable precautions are taken each year to identify and control infestations of a variety of different insect pests. Large weevils, including the red palm weevil and the co...

  18. Constructing Student Problems in Phylogenetic Tree Construction.

    ERIC Educational Resources Information Center

    Brewer, Steven D.

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

  19. Teaching K. A. Porter's "That Tree."

    ERIC Educational Resources Information Center

    Monton, Elena Ortells

    2003-01-01

    Susan Lanser's poetics of point of view provides sound basis for the unveiling of the deeper layers of significance embedded behind the formal properties of a literary text. By applying her theory to the analysis of Porter's "That Tree," this article aims to yield a practical example of its enlightening use in the classroom. (Contains 18…

  20. NRCS-EQIP Tree Fruit IPM Program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2008, the WVU Extension Service partnered with the Natural Resources Conservation Service (NRCS) to develop and implement a cost-share IPM program for the commercial tree fruit growers in West Virginia. Fifty percent of implementation costs were paid by NRCS through the Environmental Quality Ince...

  1. Silver Trees: Chemistry on a TEM Grid

    EPA Science Inventory

    The copper/carbon substrate of a TEM grid reacted with aqueous silver nitrate solution within minutes to yield spectacular tree-like silver dendrites, without using any added capping or reducing reagents. These results demonstrate a facile, aqueous, room temperature synthesis of...

  2. Tree Seed Technology Training Course: Student Outline.

    ERIC Educational Resources Information Center

    Bonner, F. T.; And Others

    This manual is intended primarily to train seed collectors, seed-plant managers, seed analysts, and nursery managers, but can serve as a resource for any training course in forest regeneration. It includes both temperate and tropical tree species of all intended uses and covers the following topics: seed biology, seed collection, seed handling,…

  3. Disease and spray coverage in pecan trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan scab (Fusicladium effusum G. Winter) is the major disease of pecan in the southeastern U.S., and severe epidemics on susceptible cultivars can result in complete yield loss. Anecdotal evidence indicates adequate scab control in the tops of tall trees in mature orchards is difficult, but no dat...

  4. Advective Mechanisms in Tree Island Formation

    NASA Astrophysics Data System (ADS)

    Stothoff, S.

    2002-05-01

    Tree islands are important landscape features in the Florida Everglades. Tres islands are formed of peat deposited on the shallow limestone bedrock, and have been stressed as the system has changed in response to anthropogenic activities due to the sensitivity of organic soils to hydrologic cycles. The plume shape aligned with flow direction for typical tree islands is characteristic of advective transport, despite the rather low flow velocities in the system. Hypothesized mechanisms for the plume shape include sediment transport downstream from the head of the island (often anchored by a bedrock rise), or nutrient transport downstream allowing plants to produce more sediments in situ. Understanding mechanisms controlling tree island shape will aid in understanding the response of tree islands to hydrologic management. An integrated system of field, laboratory, and modeling studies is underway, with the first effort aimed at bounding the importance of the simpler sediment transport processes before tackling more-complex nutrient transport processes. The numerical model integrating the field and laboratory efforts is a 3D finite volume model considering water flow in the shallow groundwater/surface-water system together with sediment transport. The model can account for variable vegetative resistance through the flow column, including the important case where a dense mat forms at the surface. Model components specific for this system and associated data requirements are presented.

  5. Investigating Tree Thinking & Ancestry with Cladograms

    ERIC Educational Resources Information Center

    Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

    2015-01-01

    Interpreting cladograms is a key skill for biological literacy. In this lesson, students interpret cladograms based on familial relationships and language relationships to build their understanding of tree thinking and to construct a definition of "common ancestor." These skills can then be applied to a true biological cladogram.

  6. Pushing the pace of tree species migration.

    PubMed

    Lazarus, Eli D; McGill, Brian J

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  7. Quad Tree Structures for Image Compression Applications.

    ERIC Educational Resources Information Center

    Markas, Tassos; Reif, John

    1992-01-01

    Presents a class of distortion controlled vector quantizers that are capable of compressing images so they comply with certain distortion requirements. Highlights include tree-structured vector quantizers; multiresolution vector quantization; error coding vector quantizer; error coding multiresolution algorithm; and Huffman coding of the quad-tree…

  8. Phytotoxic evaluation of whole pine tree substrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Decreased availability and increased cost of quality substrates are issues facing many horticulture crop producers. Peat moss and pine bark are the most widely used substrate components, yet producers have become more aware of acceptable alternative components. Processed whole pine trees have been i...

  9. Intractable Tangles in the Bird Family Tree.

    PubMed

    Roberts, Roland G

    2015-08-01

    Rapid sequential speciation events can outpace the fixation of genetic variants, resulting in a family tree that lacks clear branching patterns. A new study of bird genomes reveals such an explosive super-radiation that may coincide with the mass extinction at the end of the Cretaceous period. PMID:26284616

  10. New substitution models for rooting phylogenetic trees

    PubMed Central

    Williams, Tom A.; Heaps, Sarah E.; Cherlin, Svetlana; Nye, Tom M. W.; Boys, Richard J.; Embley, T. Martin

    2015-01-01

    The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. PMID:26323766

  11. Propagation of almond rootstocks and trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Millions of almond trees in production in California and elsewhere were propagated by nurseries using the grafting technique called budding. This gives a uniform orchard and allows the grower to select nut cultivar (scion) and rootstock combinations. Grafting is a form of clonal propagation and resu...

  12. Pablo's Tree: Mathematics in a Different Light.

    ERIC Educational Resources Information Center

    Wickett, Maryann

    1996-01-01

    Relates mathematics to literature through the story "Pablo's Tree." The students turn flat paper into three-dimensional boxes through the use of riddles, reasoning, and communication, thereby providing the teacher an easy, informal way to assess their level of thinking and understanding. (AIM)

  13. An interactive programme for weighted Steiner trees

    NASA Astrophysics Data System (ADS)

    Zanchetta do Nascimento, Marcelo; Ramos Batista, Valério; Raffa Coimbra, Wendhel

    2015-01-01

    We introduce a fully written programmed code with a supervised method for generating weighted Steiner trees. Our choice of the programming language, and the use of well- known theorems from Geometry and Complex Analysis, allowed this method to be implemented with only 764 lines of effective source code. This eases the understanding and the handling of this beta version for future developments.

  14. Why trees and shrubs but rarely trubs?

    PubMed

    Scheffer, Marten; Vergnon, Remi; Cornelissen, J Hans C; Hantson, Stijn; Holmgren, Milena; van Nes, Egbert H; Xu, Chi

    2014-08-01

    An analysis of the maximum height of woody plant species across the globe reveals that an intermediate size is remarkably rare. We speculate that this may be due to intrinsic suboptimality or to ecosystem bistability with open landscapes favouring shrubs, and closed canopies propelling trees to excessive tallness. PMID:24951396

  15. What Is the Tree of Life?

    PubMed Central

    Doolittle, W. Ford; Brunet, Tyler D. P.

    2016-01-01

    A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic. PMID:27078870

  16. Evaluation Theory Tree Re-Examined

    ERIC Educational Resources Information Center

    Christie, Christina A.; Alkin, Marvin C.

    2008-01-01

    When examining various evaluation prescriptive theories comparatively, we find it helpful to have a framework showing how they are related that highlights features that distinguish theoretical perspectives, thus a "theory" about theories. The evaluation theory tree that we presented in Alkin's recent book, "Evaluation Roots" [Eisner, E. (2004).…

  17. New substitution models for rooting phylogenetic trees.

    PubMed

    Williams, Tom A; Heaps, Sarah E; Cherlin, Svetlana; Nye, Tom M W; Boys, Richard J; Embley, T Martin

    2015-09-26

    The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. PMID:26323766

  18. DYNAMIC STANDARDIZATION OF TREE-RING SERIES

    EPA Science Inventory

    The compound growth function of Warren (W.G. Warren, 1980. ree-Ring Bull. 40:35-44) represented an attempt to develop a model-based approach that standardized tree ring width sequences and was more flexible than the monotonic functions that were then commonly used. hile the idea ...

  19. The value of our public trees

    EPA Science Inventory

    An assessment of the value and annual benefits of public trees in the Corvallis Urban Growth Boundary (UGB) was recently conducted by Don Phillips (Research Biologist at the U.S. Environmental Protection Agency [EPA] research lab in Corvallis), along with Connie Burdick (EPA geog...

  20. Providing R-Tree Support for Mongodb

    NASA Astrophysics Data System (ADS)

    Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

    2016-06-01

    Supporting large amounts of spatial data is a significant characteristic of modern databases. However, unlike some mature relational databases, such as Oracle and PostgreSQL, most of current burgeoning NoSQL databases are not well designed for storing geospatial data, which is becoming increasingly important in various fields. In this paper, we propose a novel method to provide R-tree index, as well as corresponding spatial range query and nearest neighbour query functions, for MongoDB, one of the most prevalent NoSQL databases. First, after in-depth analysis of MongoDB's features, we devise an efficient tabular document structure which flattens R-tree index into MongoDB collections. Further, relevant mechanisms of R-tree operations are issued, and then we discuss in detail how to integrate R-tree into MongoDB. Finally, we present the experimental results which show that our proposed method out-performs the built-in spatial index of MongoDB. Our research will greatly facilitate big data management issues with MongoDB in a variety of geospatial information applications.

  1. The Case of the Similar Trees.

    ERIC Educational Resources Information Center

    Meyer, Rochelle Wilson

    1982-01-01

    A possible logical flaw based on similar triangles is discussed with the Sherlock Holmes mystery, "The Muskgrave Ritual." The possible flaw has to do with the need for two trees to have equal growth rates over a 250-year period in order for the solution presented to work. (MP)

  2. Pushing the Pace of Tree Species Migration

    PubMed Central

    Lazarus, Eli D.; McGill, Brian J.

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  3. Vacuum treatments for California tree nuts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    California walnuts, almonds and pistachios must be free of insect infestation to meet consumer demands and export requirements. Fumigants such as methyl bromide have long been used to disinfest tree nuts of field pests such as codling moth and navel orangeworm, and storage pests such as Indianmeal ...

  4. TREAT (TREe-based Association Test)

    Cancer.gov

    TREAT is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association be

  5. Phylogenetic classification and the universal tree.

    PubMed

    Doolittle, W F

    1999-06-25

    From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished. PMID:10381871

  6. Substrate influences ecophysiological performance of tree seedlings.

    PubMed

    Pröll, Gisela; Hietz, Peter; Delaney, Christina M; Katzensteiner, Klaus

    2016-01-01

    Unfavourable soil conditions frequently limit tree regeneration in mountain forests on calcareous bedrock. Rocky, shallow organic soils on dolomite pose a particular problem for tree regeneration due to commonly restricted water and nutrient supplies. Moreover, an often dense layer of understorey vegetation competes for the limited resources available. Hence, an array of interacting factors impairs tree seedlings' performance on dolomite, but there is little information on the ecophysiological mechanisms. We studied the effects of substrate, competing vegetation and foliar nutrient concentrations on the photosynthetic rate (A), stomatal conductance (gs) and leaf water potentials (ψ) of sycamore (Acer pseudoplatanus L.), beech (Fagus sylvatica L.), spruce [Picea abies (L.) Karst.] and larch (Larix decidua Mill.) under controlled (well-watered/drought-stressed) conditions and under prevailing field conditions. While A and gs of well-watered spruce in the pot experiment were reduced by the mineral substrate, the organic dolomite substrate with dense competing vegetation reduced gs and ψ of sycamore, spruce and larch under drought-stressed conditions in the field. For sycamore and spruce, A and gs were strongly correlated with foliar nitrogen (N) and potassium (K) concentrations in the pot experiment. In contrast, soil water primarily affected beech and larch. Finally, dense competing vegetation negatively affected A and gs of spruce and A of larch on dolomite. Our results highlight the critical role of N, K and water availability for tree seedlings in shallow soils on calcareous bedrock. On these sites, natural tree regeneration is at particular risk from episodic drought, a likely consequence of climate change. PMID:26446268

  7. The water relations of trees on karst

    NASA Astrophysics Data System (ADS)

    Schwinning, S.

    2008-05-01

    The ecohydrology of karst has not received much attention, despite the disproportionally large effect that karst ecosystems might have on the availability of global freshwater quantity and quality. Theoretical considerations suggest that the ecohydrology of woody plants in karst, specifically where soil cover is thin and trees take root in the epikarst, could be very different from that of woody plants in systems with deep soils. I explore the mechanistic basis and possible ecohydrologic consequences of these differences, as well as present the results of a field study into the water relations of trees in karst. The study examined the water sources and water relations of Quercus fusiformis (Small) and Juniperus ashei (Buchholz) in the karst region of the eastern Edwards Plateau, Texas (USA). Stable isotope analysis of stem water suggested that both trees used evaporatively enriched water stored in the epikarst. Q. fusiformis had consistently higher predawn water potentials than J. ashei during drought. However, epikarst structure had strong effects on the predawn water potentials experienced during drought. Although the water potentials of both species recovered after drought- breaking rain events, associated shifts in stem water isotope ratios did not indicate significant uptake of rainwater from the shallow soil. A hypothesis is developed to explain this phenomenon invoking a piston-flow mechanism that pushes water stored in macropores into the pseudomatrix and into the presumed active root zones of the trees. The study suggests that tree species of the Edwards Plateau do not commonly reduce aquifer recharge by tapping directly into macropores or perched water tables, but more likely by reducing water storage in the pseudomatrix of the epikarst.

  8. Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

    PubMed Central

    Vaniya, Arpana

    2015-01-01

    Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations. PMID:26213431

  9. USE OF SEWAGE SLUDGE FOR FOREST-TREE SEEDLING PRODUCTION

    EPA Science Inventory

    Research was undertaken to determine the beneficial and harmful effects of using dewatered, digested sewage sludge in: (1) containerized production of forest tree seedlings, (2) tree seedling production in a conventional outdoor nursery, (3) establishment and growth of transplant...

  10. Radar cross section of a planar fractal tree

    NASA Astrophysics Data System (ADS)

    Demiris, John

    1989-03-01

    Electromagnetic scattering from trees and vegetation is of prime importance in radar and remote sensing. The actual problem of scattering from trees is rather complicated and involves three dimensional scattering from lossy, electrically large, and randomly oriented objects. In this thesis, the radar cross section of a planar fractal tree is considered. Although a planar tree is far from being real, scattering from it shed light on the scattering phenomenon from an actual tree. The planar tree is generated using fractal geometry and its branches are considered perfectly conducting. The tree is illuminated by a plane wave and the problem is solved using the moment method. Data is presented for the radar cross section for different branching angles of the tree and at different frequencies.

  11. Collecting, preparing, crossdating, and measuring tree increment cores

    USGS Publications Warehouse

    Phipps, R.L.

    1985-01-01

    Techniques for collecting and handling increment tree cores are described. Procedures include those for cleaning and caring for increment borers, extracting the sample from a tree, core surfacing, crossdating, and measuring. (USGS)

  12. 13. FLOOR 1: DETAIL OF POSTS SUPPORTING BRIDGE TREE TO ...

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

    13. FLOOR 1: DETAIL OF POSTS SUPPORTING BRIDGE TREE TO NORTH; NOTE BEADING AT CORNERS; WEDGES ADJUST HEIGHT OF PIVOTING END OF BRIDGE TREE - Pantigo Windmill, James Lane, East Hampton, Suffolk County, NY

  13. 5. TUNNEL TREE AT DRIVETHROUGHTREE PARK. LEGGETT, HUMBOLDT COUNTY, CALIFORNIA. ...

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

    5. TUNNEL TREE AT DRIVE-THROUGH-TREE PARK. LEGGETT, HUMBOLDT COUNTY, CALIFORNIA. LOOKING NE. - Redwood National & State Parks Roads, California coast from Crescent City to Trinidad, Crescent City, Del Norte County, CA

  14. 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.

  15. Blooming Trees Can Bring Misery to Allergy Sufferers

    MedlinePlus

    ... nih.gov/medlineplus/news/fullstory_157872.html Blooming Trees Can Bring Misery to Allergy Sufferers But expert ... 20, 2016 SUNDAY, March 20, 2016 (HealthDay News) -- Tree pollen season has arrived, but there are a ...

  16. Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

    NASA Astrophysics Data System (ADS)

    Hosoi, F.

    2014-12-01

    Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of

  17. PypeTree: a tool for reconstructing tree perennial tissues from point clouds.

    PubMed

    Delagrange, Sylvain; Jauvin, Christian; Rochon, Pascal

    2014-01-01

    The reconstruction of trees from point clouds that were acquired with terrestrial LiDAR scanning (TLS) may become a significant breakthrough in the study and modelling of tree development. Here, we develop an efficient method and a tool based on extensive modifications to the skeletal extraction method that was first introduced by Verroust and Lazarus in 2000. PypeTree, a user-friendly and open-source visual modelling environment, incorporates a number of improvements into the original skeletal extraction technique, making it better adapted to tackle the challenge of tree perennial tissue reconstruction. Within PypeTree, we also introduce the idea of using semi-supervised adjustment tools to address methodological challenges that are associated with imperfect point cloud datasets and which further improve reconstruction accuracy. The performance of these automatic and semi-supervised approaches was tested with the help of synthetic models and subsequently validated on real trees. Accuracy of automatic reconstruction greatly varied in terms of axis detection because small (length < 3.5 cm) branches were difficult to detect. However, as small branches account for little in terms of total skeleton length, mean reconstruction error for cumulated skeleton length only reached 5.1% and 1.8% with automatic or semi-supervised reconstruction, respectively. In some cases, using the supervised tools, a perfect reconstruction of the perennial tissue could be achieved. PMID:24599190

  18. Environmental fate of emamectin benzoate after tree micro injection of horse chestnut trees.

    PubMed

    Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

    2015-02-01

    Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. PMID:25363584

  19. PypeTree: A Tool for Reconstructing Tree Perennial Tissues from Point Clouds

    PubMed Central

    Delagrange, Sylvain; Jauvin, Christian; Rochon, Pascal

    2014-01-01

    The reconstruction of trees from point clouds that were acquired with terrestrial LiDAR scanning (TLS) may become a significant breakthrough in the study and modelling of tree development. Here, we develop an efficient method and a tool based on extensive modifications to the skeletal extraction method that was first introduced by Verroust and Lazarus in 2000. PypeTree, a user-friendly and open-source visual modelling environment, incorporates a number of improvements into the original skeletal extraction technique, making it better adapted to tackle the challenge of tree perennial tissue reconstruction. Within PypeTree, we also introduce the idea of using semi-supervised adjustment tools to address methodological challenges that are associated with imperfect point cloud datasets and which further improve reconstruction accuracy. The performance of these automatic and semi-supervised approaches was tested with the help of synthetic models and subsequently validated on real trees. Accuracy of automatic reconstruction greatly varied in terms of axis detection because small (length < 3.5 cm) branches were difficult to detect. However, as small branches account for little in terms of total skeleton length, mean reconstruction error for cumulated skeleton length only reached 5.1% and 1.8% with automatic or semi-supervised reconstruction, respectively. In some cases, using the supervised tools, a perfect reconstruction of the perennial tissue could be achieved. PMID:24599190

  20. ForestTreeDB: a database dedicated to the mining of tree transcriptomes.

    PubMed

    Pavy, Nathalie; Johnson, James J; Crow, John A; Paule, Charles; Kunau, Timothy; MacKay, John; Retzel, Ernest F

    2007-01-01

    ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344,878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects. PMID:17130142

  1. An Application of Decision Tree Based on ID3

    NASA Astrophysics Data System (ADS)

    Xiaohu, Wang; Lele, Wang; Nianfeng, Li

    This article deals with the application of classical decision tree ID3 of the data mining in a certain site data. It constitutes a decision tree based on information gain and thus produces some useful purchasing behavior rules. It also proves that the decision tree has a wide applicable future in the sale field on site.

  2. Global Expression of Cold-Responsive Genes in Fruit Trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Annual plants in temperate zones survive low temperature extremes in the form of seeds that over-winter. Perennial plants, like trees, must adapt their physiology and biochemistry to survive winters. How do fruit trees adapt to low temperatures? Research has shown that fruit trees alter the expressi...

  3. 29 CFR 780.208 - Forest and Christmas tree activities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 3 2012-07-01 2012-07-01 false Forest and Christmas tree activities. 780.208 Section 780... Agriculture as It Relates to Specific Situations Nursery and Landscaping Operations § 780.208 Forest and Christmas tree activities. Operations in a forest tree nursery such as seeding new beds and growing...

  4. 29 CFR 780.208 - Forest and Christmas tree activities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 3 2011-07-01 2011-07-01 false Forest and Christmas tree activities. 780.208 Section 780... Agriculture as It Relates to Specific Situations Nursery and Landscaping Operations § 780.208 Forest and Christmas tree activities. Operations in a forest tree nursery such as seeding new beds and growing...

  5. 29 CFR 780.208 - Forest and Christmas tree activities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Forest and Christmas tree activities. 780.208 Section 780... Agriculture as It Relates to Specific Situations Nursery and Landscaping Operations § 780.208 Forest and Christmas tree activities. Operations in a forest tree nursery such as seeding new beds and growing...

  6. 29 CFR 780.208 - Forest and Christmas tree activities.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 3 2014-07-01 2014-07-01 false Forest and Christmas tree activities. 780.208 Section 780... Agriculture as It Relates to Specific Situations Nursery and Landscaping Operations § 780.208 Forest and Christmas tree activities. Operations in a forest tree nursery such as seeding new beds and growing...

  7. 29 CFR 780.208 - Forest and Christmas tree activities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 3 2013-07-01 2013-07-01 false Forest and Christmas tree activities. 780.208 Section 780... Agriculture as It Relates to Specific Situations Nursery and Landscaping Operations § 780.208 Forest and Christmas tree activities. Operations in a forest tree nursery such as seeding new beds and growing...

  8. Turning Kids "Green": Tree Planting Program Targets Schools.

    ERIC Educational Resources Information Center

    Zaidi, Radha

    1994-01-01

    Describes the Grow-a-Tree Project, which teaches Canadian elementary children the important role of trees in the environment. Students grow trees from seed and learn basic concepts of science and ecology. Last year more than 45,000 children took part in the program and planted over 950,000 seeds. (LP)

  9. The Use of Binary Search Trees in External Distribution Sorting.

    ERIC Educational Resources Information Center

    Cooper, David; Lynch, Michael F.

    1984-01-01

    Suggests new method of external distribution called tree partitioning that involves use of binary tree to split incoming file into successively smaller partitions for internal sorting. Number of disc accesses during a tree-partitioning sort were calculated in simulation using files extracted from British National Bibliography catalog files. (19…

  10. Category of trees in representation theory of quantum algebras

    SciTech Connect

    Moskaliuk, N. M.; Moskaliuk, S. S.

    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.

  11. Selection of sleeping trees in pileated gibbons (Hylobates pileatus).

    PubMed

    Phoonjampa, Rungnapa; Koenig, Andreas; Borries, Carola; Gale, George A; Savini, Tommaso

    2010-06-01

    Selection and use patterns of sleeping sites in nonhuman primates are suggested to have multiple functions, such as predation avoidance, but they might be further affected by range defense as well as foraging constraints or other factors. Here, we investigate sleeping tree selection by the male and female members of one group of pileated gibbons (Hylobates pileatus) at Khao Ang Rue Nai Wildlife Sanctuary, Thailand. Data were collected on 113 nights, between September 2006 and January 2009, yielding data on 201 sleeping tree choices (107 by the female and 94 by the male) and on the characteristics of 71 individual sleeping trees. Each sleeping tree and all trees > or =40 cm diameter at breast height (DBH) in the home range were assessed (height, DBH, canopy structure, liana load) and mapped using a GPS. The gibbons preferentially selected tall (mean=38.5 m), emergent trees without lianas. The majority of the sleeping trees (53.5%) were used only once and consecutive reuse was rare (9.5%). Sleeping trees were closer to the last feeding tree of the evening than to the first feeding tree in the morning, and sleeping trees were located in the overlap areas with neighbors less often than expected based on time spent in these areas. These results suggest avoidance of predators as the main factor influencing sleeping tree selection in pileated gibbons. However, other non-mutually exclusive factors may be involved as well. PMID:20196132

  12. WDM Multicast Tree Construction Algorithms and Their Comparative Evaluations

    NASA Astrophysics Data System (ADS)

    Makabe, Tsutomu; Mikoshi, Taiju; Takenaka, Toyofumi

    We propose novel tree construction algorithms for multicast communication in photonic networks. Since multicast communications consume many more link resources than unicast communications, effective algorithms for route selection and wavelength assignment are required. We propose a novel tree construction algorithm, called the Weighted Steiner Tree (WST) algorithm and a variation of the WST algorithm, called the Composite Weighted Steiner Tree (CWST) algorithm. Because these algorithms are based on the Steiner Tree algorithm, link resources among source and destination pairs tend to be commonly used and link utilization ratios are improved. Because of this, these algorithms can accept many more multicast requests than other multicast tree construction algorithms based on the Dijkstra algorithm. However, under certain delay constraints, the blocking characteristics of the proposed Weighted Steiner Tree algorithm deteriorate since some light paths between source and destinations use many hops and cannot satisfy the delay constraint. In order to adapt the approach to the delay-sensitive environments, we have devised the Composite Weighted Steiner Tree algorithm comprising the Weighted Steiner Tree algorithm and the Dijkstra algorithm for use in a delay constrained environment such as an IPTV application. In this paper, we also give the results of simulation experiments which demonstrate the superiority of the proposed Composite Weighted Steiner Tree algorithm compared with the Distributed Minimum Hop Tree (DMHT) algorithm, from the viewpoint of the light-tree request blocking.

  13. Clonal preservation of apricot, peach and nut trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Climate change will affect the geographical area suitable for cultivation of fruit and nut trees; hence, preserving genetic diversity of horticultural trees is imperative for securing our future food supply. Many tree species are preserved as seeds but horticultural cultivars, elite and breeding lin...

  14. 16 CFR 501.2 - Christmas tree ornaments.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Christmas tree ornaments. 501.2 Section 501.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENT OF GENERAL POLICY OR... PROHIBITIONS UNDER PART 500 § 501.2 Christmas tree ornaments. Christmas tree ornaments packaged and labeled...

  15. 16 CFR 501.2 - Christmas tree ornaments.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Christmas tree ornaments. 501.2 Section 501.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENT OF GENERAL POLICY OR... PROHIBITIONS UNDER PART 500 § 501.2 Christmas tree ornaments. Christmas tree ornaments packaged and labeled...

  16. 16 CFR 501.2 - Christmas tree ornaments.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Christmas tree ornaments. 501.2 Section 501.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENT OF GENERAL POLICY OR... PROHIBITIONS UNDER PART 500 § 501.2 Christmas tree ornaments. Christmas tree ornaments packaged and labeled...

  17. Out on a Limb: Investigating the Anatomy of Tree Limbs

    ERIC Educational Resources Information Center

    Shaw, Edward L.

    2008-01-01

    The author presents several upper elementary science activities involving tree limbs that were collected after severe weather conditions. The activities involved 3rd-grade students arranging tree limb pieces in the correct order from the trunk to the tip of the limb, measuring the pieces, determining the age of a tree limb by its rings,…

  18. 16 CFR 501.2 - Christmas tree ornaments.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Christmas tree ornaments. 501.2 Section 501.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENT OF GENERAL POLICY OR... PROHIBITIONS UNDER PART 500 § 501.2 Christmas tree ornaments. Christmas tree ornaments packaged and labeled...

  19. 77 FR 20612 - National Tree-Marking Paint Committee Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-05

    ... Forest Service National Tree-Marking Paint Committee Meeting AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The National Tree-Marking Paint Committee will meet in Flagstaff, Arizona on May..., concerns about, and the handling and use of tree-marking paint by personnel of the Forest Service and...

  20. 7 CFR 1410.9 - Conversion to trees.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Conversion to trees. 1410.9 Section 1410.9... Conversion to trees. An owner or operator who has entered into a CRP contract prior to November 28, 1990, may... permanent vegetative cover, from such cover to hardwood trees, (including alley cropping and...

  1. 7 CFR 457.130 - Macadamia tree crop insurance provisions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 6 2011-01-01 2011-01-01 false Macadamia tree crop insurance provisions. 457.130... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.130 Macadamia tree crop insurance provisions. The macadamia tree crop insurance provisions for the 2011 and...

  2. 7 CFR 457.130 - Macadamia tree crop insurance provisions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Macadamia tree crop insurance provisions. 457.130... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.130 Macadamia tree crop insurance provisions. The macadamia tree crop insurance provisions for the 1999 and...

  3. 78 FR 20295 - National Tree-Marking Paint Committee Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ...; ] DEPARTMENT OF AGRICULTURE Forest Service National Tree-Marking Paint Committee Meeting AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The National Tree-Marking Paint Committee will meet in... improvements in, concerns about, and the handling and use of tree-marking paint by personnel of the...

  4. 7 CFR 1410.9 - Conversion to trees.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Conversion to trees. 1410.9 Section 1410.9... Conversion to trees. An owner or operator who has entered into a CRP contract prior to November 28, 1990, may... permanent vegetative cover, from such cover to hardwood trees, (including alley cropping and...

  5. 7 CFR 457.130 - Macadamia tree crop insurance provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 6 2013-01-01 2013-01-01 false Macadamia tree crop insurance provisions. 457.130... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.130 Macadamia tree crop insurance provisions. The macadamia tree crop insurance provisions for the 2011 and...

  6. 75 FR 17897 - National Tree-Marking Paint Committee Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-08

    ... Forest Service National Tree-Marking Paint Committee Meeting AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The National Tree-marking Paint Committee will meet in Colorado Springs..., concerns about, and the handling and use of tree-marking paint by personnel of the Forest Service and...

  7. 16 CFR 501.2 - Christmas tree ornaments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Christmas tree ornaments. 501.2 Section 501.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENT OF GENERAL POLICY OR... PROHIBITIONS UNDER PART 500 § 501.2 Christmas tree ornaments. Christmas tree ornaments packaged and labeled...

  8. 76 FR 17379 - National Tree-Marking Paint Committee Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-29

    ... Forest Service National Tree-Marking Paint Committee Meeting AGENCY: Forest Service, USDA. ACTION: Notice of meeting. SUMMARY: The National Tree-Marking Paint Committee will meet in Missoula, Montana on June... about, and the handling and use of tree-marking paint by personnel of the Forest Service and...

  9. 7 CFR 1410.9 - Conversion to trees.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Conversion to trees. 1410.9 Section 1410.9... Conversion to trees. An owner or operator who has entered into a CRP contract prior to November 28, 1990, may... permanent vegetative cover, from such cover to hardwood trees, (including alley cropping and...

  10. 7 CFR 457.130 - Macadamia tree crop insurance provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 6 2014-01-01 2014-01-01 false Macadamia tree crop insurance provisions. 457.130... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.130 Macadamia tree crop insurance provisions. The macadamia tree crop insurance provisions for the 2011 and...

  11. 7 CFR 1410.9 - Conversion to trees.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Conversion to trees. 1410.9 Section 1410.9... Conversion to trees. An owner or operator who has entered into a CRP contract prior to November 28, 1990, may... permanent vegetative cover, from such cover to hardwood trees, (including alley cropping and...

  12. 7 CFR 1410.9 - Conversion to trees.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Conversion to trees. 1410.9 Section 1410.9... Conversion to trees. An owner or operator who has entered into a CRP contract prior to November 28, 1990, may... permanent vegetative cover, from such cover to hardwood trees, (including alley cropping and...

  13. 7 CFR 457.130 - Macadamia tree crop insurance provisions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 6 2012-01-01 2012-01-01 false Macadamia tree crop insurance provisions. 457.130... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.130 Macadamia tree crop insurance provisions. The macadamia tree crop insurance provisions for the 2011 and...

  14. Trees as templates for tropical litter arthropod diversity.

    PubMed

    Donoso, David A; Johnston, Mary K; Kaspari, Michael

    2010-09-01

    Increased tree species diversity in the tropics is associated with even greater herbivore diversity, but few tests of tree effects on litter arthropod diversity exist. We studied whether tree species influence patchiness in diversity and abundance of three common soil arthropod taxa (ants, gamasid mites, and oribatid mites) in a Panama forest. The tree specialization hypothesis proposes that tree-driven habitat heterogeneity maintains litter arthropod diversity. We tested whether tree species differed in resource quality and quantity of their leaf litter and whether more heterogeneous litter supports more arthropod species. Alternatively, the abundance-extinction hypothesis states that arthropod diversity increases with arthropod abundance, which in turn tracks resource quantity (e.g., litter depth). We found little support for the hypothesis that tropical trees are templates for litter arthropod diversity. Ten tree species differed in litter depth, chemistry, and structural variability. However, the extent of specialization of invertebrates on particular tree taxa was low and the more heterogeneous litter between trees failed to support higher arthropod diversity. Furthermore, arthropod diversity did not track abundance or litter depth. The lack of association between tree species and litter arthropods suggests that factors other than tree species diversity may better explain the high arthropod diversity in tropical forests. PMID:20349247

  15. Characterization of reference gene expression in tung tree (Vernicia fordii)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tung oil from tung tree (Vernicia fordii) is widely used as a drying ingredient in paints, varnishes, and other coatings and finishes. Recent research has focused on the understanding of the biosynthesis of oil in tung trees. Many oil biosynthetic genes have been identified in tung tree but little...

  16. Importance of scion cultivar in peach tree short life

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the Southeast peach trees planted on sites previously planted to peaches often suffer from Peach Tree Short Life (PTSL) syndrome, in which ring nematode, cold injury, and bacterial canker combine to kill the scion in the spring. Rootstock plays an important role; trees on Guardian rootstock surv...

  17. Small bodies' impacts and tree-rings

    NASA Astrophysics Data System (ADS)

    Moshnikova, Maria; Shumilov, Oleg; Kasatkina, Elena; Kanatjev, Alexandr; Timonen, Mauri

    2016-04-01

    The Earth has no natural protection against cosmic bodies' impacts from space. It could be bombarded either by very small particles of cosmic dust every day or by huge bodies causing significant climatic changes. The AD 536 comet event is supposed to be the reason of the global temperature decrease of up to 3°C (Baillie, The Holocene, 1994). Using the 7500 finish supra-long chronology analysis we also observed the tree growth stress after the AD 536 event. The observation of small cosmic bodies by optical methods is most difficult as it was demonstrated in the case of the 2013 Chelyabinsk bolide. Though, there are proxy data providing detailed information about astronomical phenomena in the past. For example, the tree-ring analysis demonstrates the anomalous growth of trees after the Tunguska event in Siberia in 1908 and the same, but smaller effect after the Chulym bolide explosion in 1984 (Kasatkina, Shumilov, JETP Letters, 2007). We considered that the collisions with much smaller cosmic bodies sized from several to hundred meters may also cause similar effects. The results of our dendrochronological research at the Kola Peninsula (northwestern Russia) showed the tree growth increase in 1873 (up to 30% compared to the previous year) at a large distance. The tree-ring growth was likely stimulated either by the comet substance spread over a large territory of the Kola Peninsula and introduced into the soil or by the NO produced during the Kola bolide impact. This fact confirms the evidence of the Kola bolide impact on February 4, 1873 described in "The earthquake catalogue of the Russian Empire" (Mushketov, Orlov, 1893). We determined the distribution of the wind velocity in February 1873 using the Horizontal Neutral Wind Model 07 (HWM 07). The tree-ring analysis and the wind velocity distribution allowed us to estimate the possible trajectory of the Kola bolide flight in February 1873. Our results showed that the dendrochronological method is proved to be the

  18. Microwave Soil Moisture Retrieval Under Trees

    NASA Technical Reports Server (NTRS)

    O'Neill, P.; Lang, R.; Kurum, M.; Joseph, A.; Jackson, T.; Cosh, M.

    2008-01-01

    Soil moisture is recognized as an important component of the water, energy, and carbon cycles at the interface between the Earth's surface and atmosphere. Current baseline soil moisture retrieval algorithms for microwave space missions have been developed and validated only over grasslands, agricultural crops, and generally light to moderate vegetation. Tree areas have commonly been excluded from operational soil moisture retrieval plans due to the large expected impact of trees on masking the microwave response to the underlying soil moisture. Our understanding of the microwave properties of trees of various sizes and their effect on soil moisture retrieval algorithms at L band is presently limited, although research efforts are ongoing in Europe, the United States, and elsewhere to remedy this situation. As part of this research, a coordinated sequence of field measurements involving the ComRAD (for Combined Radar/Radiometer) active/passive microwave truck instrument system has been undertaken. Jointly developed and operated by NASA Goddard Space Flight Center and George Washington University, ComRAD consists of dual-polarized 1.4 GHz total-power radiometers (LH, LV) and a quad-polarized 1.25 GHz L band radar sharing a single parabolic dish antenna with a novel broadband stacked patch dual-polarized feed, a quad-polarized 4.75 GHz C band radar, and a single channel 10 GHz XHH radar. The instruments are deployed on a mobile truck with an 19-m hydraulic boom and share common control software; real-time calibrated signals, and the capability for automated data collection for unattended operation. Most microwave soil moisture retrieval algorithms developed for use at L band frequencies are based on the tau-omega model, a simplified zero-order radiative transfer approach where scattering is largely ignored and vegetation canopies are generally treated as a bulk attenuating layer. In this approach, vegetation effects are parameterized by tau and omega, the microwave

  19. The future of large old trees in urban landscapes.

    PubMed

    Le Roux, Darren S; Ikin, Karen; Lindenmayer, David B; Manning, Adrian D; Gibbons, Philip

    2014-01-01

    Large old trees are disproportionate providers of structural elements (e.g. hollows, coarse woody debris), which are crucial habitat resources for many species. The decline of large old trees in modified landscapes is of global conservation concern. Once large old trees are removed, they are difficult to replace in the short term due to typically prolonged time periods needed for trees to mature (i.e. centuries). Few studies have investigated the decline of large old trees in urban landscapes. Using a simulation model, we predicted the future availability of native hollow-bearing trees (a surrogate for large old trees) in an expanding city in southeastern Australia. In urban greenspace, we predicted that the number of hollow-bearing trees is likely to decline by 87% over 300 years under existing management practices. Under a worst case scenario, hollow-bearing trees may be completely lost within 115 years. Conversely, we predicted that the number of hollow-bearing trees will likely remain stable in semi-natural nature reserves. Sensitivity analysis revealed that the number of hollow-bearing trees perpetuated in urban greenspace over the long term is most sensitive to the: (1) maximum standing life of trees; (2) number of regenerating seedlings ha(-1); and (3) rate of hollow formation. We tested the efficacy of alternative urban management strategies and found that the only way to arrest the decline of large old trees requires a collective management strategy that ensures: (1) trees remain standing for at least 40% longer than currently tolerated lifespans; (2) the number of seedlings established is increased by at least 60%; and (3) the formation of habitat structures provided by large old trees is accelerated by at least 30% (e.g. artificial structures) to compensate for short term deficits in habitat resources. Immediate implementation of these recommendations is needed to avert long term risk to urban biodiversity. PMID:24941258

  20. The Future of Large Old Trees in Urban Landscapes

    PubMed Central

    Le Roux, Darren S.; Ikin, Karen; Lindenmayer, David B.; Manning, Adrian D.; Gibbons, Philip

    2014-01-01

    Large old trees are disproportionate providers of structural elements (e.g. hollows, coarse woody debris), which are crucial habitat resources for many species. The decline of large old trees in modified landscapes is of global conservation concern. Once large old trees are removed, they are difficult to replace in the short term due to typically prolonged time periods needed for trees to mature (i.e. centuries). Few studies have investigated the decline of large old trees in urban landscapes. Using a simulation model, we predicted the future availability of native hollow-bearing trees (a surrogate for large old trees) in an expanding city in southeastern Australia. In urban greenspace, we predicted that the number of hollow-bearing trees is likely to decline by 87% over 300 years under existing management practices. Under a worst case scenario, hollow-bearing trees may be completely lost within 115 years. Conversely, we predicted that the number of hollow-bearing trees will likely remain stable in semi-natural nature reserves. Sensitivity analysis revealed that the number of hollow-bearing trees perpetuated in urban greenspace over the long term is most sensitive to the: (1) maximum standing life of trees; (2) number of regenerating seedlings ha−1; and (3) rate of hollow formation. We tested the efficacy of alternative urban management strategies and found that the only way to arrest the decline of large old trees requires a collective management strategy that ensures: (1) trees remain standing for at least 40% longer than currently tolerated lifespans; (2) the number of seedlings established is increased by at least 60%; and (3) the formation of habitat structures provided by large old trees is accelerated by at least 30% (e.g. artificial structures) to compensate for short term deficits in habitat resources. Immediate implementation of these recommendations is needed to avert long term risk to urban biodiversity. PMID:24941258

  1. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

    PubMed Central

    Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

    2013-01-01

    Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

  2. Tree colonization by the Asian longhorn beetle, Anoplophora glabripennis (Coleoptera: Cerambycidae): effect of habitat and tree suitability.

    PubMed

    Faccoli, Massimo; Favaro, Riccardo; Concheri, Giuseppe; Squartini, Andrea; Battisti, Andrea

    2016-04-01

    Tree colonization and feeding activity of the invasive wood-borer Asian longhorn beetle (Anoplophora glabripennis), an Asian pest introduced into North America and Europe, was studied in a newly invaded area in Italy. The hypothesis being tested was that the reproductive success of the insect depend on habitat type and tree suitability. Adult beetles were caged on branches of host and nonhost species, in both urban and forest habitats. Two months later, number and size of feeding patches on plant tissues, eggs laid, and surviving larvae were assessed. Bark concentration of C and N was also measured from the same trees. Results indicated that the mean area of plant tissues consumed by adult feeding was significantly larger on trees growing in forest than in urban habitat, although within the same habitat there were no differences between susceptible and nonsusceptible trees. ALB tree colonization, in terms of number of eggs laid and young larvae survival, was not affected by habitat while it was higher on susceptible trees. Although trees growing in forests had a lower nitrogen concentration, they allowed colonization rates similar to those of trees growing in the urban habitat. Hence, the amount of carbon and nitrogen did not fully explain tree suitability or habitat selection. We suggest compensatory feeding as a potential mechanism that might explain this peculiar situation, as supported by a more intensive feeding activity recorded on trees in the forest. Suitability of different trees may be due to other factors, such as secondary chemical compounds. PMID:25424840

  3. Foliar nickel application can increase the incidence of peach tree short life and consequent peach tree mortality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability of postplant nickel (Ni) foliar application to suppress Mesocriconema xenoplax populations and thereby prolong tree survival of peach trees on a peach tree short life (PTSL) site was investigated from 2004-2011. The study was conducted in an orchard infested with M. xenoplax and a histo...

  4. Reset tree-based optical fault detection.

    PubMed

    Lee, Dong-Geon; Choi, Dooho; Seo, Jungtaek; Kim, Howon

    2013-01-01

    In this paper, we present a new reset tree-based scheme to protect cryptographic hardware against optical fault injection attacks. As one of the most powerful invasive attacks on cryptographic hardware, optical fault attacks cause semiconductors to misbehave by injecting high-energy light into a decapped integrated circuit. The contaminated result from the affected chip is then used to reveal secret information, such as a key, from the cryptographic hardware. Since the advent of such attacks, various countermeasures have been proposed. Although most of these countermeasures are strong, there is still the possibility of attack. In this paper, we present a novel optical fault detection scheme that utilizes the buffers on a circuit's reset signal tree as a fault detection sensor. To evaluate our proposal, we model radiation-induced currents into circuit components and perform a SPICE simulation. The proposed scheme is expected to be used as a supplemental security tool. PMID:23698267

  5. 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.

  6. Region effects influence local tree species diversity

    PubMed Central

    Ricklefs, Robert E.; He, Fangliang

    2016-01-01

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  7. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  8. Adaptive prediction trees for image compression.

    PubMed

    Robinson, John A

    2006-08-01

    This paper presents a complete general-purpose method for still-image compression called adaptive prediction trees. Efficient lossy and lossless compression of photographs, graphics, textual, and mixed images is achieved by ordering the data in a multicomponent binary pyramid, applying an empirically optimized nonlinear predictor, exploiting structural redundancies between color components, then coding with hex-trees and adaptive runlength/Huffman coders. Color palettization and order statistics prefiltering are applied adaptively as appropriate. Over a diverse image test set, the method outperforms standard lossless and lossy alternatives. The competing lossy alternatives use block transforms and wavelets in well-studied configurations. A major result of this paper is that predictive coding is a viable and sometimes preferable alternative to these methods. PMID:16900671

  9. Analysis of Japanese banks’ historical tree diagram

    NASA Astrophysics Data System (ADS)

    Ueno, Hiromichi; Mizuno, Takayuki; Takayasu, Misako

    2007-09-01

    By using the historical data from the Japanese banks’ database at “The Bankers Library” of Japanese Banker Association, we analyze the historical network of banks from 1868 to 2006. Firstly, we define a bank every year by a particle and draw a space-time evolution process of merger, division, establishment, and failure by a tree diagram structure. We found that the distribution of the tree basin size of real data and simulation result are mostly fitting well. Secondly, we analyze the raw data of financial statements of banks collected by the National Diet library. We confirm that the distributions of the amount of deposits have fat-tail every year, however, small deviations are observed relating to governmental policy.

  10. Reset Tree-Based Optical Fault Detection

    PubMed Central

    Lee, Dong-Geon; Choi, Dooho; Seo, Jungtaek; Kim, Howon

    2013-01-01

    In this paper, we present a new reset tree-based scheme to protect cryptographic hardware against optical fault injection attacks. As one of the most powerful invasive attacks on cryptographic hardware, optical fault attacks cause semiconductors to misbehave by injecting high-energy light into a decapped integrated circuit. The contaminated result from the affected chip is then used to reveal secret information, such as a key, from the cryptographic hardware. Since the advent of such attacks, various countermeasures have been proposed. Although most of these countermeasures are strong, there is still the possibility of attack. In this paper, we present a novel optical fault detection scheme that utilizes the buffers on a circuit's reset signal tree as a fault detection sensor. To evaluate our proposal, we model radiation-induced currents into circuit components and perform a SPICE simulation. The proposed scheme is expected to be used as a supplemental security tool. PMID:23698267

  11. Inferring Epidemic Contact Structure from Phylogenetic Trees

    PubMed Central

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

    2012-01-01

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

  12. Entanglement entropy on the Cayley tree

    NASA Astrophysics Data System (ADS)

    Schreiber, Yishai; Berkovits, Richard

    2016-08-01

    The properties of the entanglement entropy (EE) of a clean and disordered Cayley tree (CT) are studied. The EE shows a completely different behavior depending on the way the CT is partitioned into two regions and whether we consider the ground-state or highly excited many-particle wave function. For a clean CT the ground-state EE increases logarithmically as a function of the number of generation if a single branch is pruned off the tree, while it grows exponentially if the region around the root is trimmed. On the other hand, in both cases the highly excited states’ EE grows exponentially. In the presence of disorder the exponential behavior is preserved only for the latter dissection. The implications of these results to general graphs and disordered systems are shortly discussed.

  13. 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.

  14. Self-Adaptive Induction of Regression Trees.

    PubMed

    Fidalgo-Merino, Raúl; Núñez, Marlon

    2011-08-01

    A new algorithm for incremental construction of binary regression trees is presented. This algorithm, called SAIRT, adapts the induced model when facing data streams involving unknown dynamics, like gradual and abrupt function drift, changes in certain regions of the function, noise, and virtual drift. It also handles both symbolic and numeric attributes. The proposed algorithm can automatically adapt its internal parameters and model structure to obtain new patterns, depending on the current dynamics of the data stream. SAIRT can monitor the usefulness of nodes and can forget examples from selected regions, storing the remaining ones in local windows associated to the leaves of the tree. On these conditions, current regression methods need a careful configuration depending on the dynamics of the problem. Experimentation suggests that the proposed algorithm obtains better results than current algorithms when dealing with data streams that involve changes with different speeds, noise levels, sampling distribution of examples, and partial or complete changes of the underlying function. PMID:21263164

  15. Street-Scene Tree Segmentation from Mobile Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Guan, H.; Cao, S.; Yu, Y.; Li, J.; Liu, N.; Chen, P.; Li, Y.

    2016-06-01

    Our work addresses the problem of extracting trees from mobile laser scanning data. The work is a two step-wise strategy, including terrain point removal and tree segmentation. First, a voxel-based upward growing filtering is proposed to remove terrain points from the mobile laser scanning data. Then, a tree segmentation is presented to extract individual trees via a Euclidean distance clustering approach and Voxel-based Normalized Cut (VNCut) segmentation approach. A road section data acquired by a RIEGL VMX-450 system are selected for evaluating the proposed tree segmentation method. Qualitative analysis shows that our algorithm achieves a good performance.

  16. 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

  17. Heat or humidity, which triggers tree phenology?

    NASA Astrophysics Data System (ADS)

    Laube, Julia; Sparks, Tim H.; Estrella, Nicole; Menzel, Annette

    2014-05-01

    An overwhelming number of studies confirm that temperature is the main driver for phenological events such as leafing, flowering or fruit ripening, which was first discovered by Réaumur in 1735. Since then, several additional factors which influence onset dates have been identified, such as length of the chilling period, photoperiod, temperature of the previous autumn, nutrient availability, precipitation, sunshine and genetics (local adaptations). Those are supposed to capture some of the remaining, unexplained variance. But our ability to predict onset dates remains imprecise, and our understanding of how plants sense temperature is vague. From a climate chamber experiment on cuttings of 9 tree species we present evidence that air humidity is an important, but previously overlooked, factor influencing the spring phenology of trees. The date of median leaf unfolding was 7 days earlier at 90% relative humidity compared to 40% relative humidity. A second experiment with cuttings shows that water uptake by above-ground tissue might be involved in the phenological development of trees. A third climate chamber experiment suggests that winter dormancy and chilling might be linked to dehydration processes. Analysis of climate data from several meteorological stations across Germany proves that the increase in air humidity after winter is a reliable signal of spring, i.e. less variable or susceptible to reversal compared to temperature. Finally, an analysis of long-term phenology data reveals that absolute air humidity can even be used as a reliable predictor of leafing dates. Current experimental work tries to elucidate the involved foliar uptake processes by using deuterium oxide marked water and Raman spectroscopy. We propose a new framework, wherein plants' chilling requirements and frost tolerance might be attributed to desiccation processes, while spring development is linked to re-humidification of plant tissue. The influence of air humidity on the spring

  18. Finding cycles and trees in sublinear time.

    SciTech Connect

    Czumaj, Artur; Goldreich, Oded; Seshadhri, Comandur; Sohler, Christian; Shapira, Asaf; Ron, Dana

    2010-10-01

    We present sublinear-time (randomized) algorithms for finding simple cycles of length at least k {ge} 3 and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being C{sub k}-minor-free (resp., free from having the corresponding tree-minor). In particular, if the graph is far (i.e., {Omega}(1)-far) from being cycle-free, i.e. if one has to delete a constant fraction of edges to make it cycle-free, then the algorithm finds a cycle of polylogarithmic length in time {tilde O}({radical}N), where N denotes the number of vertices. This time complexity is optimal up to polylogarithmic factors. The foregoing results are the outcome of our study of the complexity of one-sided error property testing algorithms in the bounded-degree graphs model. For example, we show that cycle-freeness of N-vertex graphs can be tested with one-sided error within time complexity {tilde O}(poly(1/{epsilon}) {center_dot} {radical}N). This matches the known {Omega}({radical}N) query lower bound, and contrasts with the fact that any minor-free property admits a two-sided error tester of query complexity that only depends on the proximity parameter {epsilon}. For any constant k {ge} 3, we extend this result to testing whether the input graph has a simple cycle of length at least k. On the other hand, for any fixed tree T, we show that T -minor-freeness has a one-sided error tester of query complexity that only depends on the proximity parameter {epsilon}. Our algorithm for finding cycles in bounded-degree graphs extends to general graphs, where distances are measured with respect to the actual number of edges. Such an extension is not possible with respect to finding tree-minors in o({radical}N) complexity.

  19. Livermore Big Trees Park: 1998 summary results

    SciTech Connect

    Gallegos, G; MacQueen, D; Surano, K

    1999-08-13

    This report summarizes work conducted in 1998 by the Lawrence Livermore National Laboratory (LLNL) to determine the extent and origin of plutonium at concentrations above background levels at Big Trees Park in the city of Livermore. This summary includes the project background and sections that explain the sampling, radiochemical and data analysis, and data interpretation. This report is a summary report only and is not intended as a rigorous technical or statistical analysis of the data.

  20. Status tree monitoring and display system

    SciTech Connect

    Watson, C.D.; Eastman, M.C.; Woods, D.D.; Carrera, J.P.; Easter, J.R.; Lipner, M.H.; Elm, W.C.; Mundy, A.D.

    1990-02-20

    This patent describes an apparatus for producing a discrete state display for a pressurized water nuclear reactor process. It comprises: data acquisition and status tree computation means for sampling process control data, determining a value of a discrete process parameter and creating first through third accessible displays in dependence on the parameter value; and display means for displaying the first through third displays independence upon the parameter and an operator request.

  1. Photographic Remote Sensing of Sick Citrus Trees

    NASA Technical Reports Server (NTRS)

    Gausman, H. W.

    1971-01-01

    Remote sensing with infrared color aerial photography (Kodak Ektachrome Infrared Aero 8443 film) for detecting citrus tree anomalies is described. Illustrations and discussions are given for detecting nutrient toxicity symptoms, for detecting foot rot and sooty mold fungal diseases, and for distinguishing among citrus species. Also, the influence of internal leaf structure on light reflectance, transmittance, and absorptance are considered; and physiological and environmental factors that affect citrus leaf light reflectance are reviewed briefly and illustrated.

  2. Collaboration in the Magic Tree House

    ERIC Educational Resources Information Center

    Berner, Jane; Minser, Sabrina; Presser, Helen Burkart

    2008-01-01

    The Magic Tree House series is a collection of books by Mary Pope Osborne, each built around a time and place of high interest to young children, with an underlying story that makes children want to read the next book in the series to find out what is going to happen. Here, the authors describe the development of a two-week reading program for…

  3. Oxidative stability of tree nut oils.

    PubMed

    Miraliakbari, Homan; Shahidi, Fereidoon

    2008-06-25

    The oxidative stability of selected tree nut oils was examined. The oils of almond, Brazil nut, hazelnut, pecan, pine nut, pistachio, and walnut were extracted using two solvent extraction systems, namely, hexane and chloroform/methanol. The chloroform/methanol system afforded a higher oil yield for each tree nut type examined (pine nut had the highest oil content, whereas almond had the lowest). The fatty acid compositions of tree nut oils were analyzed using gas chromatography, showing that oleic acid was the predominant fatty acid in all samples except pine nut and walnut oils, which contained high amounts of linoleic acid. The tocopherol compositions were analyzed using high-performance liquid chromatography, showing that alpha- and gamma-tocopherols were the predominant tocopherol homologues present; however delta- and beta-tocopherols were also detected in some samples. The oxidative stability of nonstripped and stripped tree nut oils was examined under two conditions, namely, accelerated autoxidation and photooxidation. Progression of oxidation was monitored using tests for conjugated dienes, peroxide value, p-anisidine value, and headspace volatiles. Primary products of oxidation persisted in the earlier stages of oxidation, whereas secondary oxidation product levels increased dramatically during the later stages of oxidation. Hexanal was the major headspace aldehyde formed in all oxidized samples except walnut oil, which contained primarily propanal. Results showed that chloroform/methanol-extracted oils were more stable than hexane-extracted oils in both the accelerated autoxidation and photooxidation studies. Oils of pecan and pistachio were the most stable, whereas oils of pine nut and walnut were the least stable. PMID:18494484

  4. Computing tumor trees from single cells.

    PubMed

    Davis, Alexander; Navin, Nicholas E

    2016-01-01

    Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical oncology.Please see related Research articles: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0929-9 and http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0936-x . PMID:27230879

  5. Robustness of Tree Extraction Algorithms from LIDAR

    NASA Astrophysics Data System (ADS)

    Dumitru, M.; Strimbu, B. M.

    2015-12-01

    Forest inventory faces a new era as unmanned aerial systems (UAS) increased the precision of measurements, while reduced field effort and price of data acquisition. A large number of algorithms were developed to identify various forest attributes from UAS data. The objective of the present research is to assess the robustness of two types of tree identification algorithms when UAS data are combined with digital elevation models (DEM). The algorithms use as input photogrammetric point cloud, which are subsequent rasterized. The first type of algorithms associate tree crown with an inversed watershed (subsequently referred as watershed based), while the second type is based on simultaneous representation of tree crown as an individual entity, and its relation with neighboring crowns (subsequently referred as simultaneous representation). A DJI equipped with a SONY a5100 was used to acquire images over an area from center Louisiana. The images were processed with Pix4D, and a photogrammetric point cloud with 50 points / m2 was attained. DEM was obtained from a flight executed in 2013, which also supplied a LIDAR point cloud with 30 points/m2. The algorithms were tested on two plantations with different species and crown class complexities: one homogeneous (i.e., a mature loblolly pine plantation), and one heterogeneous (i.e., an unmanaged uneven-aged stand with mixed species pine -hardwoods). Tree identification on photogrammetric point cloud reveled that simultaneous representation algorithm outperforms watershed algorithm, irrespective stand complexity. Watershed algorithm exhibits robustness to parameters, but the results were worse than majority sets of parameters needed by the simultaneous representation algorithm. The simultaneous representation algorithm is a better alternative to watershed algorithm even when parameters are not accurately estimated. Similar results were obtained when the two algorithms were run on the LIDAR point cloud.

  6. Quantifying MCMC exploration of phylogenetic tree space.

    PubMed

    Whidden, Chris; Matsen, Frederick A

    2015-05-01

    In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks. PMID:25631175

  7. Spanning tree generating functions and Mahler measures

    NASA Astrophysics Data System (ADS)

    Guttmann, Anthony J.; Rogers, Mathew D.

    2012-12-01

    We define the notion of a spanning tree generating function (STGF) ∑anzn, which gives the spanning tree constant when evaluated at z = 1, and gives the lattice Green function (LGF) when differentiated. By making use of known results for logarithmic Mahler measures of certain Laurent polynomials, and proving new results, we express the STGFs as hypergeometric functions for all regular two and three dimensional lattices (and one higher-dimensional lattice). This gives closed form expressions for the spanning tree constants for all such lattices, which were previously largely unknown in all but one three-dimensional case. We show for all lattices that these can also be represented as Dirichlet L-series. Making the connection between STGFs and LGFs produces integral identities and hypergeometric connections, some of which appear to be new. This article is part of ‘Lattice models and integrability’, a special issue of Journal of Physics A: Mathematical and Theoretical in honour of F Y Wu's 80th birthday.

  8. Vascular active contour for vessel tree segmentation.

    PubMed

    Shang, Yanfeng; Deklerck, Rudi; Nyssen, Edgard; Markova, Aneta; de Mey, Johan; Yang, Xin; Sun, Kun

    2011-04-01

    In this paper, a novel active contour model is proposed for vessel tree segmentation. First, we introduce a region competition-based active contour model exploiting the gaussian mixture model, which mainly segments thick vessels. Second, we define a vascular vector field to evolve the active contour along its center line into the thin and weak vessels. The vector field is derived from the eigenanalysis of the Hessian matrix of the image intensity in a multiscale framework. Finally, a dual curvature strategy, which uses a vesselness measure-dependent function selecting between a minimal principal curvature and a mean curvature criterion, is added to smoothen the surface of the vessel without changing its shape. The developed model is used to extract the liver and lung vessel tree as well as the coronary artery from high-resolution volumetric computed tomography images. Comparisons are made with several classical active contour models and manual extraction. The experiments show that our model is more accurate and robust than these classical models and is, therefore, more suited for automatic vessel tree extraction. PMID:21138795

  9. Quantifying MCMC Exploration of Phylogenetic Tree Space

    PubMed Central

    Whidden, Chris; Matsen, Frederick A.

    2015-01-01

    In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks. PMID:25631175

  10. Steiner Tree for Fast Data Distribution

    NASA Astrophysics Data System (ADS)

    Fan, Hongbing; Chen, Yue-Ang

    2011-11-01

    This paper studies the multicast problem of distributing data from a source node to a group of destination nodes along a peer-to-peer (P2P) overlay network of tree topology. A star-based data distribution protocol is used, which allows a node to send data packet to all its children one after another. After all its children receive the data, the node signals them to send the data to their children. The data distribution time of this protocol is defined to be the time span starting from data dispatching at the source node and ending at data received on all destination nodes. The problem is to find a Steiner tree connecting the source node and destination nodes that minimizes data distribution time. A formulation of data distribution time is given and used as an objective function in finding a Steiner tree. The corresponding optimization problem is NP-hard. A heuristic algorithm is presented, which derives an optimal solution when data transfer delays between all pairs of nodes are the same.

  11. Blood Tracer Kinetics in the Arterial Tree

    PubMed Central

    Kellner, Elias; Gall, Peter; Günther, Matthias; Reisert, Marco; Mader, Irina; Fleysher, Roman; Kiselev, Valerij G.

    2014-01-01

    Evaluation of blood supply of different organs relies on labeling blood with a suitable tracer. The tracer kinetics is linear: Tracer concentration at an observation site is a linear response to an input somewhere upstream the arterial flow. The corresponding impulse response functions are currently treated empirically without incorporating the relation to the vascular morphology of an organ. In this work we address this relation for the first time. We demonstrate that the form of the response function in the entire arterial tree is reduced to that of individual vessel segments under approximation of good blood mixing at vessel bifurcations. The resulting expression simplifies significantly when the geometric scaling of the vascular tree is taken into account. This suggests a new way to access the vascular morphology in vivo using experimentally determined response functions. However, it is an ill-posed inverse problem as demonstrated by an example using measured arterial spin labeling in large brain arteries. We further analyze transport in individual vessel segments and demonstrate that experimentally accessible tracer concentration in vessel segments depends on the measurement principle. Explicit expressions for the response functions are obtained for the major middle part of the arterial tree in which the blood flow in individual vessel segments can be treated as laminar. When applied to the analysis of regional cerebral blood flow measurements for which the necessary arterial input is evaluated in the carotid arteries, present theory predicts about 20% underestimation, which is in agreement with recent experimental data. PMID:25299048

  12. Trimming the UCERF2 hazard logic tree

    USGS Publications Warehouse

    Porter, Keith A.; Field, Edward H.; Milner, Kevin

    2012-01-01

    The Uniform California Earthquake Rupture Forecast 2 (UCERF2) is a fully time‐dependent earthquake rupture forecast developed with sponsorship of the California Earthquake Authority (Working Group on California Earthquake Probabilities [WGCEP], 2007; Field et al., 2009). UCERF2 contains 480 logic‐tree branches reflecting choices among nine modeling uncertainties in the earthquake rate model shown in Figure 1. For seismic hazard analysis, it is also necessary to choose a ground‐motion‐prediction equation (GMPE) and set its parameters. Choosing among four next‐generation attenuation (NGA) relationships results in a total of 1920 hazard calculations per site. The present work is motivated by a desire to reduce the computational effort involved in a hazard analysis without understating uncertainty. We set out to assess which branching points of the UCERF2 logic tree contribute most to overall uncertainty, and which might be safely ignored (set to only one branch) without significantly biasing results or affecting some useful measure of uncertainty. The trimmed logic tree will have all of the original choices from the branching points that contribute significantly to uncertainty, but only one arbitrarily selected choice from the branching points that do not.

  13. Decoding the genomic tree of life

    PubMed Central

    Simonson, Anne B.; Servin, Jacqueline A.; Skophammer, Ryan G.; Herbold, Craig W.; Rivera, Maria C.; Lake, James A.

    2005-01-01

    Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life. PMID:15851667

  14. CUDT: A CUDA Based Decision Tree Algorithm

    PubMed Central

    Sheu, Ruey-Kai; Chiu, Chun-Chieh

    2014-01-01

    Decision tree is one of the famous classification methods in data mining. Many researches have been proposed, which were focusing on improving the performance of decision tree. However, those algorithms are developed and run on traditional distributed systems. Obviously the latency could not be improved while processing huge data generated by ubiquitous sensing node in the era without new technology help. In order to improve data processing latency in huge data mining, in this paper, we design and implement a new parallelized decision tree algorithm on a CUDA (compute unified device architecture), which is a GPGPU solution provided by NVIDIA. In the proposed system, CPU is responsible for flow control while the GPU is responsible for computation. We have conducted many experiments to evaluate system performance of CUDT and made a comparison with traditional CPU version. The results show that CUDT is 5∼55 times faster than Weka-j48 and is 18 times speedup than SPRINT for large data set. PMID:25140346

  15. Extremal paths on a random Cayley tree

    NASA Astrophysics Data System (ADS)

    Majumdar, Satya N.; Krapivsky, P. L.

    2000-12-01

    We investigate the statistics of extremal path(s) (both the shortest and the longest) from the root to the bottom of a Cayley tree. The lengths of the edges are assumed to be independent identically distributed random variables drawn from a distribution ρ(l). Besides, the number of branches from any node is also random. Exact results are derived for arbitrary distribution ρ(l). In particular, for the binary \\{0,1\\} distribution ρ(l)=pδl,1+(1-p)δl,0, we show that as p increases, the minimal length undergoes an unbinding transition from a ``localized'' phase to a ``moving'' phase at the critical value, p=pc=1-b-1, where b is the average branch number of the tree. As the height n of the tree increases, the minimal length saturates to a finite constant in the localized phase (ppc) where the velocity vmin(p) is determined via a front selection mechanism. At p=pc, the minimal length grows with n in an extremely slow double-logarithmic fashion. The length of the maximal path, on the other hand, increases linearly as vmax(p)n for all p. The maximal and minimal velocities satisfy a general duality relation, vmin(p)+vmax(1-p)=1, which is also valid for directed paths on finite-dimensional lattices.

  16. 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.

  17. Does coring contribute to tree mortality?

    USGS Publications Warehouse

    van Mantgem, P.J.; Stephenson, N.L.

    2004-01-01

    We assess the potential of increment coring, a common method for measuring tree ages and growth, to contribute to mortality. We used up to 21 years of annual censuses from two cored and two uncored permanent plots in the Sierra Nevada of California, to detect changes in mortality rates 12 years following coring for individuals >5 cm DBH from two coniferous species, Abies concolor (Gordon & Glend.) Lindl. (white fir) and Abies magnifica A. Murr. (red fir). Using a randomized before-after control impact (BACI) design, we found no differences in mortality rates following coring for 825 cored and 525 uncored A. concolor and 104 cored and 66 uncored A. magnifica. These results support the view that collecting tree cores can be considered nondestructive sampling, but we emphasize that our 12-year postcoring records are short compared with the maximum life-span of these trees and that other species in different environments may prove to be more sensitive to coring. ?? 2004 NRC Canada.

  18. Arginine, scurvy and Cartier's "tree of life"

    PubMed Central

    Durzan, Don J

    2009-01-01

    Several conifers have been considered as candidates for "Annedda", which was the source for a miraculous cure for scurvy in Jacques Cartier's critically ill crew in 1536. Vitamin C was responsible for the cure of scurvy and was obtained as an Iroquois decoction from the bark and leaves from this "tree of life", now commonly referred to as arborvitae. Based on seasonal and diurnal amino acid analyses of candidate "trees of life", high levels of arginine, proline, and guanidino compounds were also probably present in decoctions prepared in the severe winter. The semi-essential arginine, proline and all the essential amino acids, would have provided additional nutritional benefits for the rapid recovery from scurvy by vitamin C when food supply was limited. The value of arginine, especially in the recovery of the critically ill sailors, is postulated as a source of nitric oxide, and the arginine-derived guanidino compounds as controlling factors for the activities of different nitric oxide synthases. This review provides further insights into the use of the candidate "trees of life" by indigenous peoples in eastern Canada. It raises hypotheses on the nutritional and synergistic roles of arginine, its metabolites, and other biofactors complementing the role of vitamin C especially in treating Cartier's critically ill sailors. PMID:19187550

  19. Adaptive significance of root grafting in trees

    SciTech Connect

    Loehle, C.; Jones, R.

    1988-12-31

    Root grafting has long been observed in forest trees but the adaptive significance of this trait has not been fully explained. Various authors have proposed that root grafting between trees contributes to mechanical support by linking adjacent root systems. Keeley proposes that this trait would be of greatest advantage in swamps where soils provide poor mechanical support. He provides as evidence a greenhouse study of Nyssa sylvatica Marsh in which seedlings of swamp provenance formed between-individual root grafts more frequently than upland provenance seedlings. In agreement with this within-species study, Keeley observed that arid zone species rarely exhibit grafts. Keeley also demonstrated that vines graft less commonly than trees, and herbs never do. Since the need for mechanical support coincides with this trend, these data seem to support his model. In this paper, the authors explore the mechanisms and ecological significance of root grafting, leading to predictions of root grafting incidence. Some observations support and some contradict the mechanical support hypothesis.

  20. Enumerating tree-like polyphenyl isomers

    NASA Astrophysics Data System (ADS)

    Deng, Kecai; Qian, Jianguo; Zhang, Fuji

    2012-12-01

    Enumeration of molecules is one of the fundamental problems in bioinformatics and plays an important role in drug discovery, experimental structure elucidation (e.g., by using NMR or mass spectrometry), molecular design and virtual library construction. We consider the enumeration of tree-like polyphenyls (C6nH4n+2). For this purpose, we define two generating functions T(x) and R(x) involving the numbers tn and rn of tree-like polyphenyls (TL-polyphenyls) and monosubstituted tree-like polyphenyls (MTL-polyphenyls), respectively. By characterizing the symmetry groups with respect to TL-polyphenyls and MTL-polyphenyls, we establish two functional equations for these two generating functions. This yields for the first time an efficient recursion formula for calculating the numbers tn and rn. The two functional equations are also the fundamentals for analyzing their asymptotic behaviors, from which we derive the precise asymptotic values for both rn and tn. The resulting asymptotic values are shown to fit well to the numerical results obtained by using our recursion formula. Finally, we give an explicit enumerating expression for TL-polyphenyls of a particular type: the linear polyphenyls.

  1. Exploring tree species signature using waveform LiDAR data

    NASA Astrophysics Data System (ADS)

    Zhou, T.; Popescu, S. C.; Krause, K.

    2015-12-01

    Successful classification of tree species with waveform LiDAR data would be of considerable value to estimate the biomass stocks and changes in forests. Current approaches emphasize converting the full waveform data into discrete points to get larger amount of parameters and identify tree species using several discrete-points variables. However, ignores intensity values and waveform shapes which convey important structural characteristics. The overall goal of this study was to employ the intensity and waveform shape of individual tree as the waveform signature to detect tree species. The data was acquired by the National Ecological Observatory Network (NEON) within 250*250 m study area located in San Joaquin Experimental Range. Specific objectives were to: (1) segment individual trees using the smoothed canopy height model (CHM) derived from discrete LiDAR points; (2) link waveform LiDAR with above individual tree boundaries to derive sample signatures of three tree species and use these signatures to discriminate tree species in a large area; and (3) compare tree species detection results from discrete LiDAR data and waveform LiDAR data. An overall accuracy of the segmented individual tree of more than 80% was obtained. The preliminary results show that compared with the discrete LiDAR data, the waveform LiDAR signature has a higher potential for accurate tree species classification.

  2. Improving multiple sequence alignment by using better guide trees

    PubMed Central

    2015-01-01

    Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively according to the topology of the tree. It is believed that guide trees are very important to progressive alignment; a better guide tree will give an alignment with higher accuracy. Recently, we have proposed an adaptive method for constructing guide trees. This paper studies the quality of the guide trees constructed by such method. Our study showed that our adaptive method can be used to improve the accuracy of many different progressive MSA tools. In fact, we give evidences showing that the guide trees constructed by the adaptive method are among the best. PMID:25859903

  3. Urban tree residues: Results of the first national inventory

    SciTech Connect

    Whittier, J.; Rue, D.; Haase, S.

    1994-12-31

    The volume and characteristics of urban tree residues associated with tree pruning and other urban forestry activities have never been well documented, yet disposal of this residue is subject to increasing regulatory actions. The regulatory actions have a considerable impact on the activities of commercial, utility, and municipal tree care operations. This paper reports the results of the first national inventory of the volume and characteristics of urban tree residues. Residues are classified as follows: chips, logs, mixed wood, tops and brush, leaves, lawn clippings, and stumps. Generators of residues include the following: commercial tree care firms, municipal park and recreation departments, municipal tree care divisions, county tree care divisions, electric/telephone utility power line maintenance departments, nurseries, orchards, and landscapers. The national inventory assesses volume, characteristics, and disposal of the residues on both a regional basis as well as by size of metropolitan area. Finally, irregular residue inputs associated with natural disasters are discussed.

  4. Visualising very large phylogenetic trees in three dimensional hyperbolic space

    PubMed Central

    Hughes, Timothy; Hyun, Young; Liberles, David A

    2004-01-01

    Background Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. Results We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. Conclusion Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED). PMID:15117420

  5. Stable feature selection for clinical prediction: exploiting ICD tree structure using Tree-Lasso.

    PubMed

    Kamkar, Iman; Gupta, Sunil Kumar; Phung, Dinh; Venkatesh, Svetha

    2015-02-01

    Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can

  6. Supercooling Capacity Increases from Sea Level to Tree Line in the Hawaiian Tree Species Metrosideros polymorpha.

    PubMed

    Melcher; Cordell; Jones; Scowcroft; Niemczura; Giambelluca; Goldstein

    2000-05-01

    Population-specific differences in the freezing resistance of Metrosideros polymorpha leaves were studied along an elevational gradient from sea level to tree line (located at ca. 2500 m above sea level) on the east flank of the Mauna Loa volcano in Hawaii. In addition, we also studied 8-yr-old saplings grown in a common garden from seeds collected from the same field populations. Leaves of low-elevation field plants exhibited damage at -2 degrees C, before the onset of ice formation, which occurred at -5.7 degrees C. Leaves of high-elevation plants exhibited damage at ca. -8.5 degrees C, concurrent with ice formation in the leaf tissue, which is typical of plants that avoid freezing in their natural environment by supercooling. Nuclear magnetic resonance studies revealed that water molecules of both extra- and intracellular leaf water fractions from high-elevation plants had restricted mobility, which is consistent with their low water content and their high levels of osmotically active solutes. Decreased mobility of water molecules may delay ice nucleation and/or ice growth and may therefore enhance the ability of plant tissues to supercool. Leaf traits that correlated with specific differences in supercooling capacity were in part genetically determined and in part environmentally induced. Evidence indicated that lower apoplastic water content and smaller intercellular spaces were associated with the larger supercooling capacity of the plant's foliage at tree line. The irreversible tissue-damage temperature decreased by ca. 7 degrees C from sea level to tree line in leaves of field populations. However, this decrease appears to be only large enough to allow M. polymorpha trees to avoid leaf tissue damage from freezing up to a level of ca. 2500 m elevation, which is also the current tree line location on the east flank of Mauna Loa. The limited freezing resistance of M. polymorpha leaves may be partially responsible for the occurrence of tree line at a relatively

  7. The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa

    NASA Astrophysics Data System (ADS)

    Ter Steege, Hans; Vaessen, Rens W.; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C. A.; Jørgensen, Peter Møller; Salomão, Rafael P.

    2016-07-01

    Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species’ range size is a better predictor of the number of times it has been collected than the species’ estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites.

  8. The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa.

    PubMed

    Ter Steege, Hans; Vaessen, Rens W; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C A; Jørgensen, Peter Møller; Salomão, Rafael P

    2016-01-01

    Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species' range size is a better predictor of the number of times it has been collected than the species' estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites. PMID:27406027

  9. The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa

    PubMed Central

    ter Steege, Hans; Vaessen, Rens W.; Cárdenas-López, Dairon; Sabatier, Daniel; Antonelli, Alexandre; de Oliveira, Sylvia Mota; Pitman, Nigel C. A.; Jørgensen, Peter Møller; Salomão, Rafael P.

    2016-01-01

    Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species’ range size is a better predictor of the number of times it has been collected than the species’ estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites. PMID:27406027

  10. Error Tree: A Tree Structure for Hamming and Edit Distances and Wildcards Matching.

    PubMed

    Al-Okaily, Anas

    2015-12-01

    Approximate pattern matching is a fundamental problem in the bioinformatics and information retrieval applications. The problem involves different matching relations such as Hamming distance, edit distances, and the wildcards matching problem. The input is usually a text of length n over a fixed alphabet of length Σ, a pattern of length m, and an integer k. The output is to find all positions that have ≤ k Hamming distance, edit distance, or wildcards matching with P. Many algorithms and indexes have been proposed to solve the problems more efficiently, but due to the space and time complexities of the problems, most tools adopted heuristics approaches based on, for instance, suffix tree, suffix array, or Burrows Wheeler Transform to reach practical implementations. Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, using less space and faster computation time. The algorithm proposes for Hamming distance and wildcards matching a tree structure that needs [Formula: see text] words and takes [Formula: see text] in the average case) of query time for any online/offline pattern, where occ is the number of outputs. In addition, a tree structure of [Formula: see text] words and [Formula: see text] in the average case) query time for edit distance for any online/offline pattern. PMID:26402070

  11. Riparian Ficus Tree Communities: The Distribution and Abundance of Riparian Fig Trees in Northern Thailand

    PubMed Central

    Pothasin, Pornwiwan; Compton, Stephen G.; Wangpakapattanawong, Prasit

    2014-01-01

    Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010–2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance. PMID:25310189

  12. Impacts of Tree Height-Dbh Allometry on Lidar-Based Tree Aboveground Biomass Modeling

    NASA Astrophysics Data System (ADS)

    Fang, R.

    2016-06-01

    Lidar has been widely used in tree aboveground biomass (AGB) estimation at plot or stand levels. Lidar-based AGB models are usually constructed with the ground AGB reference as the response variable and lidar canopy indices as predictor variables. Tree diameter at breast height (dbh) is the major variable of most allometric models for estimating reference AGB. However, lidar measurements are mainly related to tree vertical structure. Therefore, tree height-dbh allometric model residuals are expected to have a large impact on lidar-based AGB model performance. This study attempts to investigate sensitivity of lidar-based AGB model to the decreasing strength of height-dbh relationship using a Monte Carlo simulation approach. Striking decrease in R2 and increase in relative RMSE were found in lidar-based AGB model, as the variance of height-dbh model residuals grew. I, therefore, concluded that individual tree height-dbh model residuals fundamentally introduce errors to lidar-AGB models.

  13. Do tree ring chronologies have missing rings that distort volcanic cooling signal?: Tree ring records not distorted by missing rings

    NASA Astrophysics Data System (ADS)

    Balcerak, Ernie

    2013-09-01

    Tree ring records are often used as a proxy for past climate. Trees form a new growth ring each year, and ring widths are related to temperature and other conditions at cold sites. Some recent studies have noted that tree ring width chronologies and resulting climate reconstructions do not appear to show the widespread cooling in the past millennium that would be expected following large volcanic eruptions. One hypothesis suggests that regional cooling after a volcanic eruption could be so severe that many trees do not form a ring at all, which leads researchers to misdate the tree ring chronology.

  14. Efficient algorithms for dilated mappings of binary trees

    NASA Technical Reports Server (NTRS)

    Iqbal, M. Ashraf

    1990-01-01

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

  15. Effects of land management on large trees and carbon stocks

    NASA Astrophysics Data System (ADS)

    Kauppi, P. E.; Birdsey, R. A.; Pan, Y.; Ihalainen, A.; Nöjd, P.; Lehtonen, A.

    2014-02-01

    Large trees are important and unique organisms in forests, providing ecosystem services including carbon dioxide removal from the atmosphere and long-term storage. There is concern about reports of global decline of big trees. Based on observations from Finland and the United States we report that trends of big trees during recent decades have been surprisingly variable among regions. In southern Finland, the growing stock volume of trees larger than 30 cm at breast height increased nearly five-fold during the second half of the 20th century, yet more recently ceased to expand. In the United States, large hardwood trees have become increasingly common since the 1950s, while large softwood trees declined until the mid 1990's as a consequence of harvests in the Pacific region, and then rebounded when harvesting there was reduced. We conclude that in the regions studied, the history of land use and forest management governs changes of tree populations especially with reference to large trees. Large trees affect greatly the carbon density of forests and usually have deeper roots and relatively lower mortality than small trees. An accumulating stock of large trees in forests may have negligible direct biophysical effects on climate because from changes in transpiration or forest albedo. Large trees have particular ecological importance and often constitute an unusually large proportion of biomass carbon stocks in a forest. Understanding the changes in big tree distributions in different regions of the world and the demography of tree populations makes a contribution to estimating the past impact and future potential of the role of forests in the global carbon budget.

  16. Hypersensitivity to common tree pollens in New York City patients.

    PubMed

    Lin, Robert Y; Clauss, Allison E; Bennett, Edward S

    2002-01-01

    Testing for tree pollen hypersensitivity typically requires the use of several tree pollens. Identifying patterns of cross-sensitivity to tree pollens could reduce the number of trees used for testing. The goal of this study was to relate reported tree pollen levels to hypersensitivity patterns. Three hundred seventy-one allergy patients were tested serologically for hypersensitivity toward prevalent tree pollens in the surrounding New York area over the years 1993-2000. Specific tree pollens that were examined included oak (Quercus alba), birch (Betula verrucosa), beech (Fagus grandifolia), poplar (Populus deltoides), maple (Acer negundo), ash (Fraxinus americana), hickory (Carya pecan), and elm (Ulmus americana). Statistical analysis of the levels of hypersensitivity was performed to identify correlations and grouping factors. Pollen levels, obtained from published annual pollen and spore reports, were characterized and related to the prevalence of hypersensitivity for the various trees. The highest prevalence of hypersensitivity (score > or = class 1) was for oak (34.3%), birch (32.9%), and maple (32.8%) tree pollens. Lower prevalences were observed for beech (29.6%), hickory (27.1%), ash (26%), elm (24.6%), and poplar (20.6%) trees. Significant correlations were observed between oak, birch, and beech radioallergosorbent test scores. Factor analysis identified two independent pollen groups with oak, birch, and beech consisting of one group and the other five tree pollens constituting the other group. Peak pollen counts clearly were highest for oak, birch, and maple trees. The peak pollen counts corresponded roughly to seropositivity prevalences for the tree pollens. When elm, poplar, and beech test scores were not used to identify patients who were allergic to tree pollens, only 1 of 106 patients with any positive tree radioallergosorbent test score was missed. It is concluded that in the New York City area, hypersensitivity to tree pollens most often is

  17. Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

    PubMed Central

    Pollard, Daniel A; Eisen, Michael B

    2006-01-01

    The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this

  18. Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation.

    PubMed

    Waters, Jonathan M; Rowe, Diane L; Burridge, Christopher P; Wallis, Graham P

    2010-10-01

    Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA. PMID:20603441

  19. Environmental Fate of Emamectin Benzoate After Tree Micro Injection of Horse Chestnut Trees

    PubMed Central

    Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

    2015-01-01

    Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. Environ Toxicol Chem 2014;9999:1–6. © 2014 The Authors. Published 2014 SETAC PMID:25363584

  20. More Trees, More Poverty? The Socioeconomic Effects of Tree Plantations in Chile, 2001-2011

    NASA Astrophysics Data System (ADS)

    Andersson, Krister; Lawrence, Duncan; Zavaleta, Jennifer; Guariguata, Manuel R.

    2016-01-01

    Tree plantations play a controversial role in many nations' efforts to balance goals for economic development, ecological conservation, and social justice. This paper seeks to contribute to this debate by analyzing the socioeconomic impact of such plantations. We focus our study on Chile, a country that has experienced extraordinary growth of industrial tree plantations. Our analysis draws on a unique dataset with longitudinal observations collected in 180 municipal territories during 2001-2011. Employing panel data regression techniques, we find that growth in plantation area is associated with higher than average rates of poverty during this period.