Science.gov

Sample records for jacaranda mimosifolia tree

  1. Phylogenetic placement of Itajahya: An unusual Jacaranda fungal associate.

    PubMed

    Marincowitz, Seonju; Coetzee, Martin P A; Wilken, P Markus; Wingfield, Brenda D; Wingfield, Michael J

    2015-12-01

    Itajahya is a member of Phallales (Agaricomycetes), which, based on the presence of a calyptra and DNA sequence data for I. rosea, has recently been raised to generic status from a subgenus of Phallus. The type species of the genus, I. galericulata, is commonly known as the Jacaranda stinkhorn in Pretoria, South Africa, which is the only area where the fungus is known outside the Americas. The common name is derived from its association with the South American originating Jacaranda mimosifolia trees in the city. The aim of this study was to consider the unusual occurrence of the fungus in South Africa, to place it on the available Phallales phylogeny and to test whether it merits generic status. Fresh basidiomes were collected during the summer of 2015 and sequenced. Phylogenetic analyses were based on sequence data for the nuc-LSU-rDNA (LSU) and ATPase subunit 6 (ATP6) regions. The results showed that I. rosea and I. galericulata are phylogenetically related. They are also clearly distinguished from other members of Phallales such as Phallus spp. and Dictyophora spp., and so our new data supports the raising of Itajahya to the generic level. PMID:26734541

  2. Antioxidant and Cytotoxic Activity of Hydroethanolic Extract from Jacaranda decurrens Leaves

    PubMed Central

    Casagrande, Junior Cesar; Macorini, Luis Fernando Benitez; Antunes, Katia Avila; dos Santos, Uilson Pereira; Campos, Jaqueline Ferreira; Dias-Júnior, Nelson Miguel; Sangalli, Andréia; Lima Cardoso, Claudia Andrea; do Carmo Vieira, Maria; Rabelo, Luiza Antas; Paredes-Gamero, Edgar Julian; dos Santos, Edson Lucas; de Picoli Souza, Kely

    2014-01-01

    Background and Purpose Leaves of Jacaranda decurrens are used in traditional Brazilian medicine to treat metabolic diseases related to increased reactive oxygen species. The present study evaluated the antioxidant and cytotoxic potential of hydroethanolic extract from the leaves of Jacaranda decurrens subsp. symmetrifoliolata. Experimental Approach Phenolic compounds, flavonoids and saponins were evaluated in an ethanol∶water (80∶20, v/v) extract from the leaves of Jacaranda decurrens subsp. symmetrifoliolata (E-Jds). The antioxidant activity of E-Jds was investigated by assessing the following: 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity; protection against 2,2′-azobis (2-amidinopropane) dihydrochloride (AAPH)-induced hemolysis of erythrocytes; in vitro and in vivo malondialdehyde dosage; and the ability to activate antioxidant enzymes. K562 leukemia cells were used for the cytotoxic evaluation of E-Jds and for the assessment of the cell death profile through flow cytometry. Key Results Phenolic and flavonoid compounds were quantified as 14.38% and 2.15%, respectively, of E-Jds. These phenolic and flavonoid compounds proved to be able to scavenge DPPH free radicals with an IC50 of 9.3±3.3 µg/mL, to protect up to 50% of erythrocytes against AAPH-induced hemolysis and to reduce in vitro and in vivo malondialdehyde levels up to 84% and 22%, respectively. E-Jds also increased glutathione peroxidase enzyme activity, with a concomitant decrease in superoxide dismutase and catalase activity, and exhibited dose-dependent cytotoxic activity on K562 erythroleukemia cells with cell death occurring via both late apoptosis and necrosis. Conclusions E-Jds exhibits in vitro and in vivo antioxidant potential, which may be the mechanism mediating the metabolic activities reported in folk medicine. Furthermore, the cytotoxic activity identified in this study contributes with the knowledge of antiproliferative activities that have been described in the literature for the genus Jacaranda. PMID:25402205

  3. Histological features, starch accumulation and sprouting in the early root development of Jacaranda ulei (Bignoniaceae).

    PubMed

    Silva, Paulo R D da; Stefenon, Valdir M

    2014-03-01

    The plant species occurring in the savanna region of the Cerrado biome in Brazil present typical morphological and physiological adaptations to a dry climate with seasonal occurrence of wildfires. In this study, the histological features of the root system, the main sites of synthesis and storage of starch and the initial phases of the bud development were characterized in Jacaranda ulei. The anatomical features observed in the root system of J. ulei are related to the needs of the species to survive in the Cerrado. The histochemical analyses demonstrated high synthesis of glucose and glycoprotein after the third day of in vitro culture, in the proximal cells of the cortical parenchyma of the exoderm. Meristematic primordia were observed in the ninth day and the beginning of the meristem formation was observed after 21 days of in vitro culture. Jacaranda ulei displays morphological, anatomical and storage features typical from resprouter species. However, it may be vulnerable to unsustainable exploitation. Considering the importance of this species for local people, more studies regarding its therapeutic properties should be performed, including the planning of appropriate programs for the species management and the production of selected clones through in vitro micropropagation. PMID:24676167

  4. Profile of volatile components of hydrodistilled and extracted leaves of Jacaranda acutifolia and their antimicrobial activity against foodborne pathogens.

    PubMed

    Singab, Abdel Nasser B; Mostafa, Nada M; Eldahshan, Omayma A; Ashour, Mohamed L; Wink, Michael

    2014-07-01

    Volatile constituents of the essential oil and n-hexane extract of Jacaranda acutifolia Humb. and Bonpl. (Bignoniaceae) leaves were determined, and their antimicrobial activities were investigated using an agar diffusion method. The minimum inhibitory concentrations (MIC) were determined and compared with those of standard antibiotics (penicillin, gentamicin and nystatin). The chemical composition of the oils was analyzed by capillary gas chromatography (GLC-FID) and gas chromatography-mass spectrometry (GLC-MS). Thirty-four components, comprising almost 93.8% of the total peak area, were identified in the leaf essential oil. The main components were methyl linolenate (26.7%), 1-octen-3-ol (10.8%), methyl phenyl acetate (9.9%), beta-linalool (5.5%) and palmitic acid (4.7%). The n-hexane extract revealed similar oil constituents, but also p-benzoquinone, phenyl acetic acid, resorcinol and homogentisic acid. The oil showed some activity against Staphylococcus aureus and Escherichia coli with MIC values of 2.2 and 2.9 mg/mL, respectively, and moderate activity against Candida albicans, Salmonella typhimurium and Shigella flexneri. The n-hexane extract showed moderate activities against all tested microorganisms, with MIC values ranging from 3.5 to 10.2 mg/mL. The antimicrobial activities of the hydrodistilled and extracted leaves make their local traditional uses rational. PMID:25230515

  5. Subacute and Reproductive Oral Toxicity Assessment of the Hydroethanolic Extract of Jacaranda decurrens Roots in Adult Male Rats

    PubMed Central

    Santos, Joyce Alencar; Arruda, Aline; Cardoso, Claudia Andrea Lima; Vieira, Maria do Carmo; Piccinelli, Ana Cludia; Figueiredo de Santana Aquino, Diana; Kassuya, Cndida Aparecida Leite; Arena, Arielle Cristina

    2013-01-01

    Jacaranda decurrens subsp. symmetrifoliolata Farias & Proena (Bignoniaceae) is a species traditionally used for the treatment of inflammatory and infectious diseases. Previous findings from our group reported scientifically that J. decurrens has anti-inflammatory efficacy. However, more toxicological studies are needed to support and ensure its safe use. The present study was carried out to evaluate the toxic effects of a prolonged treatment with hydroethanolic root extract of J. decurrens (EJD) on hematological, biochemical, and reproductive parameters in adult male rats. The animals received by oral gavage 0; 250; 500; or 1000?mg/kg body weight of EJD for 28 days. After the treatment, biochemical, hematological, histopathological, and reproductive parameters were analyzed. The EJD treatment did not cause adverse effects on body weight gain, feed and water consumption, hematological and biochemical profiles, or histopathological analysis of liver and kidney. Similarly, there were no statistically significant differences in reproductive parameters, such as sperm production, number of sperm in the epididymis, and sperm morphology. These results demonstrate the absence of subacute toxicity as a result of the oral treatment with EJD for 28 days in adult male rats. However, other studies should be performed to evaluate the total safety of this plant. PMID:24348699

  6. 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

  7. 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;

  8. Test tree

    SciTech Connect

    Schwendemann, K. L.

    1985-01-22

    A subsurface test tree so compact in its vertical dimension that the entire tree can be positioned below the blind rams in a blowout preventer stack. When the stinger is removed the remaining valve section of the tree will be below the blind rams in any conventional blowout preventer stack. The valve operators are split, one carried by the stinger and one carried in the valve housing with the arrangement of operator and valve in the housing providing an extremely small vertical dimension. A dome charge is effective on a piston to drive a ball valve to closed position to cut a line extending through the ball valve and to provide sequential operation between the ball valve on bottom and the valve thereabove which may be a flapper valve so that the lower valve closes and the line is cut before the upper valve closes. In one form the invention includes a subsurface safety valve below the test tree operated by one of control or balance pressure fluid.

  9. Tea tree oil

    MedlinePLUS

    Tea tree oil is derived from the leaves of the tea tree. The tea tree was named by eighteenth century sailors, ... to make black and green teas. Tea tree oil is applied to the skin (used topically) for ...

  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. What Makes a Tree a Tree?

    ERIC Educational Resources Information Center

    NatureScope, 1986

    1986-01-01

    Provides: (1) background information on trees, focusing on the parts of trees and how they differ from other plants; (2) eight activities; and (3) ready-to-copy pages dealing with tree identification and tree rings. Activities include objective(s), recommended age level(s), subject area(s), list of materials needed, and procedures. (JN)

  12. 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…

  13. Additive Similarity Trees

    ERIC Educational Resources Information Center

    Sattath, Shmuel; Tversky, Amos

    1977-01-01

    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  14. Categorizing ideas about trees: a tree of trees.

    PubMed

    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

  15. 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).

  16. 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

  17. 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

  18. Bronchi, Bronchial Tree, & Lungs

    MedlinePLUS

    ... Modules Resources Archived Modules Updates Bronchi, Bronchial Tree, & Lungs Bronchi and Bronchial Tree In the mediastinum , at ... the walls of the alveolar ducts and alveoli. Lungs The two lungs, which contain all the components ...

  19. 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)

  20. 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.

  1. Tree Nut Allergies

    MedlinePLUS

    ... likelihood of cross-contact with tree nuts during manufacturing and processing. Avoiding Tree Nuts The federal Food ... Word True Stories Stay Informed Newsletters Alerts Alerts Feed Alerts Archive Ingredient Notices Ingredient Notices Feed FARE ...

  2. 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

  3. Pecan tree biomass estimates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Allometric equations were developed for orchard-grown pecan [Carya illinoinensis (Wangenh.) C. Koch] trees. Trees, ranging in size from 22 to 33 cm in trunk diameter 1.4 m above the ground, were destructively harvested from two sites. The entire above-ground portion of the trees was harvested and...

  4. 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…

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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#11;erent problems that rely on contour trees can be solved in parallel with minimal communication.

  10. 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

  11. Long-term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations.

    PubMed

    Vinson, C C; Kanashiro, M; Sebbenn, A M; Williams, T C R; Harris, S A; Boshier, D H

    2015-08-01

    The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests. PMID:24424164

  12. 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

  13. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Ziya; Ben-Naim, Eli

    2015-03-01

    We investigate the fragmentation of a random recursive tree by repeated removal of nodes, resulting in a forest of disjoint trees. The initial tree is generated by sequentially attaching new nodes to randomly chosen existing nodes until the tree contains N nodes. As nodes are removed, one at a time, the tree dissolves into an ensemble of separate trees, namely a forest. We study the statistical properties of trees and nodes in this heterogeneous forest. In the limit N --> ? , we find that the system is characterized by a single parameter: the fraction of remaining nodes m. We obtain analytically the size density ?s of trees of size s, which has a power-law tail ?s ~s-? , with exponent ? = 1 + 1 / m . Therefore, the tail becomes steeper as further nodes are removed, producing an unusual scaling exponent that increases continuously with time. Furthermore, we investigate the fragment size distribution in a growing tree, where nodes are added as well as removed, and find that the distribution for this case is much narrower.

  14. Forest tree biotechnology.

    PubMed

    Dean, J F; LaFayette, P R; Eriksson, K E; Merkle, S A

    1997-01-01

    The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium. PMID:9204750

  15. Grizzly Giant Tree

    USGS Multimedia Gallery

    This giant sequoia is named the Grizzly Giant, the oldest sequoia tree in the Mariposa Grove of Big Trees, located within Yosemite National Park. It is believed to be between 1,900 and 2,400 years old. ...

  16. 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)

  17. 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...

  18. 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…

  19. 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…

  20. 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.…

  1. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Z.; Ben-Naim, E.

    2015-01-01

    We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N\\to ? . We obtain analytically the size density {{? }s} of trees of size s. The size density has power-law tail {{? }s} {{s}-? } with exponent ? =1+\\frac{1}{m}. Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent ? increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees.

  2. 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.

  3. Trees in Our Lives.

    ERIC Educational Resources Information Center

    NatureScope, 1986

    1986-01-01

    Provides: (1) background information on how trees have influenced human history and how trees affect people today; (2) four activities dealing with these topics; and (3) a ready-to-copy page related to paper and plastics. Activities include an objective, recommended age level(s), subject area(s), list of materials needed, and procedures. (JN)

  4. Tea Tree Oil

    MedlinePLUS

    ... the arms and legs causing a lack of balance and coordination. One patient went into a coma after drinking half a cup of tea tree oil. Topical use of diluted tea tree oil is generally considered safe for most adults. However, one case study did report a young ...

  5. 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

  6. 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.

  7. 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.

  8. Wounded forests, starving trees

    SciTech Connect

    Shigo, A.L.

    1985-11-01

    Acid rain, insects, and fungi are real problems that can kill trees. Wounded and starving trees are also realities and part of the total picture. Forest decline is a many-sided problem, yet recent attention has focused on only a few visible factors. The blame for diebacks and declines can not always be placed on well-publicized short-term agents. Forestry practices may also play an important part in today's current tree problems. This paper examined past forestry practices to see if they could have predisposed forests to stress and therefore been a major factor in current forest problems. 8 references, 10 figures.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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)

  14. 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

  15. 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.

  16. Trees as energy crops

    SciTech Connect

    Standiford, R.B.; Donaldson, D.R.

    1982-01-01

    A report is presented of studies on the energy production of forest trees in California. The volume yield of the fastest growing species (Eucalyptus) was 23 cubic metres per hectare and energy yield 20 million kcal per hectare per annum.

  17. 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

  18. Generalized constructive tree weights

    NASA Astrophysics Data System (ADS)

    Rivasseau, Vincent; Tanasa, Adrian

    2014-04-01

    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.

  19. 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

  20. Oscillation damping in trees.

    PubMed

    Spatz, Hanns-Christof; Theckes, Benoit

    2013-06-01

    Oscillation damping is of vital importance for trees to withstand strong gusty winds. Tree adaptation to wind loading takes place over a long time and during a storm only passive damping mechanisms can reduce the impact of the wind on trunk and roots. Structural damping, a phenomenon, which is associated with the conspicuous movements of the branches relative to the trunk is of particular importance. Primary and higher order branches can be seen as multiple tuned mass dampers. Moreover, as the frequency bands overlap within branches and between primary branches and the entire tree, resonance energy transfer can distribute mechanical energy over the entire tree, such that it is dissipated more effectively than in a tree with stiff branches and not so much focused on the tree trunk and the roots. Theoretical studies using modal analysis and finite element methods have supported these assertions. Next to "multiple mass damping" and "multiple resonance damping", both characterized by linear coupling between the elements, a third non linear mode, operative at large amplitudes has been identified: "damping by branching". In all these not mutually exclusive concepts frequency tuning between the elements appears to be a fundamental requisite. PMID:23602100

  1. 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…

  2. The inference of gene trees with species trees.

    PubMed

    Szll?si, 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

  3. Measuring inconsistency in phylogenetic trees.

    PubMed

    Willson, S J

    1998-01-01

    Suppose that we seek a tree T giving the phylogenetic relationships among the species in a set S. A common method selects for such a tree a maximum parsimony tree using the genome of the species in S. Suppose that K is a proper subset of S. Then T induces a tree U which gives the same relationships among the species in K but omits the species of S which are not in K. Unfortunately, when T is a maximum parsimony tree for the species in S, then U need not be a maximum parsimony tree for the species in K. This phenomenon exhibits an inconsistency in the criterion of maximum parsimony-maximum parsimony trees for different groups of species may be "inconsistent". It implies that the addition of a new species scan change relationships already "established" for prior species if the trees are obtained by the criterion of maximum parsimony. The phenomenon occurs both in artificial examples and with real data. An alternative method for generating phylogenetic trees seeks to minimize such inconsistencies. For each group J consisting of four of the species, we find a tree T(J) describing the relationship only among the four species in J, for example by the use of maximum parsimony on those four species alone. In favorable cases one may combine all the trees T(J) into a single tree T that is consistent with all the trees T(J). If such a tree T exists, then it is unique, and there is a computationally efficient algorithm for finding the tree T. In unfavorable bases such a tree T does not exist, but there may still be a tree containing only "mild" inconsistencies with the trees T(J). A numerical measure is given for the inconsistency I(T) of a tree T in terms of the treelengths of the various trees with set J of leaves in comparison with the tree T. We may then seek a "minimally inconsistent tree T" that minimizes the inconsistency I(T). We describe procedures which find a tree T with low inconsistency I(T). Examples are provided using both artificial strings and data from the complete mitochondrial DNA sequences for 16 species. In particular, minimally inconsistent trees are identified for the 16 species. The definition permits a proof that the trees are in fact minimally inconsistent. The criterion can be applied in both a relative and an absolute sense. PMID:9473388

  4. 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

  5. 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

  6. 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 grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews)+Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla+Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.'s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ⩽ 15% of the conflicts among Song et al.'s (2012) 447 gene trees. Unfortunately, Song et al.'s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles' heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations. PMID:26238460

  7. Lava trees and tree molds ("cannon stones") of Mt. Etna

    NASA Astrophysics Data System (ADS)

    Carveni, Pietro; Mele, Giuliana; Benfatto, Santo; Imposa, Sebastiano; Salleo Puntillo, Maria

    2011-08-01

    Unique volcanic structures, known in the literature as "lava trees" and "tree molds", have formed at several sites on Mt. Etna volcano (northeastern Sicily, Italy). They form when a fluid lava flow runs over a tree, wraps around it and, while the wood burns off, solidifies forming a hollow cast of the tree. The inhabitants of the Etna area call these formations "pietre cannone" ("cannon stones") because of their cylindrical shape. The first documentation of lava trees is from Hawaii, but the first eye-witnessed accounts of their formation are, to our knowledge, from Etna's 1865 eruption. Although many of the literature examples of lava trees and tree molds formed in pahoehoe, many of those reported in this work formed in a'a. The sites where we have found the lava tree molds are located within the territory of the Etna Regional Park; most occur next to walking trails and have a high potential for geotourism.

  8. 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

  9. 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

  10. Tree of pain.

    PubMed

    Newnham, David

    2016-01-20

    I like trees as much as anyone. But, thanks to the graceful ash outside our kitchen window, I have now joined the merry band of tennis elbow sufferers who, at any one time, make up one third of the population. PMID:26786443

  11. 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

  12. 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

  13. 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)

  14. 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…

  15. 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…

  16. 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.

  17. 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...

  18. Sizing Up Trees.

    ERIC Educational Resources Information Center

    Nelson, Don

    1995-01-01

    Presents a way for teachers to capitalize on children's intrinsic fascination with big things by measuring the world's largest living plants--trees. Students develop an appreciation of nature, work together cooperatively, and practice science process skills. Outlines the procedure and equipment including pencils, metersticks, and string. (NB)

  19. Multiquarks and Steiner trees

    NASA Astrophysics Data System (ADS)

    Richard, Jean-Marc

    2010-10-01

    A brief review review is presented of models tentatively leading to stable multiquarks. A new attempt is presented, based on a Steiner-tree model of confinement, which is inspired by by QCD. It leads to more attraction than the empirical colour-additive model used in earlier multiquark calculations, and predict several multiquark states in configurations with different flavours.

  20. Flat Tree Oyster (Isognomon alatus)

    USGS Multimedia Gallery

    At high tide, the red bark of the Red Mangrove Trees is submerged, creating a brilliant reflection at the water's surface. Flat Tree Oysters (Isognomon alatus) grow on the upper portions of the roots....

  1. 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.; Rger, N.; lvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, .; 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 cycleparticularly net primary productivity and carbon storageincreasingly 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 trees 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.

  2. 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.

  3. 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…

  4. 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,

  5. 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)

  6. 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,…

  7. 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)

  8. 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:…

  9. 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

  10. 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; Rger, 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

  11. Gene tree correction for reconciliation and species tree inference

    PubMed Central

    2012-01-01

    Background Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in embedding inferred gene trees into a known species tree, revealing the evolution of the gene family by duplications and losses. When a species tree is not known, a natural algorithmic problem is to infer a species tree from a set of gene trees, such that the corresponding reconciliation minimizes the number of duplications and/or losses. The main drawback of reconciliation is that the inferred evolutionary scenario is strongly dependent on the considered gene trees, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. Results In this paper, we take advantage of certain gene trees properties in order to preprocess them for reconciliation or species tree inference. We flag certain duplication vertices of a gene tree, the non-apparent duplication (NAD) vertices, as resulting from the misplacement of leaves. In the case of species tree inference, we develop a polynomial-time heuristic for removing the minimum number of species leading to a set of gene trees that exhibit no NAD vertices with respect to at least one species tree. In the case of reconciliation, we consider the optimization problem of removing the minimum number of leaves or species leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case. PMID:23167951

  12. 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.; Rger, N.; lvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S. J.; Duque, .; 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.

  13. 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

  14. 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

  15. 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…

  16. Structural regression trees

    SciTech Connect

    Kramer, S.

    1996-12-31

    In many real-world domains the task of machine learning algorithms is to learn a theory for predicting numerical values. In particular several standard test domains used in Inductive Logic Programming (ILP) are concerned with predicting numerical values from examples and relational and mostly non-determinate background knowledge. However, so far no ILP algorithm except one can predict numbers and cope with nondeterminate background knowledge. (The only exception is a covering algorithm called FORS.) In this paper we present Structural Regression Trees (SRT), a new algorithm which can be applied to the above class of problems. SRT integrates the statistical method of regression trees into ILP. It constructs a tree containing a literal (an atomic formula or its negation) or a conjunction of literals in each node, and assigns a numerical value to each leaf. SRT provides more comprehensible results than purely statistical methods, and can be applied to a class of problems most other ILP systems cannot handle. Experiments in several real-world domains demonstrate that the approach is competitive with existing methods, indicating that the advantages are not at the expense of predictive accuracy.

  17. 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.

  18. From event-labeled gene trees to species trees

    PubMed Central

    2012-01-01

    Background Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data. Results We show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses. Conclusions The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed.

  19. Save a Tree

    NASA Astrophysics Data System (ADS)

    Williams, Kathryn R.

    1999-10-01

    Starting in September 1925, JCE reproduced pictures of famous chemists or chemistry-related works of art as frontispieces. Often, the Journal included a biography or other article about the picture. The August 1945 frontispiece featured the largest cork oak in the United States. An accompanying article described the goals of the Cork Project to plant cork trees in suitable locations in the U.S., to compensate for uncertain European and African sources during World War II. The final frontispiece appeared in December 1956. To view supplementary material, please refer to JCE Online's supplementary links.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Looking/Learning Drawing: Trees.

    ERIC Educational Resources Information Center

    Hurwitz, Al; Blume, Sharon

    1985-01-01

    Secondary students are asked to study and compare three reproductions--Van Gogh's "Grove of Cypresses," Da Vinci's "Study of a Tree," and Mondrian's "Tree II." The activity will help students develop their powers of observation and analysis, powers that can be applied to their own drawings. (RM)

  8. The limits to tree height.

    PubMed

    Koch, George W; Sillett, Stephen C; Jennings, Gregory M; Davis, Stephen D

    2004-04-22

    Trees grow tall where resources are abundant, stresses are minor, and competition for light places a premium on height growth. The height to which trees can grow and the biophysical determinants of maximum height are poorly understood. Some models predict heights of up to 120 m in the absence of mechanical damage, but there are historical accounts of taller trees. Current hypotheses of height limitation focus on increasing water transport constraints in taller trees and the resulting reductions in leaf photosynthesis. We studied redwoods (Sequoia sempervirens), including the tallest known tree on Earth (112.7 m), in wet temperate forests of northern California. Our regression analyses of height gradients in leaf functional characteristics estimate a maximum tree height of 122-130 m barring mechanical damage, similar to the tallest recorded trees of the past. As trees grow taller, increasing leaf water stress due to gravity and path length resistance may ultimately limit leaf expansion and photosynthesis for further height growth, even with ample soil moisture. PMID:15103376

  9. Mixtures of (Constrained) Ultrametric Trees.

    ERIC Educational Resources Information Center

    Wedel, Michel; DeSarbo, Wayne S.

    1998-01-01

    Presents a method for the estimation of ultrametric trees calibrated on subjects' pairwise proximity judgments of stimuli, capturing subject heterogeneity using a finite mixture formulation. An empirical example from published data shows the ability to deal with external constraints on the tree topology. (Author/SLD)

  10. Hazard Tree Management for Camps.

    ERIC Educational Resources Information Center

    Kong, Earl

    2002-01-01

    The principles behind a camp's hazard tree program are, first, identifying and removing those hazards that offer a clear, immediate threat, and then creating a management plan for the other trees. The plan should be written and contain goals and objectives, field evaluations, and treatments. Follow-up evaluations should be done annually and after

  11. 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)

  12. Genome Trees from Conservation Profiles

    PubMed Central

    Tekaia, Fredj; Yeramian, Edouard

    2005-01-01

    The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component presence-absence protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings. PMID:16362074

  13. The tree of one percent

    PubMed Central

    Dagan, Tal; Martin, William

    2006-01-01

    Two significant evolutionary processes are fundamentally not tree-like in nature - lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree. PMID:17081279

  14. 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

  15. 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…

  16. Tree preserving embedding.

    PubMed

    Shieh, Albert D; Hashimoto, Tatsunori B; Airoldi, Edoardo M

    2011-10-11

    The goal of dimensionality reduction is to embed high-dimensional data in a low-dimensional space while preserving structure in the data relevant to exploratory data analysis such as clusters. However, existing dimensionality reduction methods often either fail to separate clusters due to the crowding problem or can only separate clusters at a single resolution. We develop a new approach to dimensionality reduction: tree preserving embedding. Our approach uses the topological notion of connectedness to separate clusters at all resolutions. We provide a formal guarantee of cluster separation for our approach that holds for finite samples. Our approach requires no parameters and can handle general types of data, making it easy to use in practice and suggesting new strategies for robust data visualization. PMID:21949369

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K.; Warnow, T.J.

    1993-03-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n{sup 3}) time and from POM experiments in O(n{sup 4}) time.

  2. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K. ); Warnow, T.J. )

    1993-01-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n[sup 3]) time and from POM experiments in O(n[sup 4]) time.

  3. 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.

  4. Through bore subsea christmas trees

    SciTech Connect

    Huber, D.S.; Simmers, G.F.C.; Johnson, C.S.

    1985-01-01

    The workovers of subsea completed wells are expensive and time consuming as even the most routine tasks must be carried out by a semi-submersible. This paper describes the economic, safety and operational advantages which led to the development and successful first installation of 'through bore' subsea production trees. The conventional wet subsea trees have proved to be very reliable over the past ten years of operation in the Argyll, Duncan and Innes fields, however the completion strings require pulling on the average about once every three to five years. The conventional subsea tree/tubing hanger set up design requires the tree to be tripped and a rig BOP stack run to pull the tubing. This operation is time consuming, very weather sensitive and leaves the well temporarily without a well control stack on the wellhead. The 7 1/16'' 'through bore' subsea tree was developed to minimize the tubing pulling workover time and several trees have been run successfully since the latter part of 1984. The time saving on a tubing pulling workover is three days. In addition, the design considerably reduces the hazards and equipment damage risk inherent in the conventional design. Hamilton Brothers and National Supply Company in Aberdeen designed the equipment which must be considered a new generation of subsea production trees.

  5. Terrestrial apes and phylogenetic trees

    PubMed Central

    Arsuaga, Juan Luis

    2010-01-01

    The image that best expresses Darwins thinking is the tree of life. However, Darwins 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

  6. Falls from trees and tree associated injuries in rural Melanesians.

    PubMed

    Barss, P; Dakulala, P; Doolan, M

    Falls from trees and other tree related injuries are the most common cause of trauma in some parts of rural Melanesia. A four year review of all admissions for trauma to the Provincial Hospital at Alotau, Milne Bay Province, Papua New Guinea, showed that 27% were due to falls from trees, and a further 10% were due to related injuries, such as being struck by a falling branch or a coconut. A questionnaire distributed to rural health centres showed that during the study period at least 28 villagers died from falls from trees before reaching hospital. Head and chest trauma were common causes of death. Many injured patients were boys. Forearm fractures were the most common injuries, but more serious injuries were also frequently encountered. Trees responsible for most deaths and injuries included the coconut palm, betel palm, mango, and breadfruit. There are many strategies for preventing such injuries; perhaps the most important is to stop small boys climbing tall trees. Such falls are a serious occupational hazard for many subsistence farmers. PMID:6440619

  7. 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 biogeniclivinginfrastructure 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.

  8. A valuable tree by gum!

    PubMed

    Forrest, M

    2000-06-01

    Which majestic ornamental tree, conspicuous in the Australian landscape, has ten million hectares in cultivation worldwide--yielding timber, fuel, essential oil and cut foliage? It could only be eucalyptus. PMID:11190248

  9. 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.

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

    PubMed

    Leach, Adam D; Banbury, Barbara L; Felsenstein, Joseph; de Oca, Adrin 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 presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. PMID:26227865

  11. 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 presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. PMID:26227865

  12. Parallel TreeSPH

    NASA Astrophysics Data System (ADS)

    Dav, Romeel; Dubinski, John; Hernquist, Lars

    1997-08-01

    We describe PTreeSPH, a gravity treecode combined with an SPH hydrodynamics code designed for parallel supercomputers having distributed memory. Our computational algorithm is based on the popular TreeSPH code of Hernquist & Katz (1989)[ApJS, 70, 419]. PTreeSPH utilizes a domain decomposition procedure and a synchronous hypercube communication paradigm to build self-contained subvolumes of the simulation on each processor at every timestep. Computations then proceed in a manner analogous to a serial code. We use the Message Passing Interface (MPI) communications package, making our code easily portable to a variety of parallel systems. PTreeSPH uses individual smoothing lengths and timesteps, with a communication algorithm designed to minimize exchange of information while still providing all information required to accurately perform SPH computations. We have incorporated periodic boundary conditions with forces calculated using a quadrupole Ewald summation method, and comoving integration under a variety of cosmologies. Following algorithms presented in Katz et al. (1996)[ApJS, 105, 19], we have also included radiative cooling, heating from a parameterized ionizing background, and star formation. A cosmological simulation from z = 49 to z = 2 with 64 3 gas particles and 64 3 dark matter particles requires 1800 node-hours on a Cray T3D, with a communications overhead of 8%, load balanced to ? 95% level. When used on the new Cray T3E, this code will be capable of performing cosmological hydrodynamical simulations down to z = 0 with 2 10 6 particles, or to z = 2 with 10 7 particles, in a reasonable amount of time. Even larger simulations will be practical in situations where the matter is not highly clustered or when periodic boundaries are not required.

  13. 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.

  14. Tunnel of the California Tunnel Tree

    USGS Multimedia Gallery

    In this image, the tunnel through the California Tunnel Tree may be seen. The tunnel was cut through the giant sequoia tree in 1895 to allow coaches, and eventually cars, to drive through the tree as part of a marketing stunt. The California Tunnel Tree is the only living giant sequoia with a t...

  15. Critical wind speed at which trees break

    NASA Astrophysics Data System (ADS)

    Virot, E.; Ponomarenko, A.; Dehandschoewercker, É.; Quéré, D.; Clanet, C.

    2016-02-01

    Data from storms suggest that the critical wind speed at which trees break is constant (≃42 m /s ), regardless of tree characteristics. We question the physical origin of this observation both experimentally and theoretically. By combining Hooke's law, Griffith's criterion, and tree allometry, we show that the critical wind speed indeed hardly depends on the height, diameter, and elastic properties of trees.

  16. 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)…

  17. 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

  18. Tree Growth Rings: What They Tell Us.

    ERIC Educational Resources Information Center

    Sunal, Dennis W.; Sunal, Cynthia Szymanski

    1991-01-01

    Activities in which students can learn to determine the history of a tree from the growth pattern recorded in the rings of a cross-section of a tree are described. Activities include background information, objectives, a list of needed materials per group, and procedures. Cross-sections of four different tree types are included if real tree

  19. 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 was divided into three sections to separate parts with different moisture (heartwood and sapwood) or empty space (decays). For easier manipulation with the antenna we developed a special ruler for measuring the distance along the scans. Instead of the surveying wheel we read the distance with a camera, which was fixed on the antenna and focused on the ruler with a binary pattern. Hence, during whole measurement and the data processing we were able to identify an accurate position on the tree in view of the scan. Some preliminary measurements on the trees were also conducted. They were performed using a GSSI 900 MHz antenna. Several tree species (beech, horse-chestnut, birch, ...) in Louvain-la-Neuve and Brussels, Belgium, have been investigated to see the internal structure of the tree decays. The measurements were carried out mainly by circumferential measurement around the trunk and also by vertical measurement along the trunk for approximate detection of the cavity. The comparison between the numerical simulations, simplified tree trunk model and real data from trees is presented. This research is funded by the Fonds de la Recherche Scientifique (FNRS, Belgium) and benefits from networking activities carried out within the EU COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar".

  20. 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.

  1. 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).

  2. 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.

  3. 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...

  4. 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

  5. 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.

  6. 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.

  7. 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 (?n)n ? 0, in which tree ?n 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

  8. 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 results will be shown.

  9. 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.

  10. Interpreting the universal phylogenetic tree.

    PubMed

    Woese, C R

    2000-07-18

    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

  11. 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.

  12. Peanut and tree nut allergy.

    PubMed

    Cox, Amanda; Sicherer, Scott H

    2015-01-01

    Allergy to peanut and tree nuts is a major worldwide health concern. The prevalence of these allergies may be increasing, but the reasons for these increases remain unclear. This group of foods accounts for a large proportion of severe and fatal food-allergic reactions. These allergies present most often during childhood but can occur at any age. Resolution is possible but uncommon, and frequent lifetime reactions caused by accidental ingestion are a serious problem. The major allergens of peanut and most tree nuts have been identified, allowing for insights into patient diagnoses, clinical outcomes, and potential future immunotherapies. PMID:26022873

  13. Dating the tree of life.

    PubMed

    Benton, Michael J; Ayala, Francisco J

    2003-06-13

    The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger. PMID:12805535

  14. Tree hydraulics: how sap rises

    NASA Astrophysics Data System (ADS)

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crowna 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.

  15. 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.

  16. 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

  17. 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…

  18. AncesTrees: ancestry estimation with randomized decision trees.

    PubMed

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

    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

  19. 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,

  20. Cedar Tree in Bryce Canyon

    USGS Multimedia Gallery

    A cedar tree in Bryce Canyon National Park. Bryce Canyon is a unique sandstone formation in southern Utah. It is home to a large number of hoodoos, which are oddly shaped pillars of rock that formed due to different erosion rates for the dolomite that caps them and the sandstone that forms their ba...

  1. 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)

  2. 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.

  3. 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…

  4. 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…

  5. 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

  6. Support Vector Machine Classification Trees.

    PubMed

    de Boves Harrington, Peter

    2015-11-01

    Proteomic and metabolomic studies based on chemical profiling require powerful classifiers to model accurately complex collections of data. Support vector machines (SVMs) are advantageous in that they provide a maximum margin of separation for the classification hyperplane. A new method for constructing classification trees, for which the branches comprise SVMs, has been devised. The novel feature is that the distribution of the data objects is used to determine the SVM encoding. The variance and covariance of the data objects are used for determining the bipolar encoding required for the SVM. The SVM that yields the lowest entropy of classification becomes the branch of the tree. The SVM-tree classifier has the added advantage that nonlinearly separable data may be accurately classified without optimization of the cost parameter C or searching for a correct higher dimensional kernel transform. It compares favorably to a regularized linear discriminant analysis, SVMs in a one against all multiple classifier, and a fuzzy rule-building expert system, a tree classifier with a fuzzy margin of separation. SVMs offer a speed advantage, especially for data sets that have more measurements than objects. PMID:26461495

  7. 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

  8. 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

  9. 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)

  10. 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)

  11. 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…

  12. Proceedings: Water treeing and aging

    SciTech Connect

    Bulinski, A.T.

    1991-10-01

    This report presents the record of the workshop Water Treeing and Aging.'' The workshop was held in Phoenix, Arizona on December 9--11, 1990 and was sponsored by the Distribution Program of the Electrical Systems Division of the Electric Power Research Institute (EPRI). Attendance at the workshop was by invitation only. Twenty two attendees from seven countries, from universities, research organizations, electric utilities and polymeric materials suppliers took part in this workshop. The workshop was designed to assess progress in the understanding of water treeing phenomena and polymeric cable insulation aging since the last meeting of a similar forum of experts, which was organized by the Office of Exploratory Research of EPRI in December 1985. The objective of the present workshop was to assess progress and to provide direction for further studies in this field. The discussions covered a wide range of subjects including water tree structure, initiation, growth and breakdown mechanisms, accelerated aging tests for new materials and cables, diagnostic tests, detection of deterioration, tree retardants, field repairs and preventive measures. The workshop discussions were recorded, transcribed, edited and included in this report. The records of the discussions within the breakout groups are also included (Appendices A and B) as they contain information regarding experience from different labs which may be valuable to the reader.

  13. GumTree: Data reduction

    NASA Astrophysics Data System (ADS)

    Rayner, Hugh; Hathaway, Paul; Hauser, Nick; Fei, Yang; Franceschini, Ferdi; Lam, Tony

    2006-11-01

    Access to software tools for interactive data reduction, visualisation and analysis during a neutron scattering experiment enables instrument users to make informed decisions regarding the direction and success of their experiment. ANSTO aims to enhance the experiment experience of its facility's users by integrating these data reduction tools with the instrument control interface for immediate feedback. GumTree is a software framework and application designed to support an Integrated Scientific Experimental Environment, for concurrent access to instrument control, data acquisition, visualisation and analysis software. The Data Reduction and Analysis (DRA) module is a component of the GumTree framework that allows users to perform data reduction, correction and basic analysis within GumTree while an experiment is running. It is highly integrated with GumTree, able to pull experiment data and metadata directly from the instrument control and data acquisition components. The DRA itself uses components common to all instruments at the facility, providing a consistent interface. It features familiar ISAW-based 1D and 2D plotting, an OpenGL-based 3D plotter and peak fitting performed by fityk. This paper covers the benefits of integration, the flexibility of the DRA module, ease of use for the interface and audit trail generation.

  14. 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

  15. 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)

  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. 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...

  18. 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

  19. Wellhead and tree standards updated

    SciTech Connect

    Dach, A.J. Jr.; Haeberle, T.

    1996-03-11

    Revisions in the API 6A, 17th Edition, have resolved a number of long-term problems and expanded its scope and coverage of wellhead and christmas tree equipment. The 17th Edition, Feb. 1, 1996, represents the state-of-the-art in international requirements for wellhead and christmas tree equipment. The design, materials, and quality control aspects of API 6A have all been improved with an emphasis on making the document more acceptable around the world. However, there are unresolved issues that raise many questions about the future direction of efforts aimed at international standardization of wellhead and christmas tree equipment. Unfortunately, these unresolved issues confuse both manufacturers and companies purchasing this equipment. This ultimately increases wellhead and christmas tree costs, so it is to everyone`s advantage to resolve these issues. This article describes the significant revisions that are included in API 6A, 17th Edition. Also discussed are the regulatory, standardization, and customer acceptance issues that cloud the future of API 6A, 17th Edition.

  20. Feathered Hollow in Living Tree

    USGS Multimedia Gallery

    Hollow in living tree in gallery forest of tributary to Tebicuary river. Grey feathers stuck along bottom of entrance suggest that it may be used by a bird. Paraguay is home to at least 589 breeding bird species and 120 migratory bird species. The Ñeembucú Region is typified by extensi...

  1. 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…

  2. Secondhand Trees, Firsthand Learning. Holiday Evergreens Revitalized.

    ERIC Educational Resources Information Center

    Graves, C. John

    1990-01-01

    Described is an activity that uses discarded evergreen trees from Christmas. Tree age and growth characteristics are investigated by looking at the number of whorls and rings of the trunks. Extensions and follow-up activities are included. (KR)

  3. Modelling Stem Cells Lineages with Markov Trees

    NASA Astrophysics Data System (ADS)

    Olariu, Victor; Coca, Daniel; Billings, Stephen A.; Kadirkamanathan, Visakan

    A variational Bayesian EM with smoothed probabilities algorithm for hidden Markov trees (HMT) is proposed for incomplete tree structured data. The full posterior of the HMT parameters is determined and the underflow problems associated with previous algorithms are eliminated. Example results for the prediction of the types of cells in real stem cell lineage trees are presented.

  4. 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...

  5. Data multiplexer using a tree switch

    NASA Technical Reports Server (NTRS)

    Easton, R. A.; Hilbert, E. E.

    1973-01-01

    Self-decoding FET-hybrid or integrated-circuit tree configuration uses minimum number of components and can be sequenced by clock or computer. Redundancy features can readily be incorporated into tree configuration; as tree grows in size and more sensors are included, percentage of parts that will affect given percentage of sensors steadily decreases.

  6. 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 ...

  7. 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 ...

  8. 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 ...

  9. Neighborhoods of trees in circular orderings.

    PubMed

    Bastkowski, Sarah; Baskowski, Sarah; Moulton, Vincent; Spillner, Andreas; Wu, Taoyang

    2015-01-01

    In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species [Formula: see text] is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set [Formula: see text]. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (NNI), the subtree prune and regraft (SPR) and the tree bisection and reconnection (TBR) operations. We show that the size of such a neighborhood of a binary tree associated with the NNI operation is independent of the tree's topology, but that this is not the case for the SPR and TBR operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the SPR and TBR operations and characterize those trees for which these bounds are attained. PMID:25477080

  10. 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

  11. 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.

  12. Tree decline in North America.

    PubMed

    Chevone, B I; Linzon, S N

    1988-01-01

    Air-borne, phytotoxic pollutants are known to adversely affect forest tree growth in North America. On a local scale, exposure to high concentrations of toxic gases, such as sulphur dioxide and fluoride, result in foliar injury, branch dieback, reduced radial growth and increased mortality in a variety of tree species. On a regional scale, the photochemical oxidant, ozone, is responsible for growth decline of pollutant-sensitive eastern white pine genotypes in the eastern United States, and of ponderosa and Jeffrey pines in the mountains of southern and central California. The etiology associated with the reported declines of high elevation red spruce in the Appalachian Mountains and of sugar maple in the northeastern United States and southeastern Canada is incompletely known at present. A complex of predisposing and inciting factors, including temperature and moisture stress, edaphic conditions, aluminium toxicity, insect depredation, and air-borne pollutants are probably involved in these declines. PMID:15092654

  13. 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

  14. 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…

  15. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... measure for all Christmas tree crops is a plant. (c) A Christmas tree having any value as a Christmas tree... 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...

  16. Anatomical modeling of the bronchial tree

    NASA Astrophysics Data System (ADS)

    Hentschel, Gerrit; Klinder, Tobias; Blaffert, Thomas; Blow, 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 nave 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.

  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. 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.

  19. 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

  20. Dendrochemistry: Seeing the forest through the trees

    NASA Astrophysics Data System (ADS)

    Hauck, Danielle K.

    Dendrochemistry is a term used to describe the compositional analysis of tree-rings and its application to biomonitoring of the tree's environment. The central hypothesis of this study is that the concentrations of silver and gold in tree-rings in the Mediterranean region record the history of African dust storms. Although there have been previous studies of tree-ring composition using both NAA and other analytical techniques, to the author's knowledge, this is the first dendrochemical study to consider the effects of dust storms on tree-ring chemistry. However, the results, as with many other dendrochemical studies, are promising at best. The tree-ring concentrations in a single tree in west-central Turkey were highly correlated with the local aerosol index obtained from the Total Ozone Mapping Spectrometer (TOMS). This suggests that silver and gold concentrations in carefully selected trees may serve as a proxy indicator of dust storm activity and indirectly, the phase of the North Atlantic Oscillation. Three other trees from the same forest did not have any silver or gold concentration peaks and possible reasons for this discrepancy are discussed. The correlation with dust storms is still uncertain because it was impossible to gather appropriate information about soil characteristics or additional trees for sampling to prove or disprove the hypothesis. However, the chemistries of silver and gold are discussed to elucidate why they may be uniquely good at recording environmental signals in tree-rings. Some promising results for detecting volcanic eruptions in tree-rings were obtained on tree samples of a shorter duration (20-30 years) from Catacik Turkey that were prepared for irradiation under improved conditions of cleanliness. These tree samples were analyzed later in the project after sample preparation procedures were altered to reduce the possibility of sample contamination. Concentration peaks in the Catacik samples were correlated with the timing of the Pinatubo eruption (1991) and the El Chichon eruption in 1982. However, many of the concentration peaks were in single trees and could not be verified by comparison to other trees that grew nearby. The relative success of correlating concentration peaks in these shorter tree sequences may have been due to the improved sample preparation procedures. Another possible explanation is that concentration peaks do not remain in the tree-rings over time due to diffusion or mobilization by the tree. This would make it more difficult to find or identify possible environmental signals in the older rings of a long tree sequence. Unfortunately, this study contributes to the overwhelming number of feasibility studies that have been performed since the 1950s. There is still no consensus regarding the mechanisms responsible for recording environmental events in tree-rings beyond passive uptake. The feasibility of dendrochemistry will be more firmly established by moving forward with thoughtfully planned control studies. The refined NAA procedures developed here are necessary for future experiments which should strive to understand the actual mechanisms responsible for uptake. There are several different aspects of dendrochemistry that could be tested with control studies and that would be useful for interpreting tree-ring chemistry. For instance, dendrochemical studies could focus on the variation in specific elements between trees and the creation of composite forest chronologies for the appropriate elements. If this was successful, it would indicate that tree-ring compositions faithfully record environmental conditions in some cases and for some elements. A possible correlation was found between the Ag and Au concentration in tree-rings and the intensity and frequency of dust storms. However, the promising results were only found for one tree out of four sampled in the Catacik forest. A future study could be dedicated to verifying the presence of the Ag and Au signals in other trees in the same forest. Future studies could also analyze the ground water near sample sites to mon

  1. 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.

  2. 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

  3. MixtureTree Annotator: A Program for Automatic Colorization and Visual Annotation of MixtureTree

    PubMed Central

    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

  4. 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.

  5. Interception losses of rainfall from Cashew trees

    NASA Astrophysics Data System (ADS)

    Rao, A. Sambasiva

    1987-04-01

    The rainfall interception losses from Cashew trees were quantified, based on the records of 105 selected storms within the range ? 25.0 mm, occurring in a humid tropical region at Kottamparamba, India. The storage capacity of the Cashew trees was worked out as 0.8 mm and the throughfall coefficient as 0.391. The trees under observation were 15-20 years of age with a leaf area index of 1.0-1.25. About 31% of the storm rainfall for storms ? 25.0 mm was intercepted by the Cashew trees and lost to the atmosphere. The measured interception losses from the trees were compared with the estimated interception losses using the analytical model of Gash (1979). The predicted interception losses from the Cashew trees were within 10% for storms with total rainfall ? 10.0 mm and within 22% for storms with a rainfall of 10.1-25.0 mm.

  6. Hierarchical clustering in minimum spanning trees

    NASA Astrophysics Data System (ADS)

    Yu, Meichen; Hillebrand, Arjan; Tewarie, Prejaas; Meier, Jil; van Dijk, Bob; Van Mieghem, Piet; Stam, Cornelis Jan

    2015-02-01

    The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.

  7. 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.

  8. Pore tree structure of porous char

    SciTech Connect

    Simons, G.A.

    1982-01-01

    A theory is presented which describes the tree-like pore structure of carbon char. Each pore that reaches the exterior surface of a char particle is depicted as the trunk of a tree. A statistically derived and empirically verified pore distribution function specifies the size distribution of the tree trunks on the particle surface. A continuous branching description of the pore tree predicts the number and size of the pores as a function of the skewed distance into the pore tree. The pore structure is completely specified through measured values of the porosity theta, internal surface area s/sub p/, and the particle radius a. The oxidation rate of carbon char is shown to be sensitive to the structure of the pore tree and the present theory is shown to accurately model the oxidation data base.

  9. 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.

  10. 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.

  11. 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%.

  12. Tree-Structured Infinite Sparse Factor Model

    PubMed Central

    Zhang, XianXing; Dunson, David B.; Carin, Lawrence

    2013-01-01

    A tree-structured multiplicative gamma process (TMGP) is developed, for inferring the depth of a tree-based factor-analysis model. This new model is coupled with the nested Chinese restaurant process, to nonparametrically infer the depth and width (structure) of the tree. In addition to developing the model, theoretical properties of the TMGP are addressed, and a novel MCMC sampler is developed. The structure of the inferred tree is used to learn relationships between high-dimensional data, and the model is also applied to compressive sensing and interpolation of incomplete images. PMID:25279389

  13. LISP-based fault tree development environment

    SciTech Connect

    Dixon, B.W.

    1986-01-01

    This paper describes an integrated graphical environment which can be used to build, modify, and analyze fault trees on a stand-alone work-station. The environment is written in LISP, utilizing graphics and menu features commonly found on LISP workstations. A unique fault tree solution algorithm is presented that efficiently utilizes a list-based tree structure and search space, and rule-based pruning to allow for rapid analysis of larger trees. Design and efficiency issues are discussed. 5 refs., 11 figs.

  14. Why are so many trees hollow?

    PubMed Central

    Ruxton, Graeme D.

    2014-01-01

    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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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...

  3. 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 (kerborg 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, Szll?si 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 analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/. PMID:25963975

  4. 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

  5. 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

  6. 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.

  7. 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...

  8. 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.

  9. 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…

  10. 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

  11. 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)

  12. Sewing String Tree Vertices with Ghosts

    NASA Astrophysics Data System (ADS)

    Sandoval Junior, Leonidas

    2002-03-01

    It is shown how to sew string vertices with ghosts at tree level in order to produce new tree vertices using the Group Theoretic approach to String Theory. It is then verified the BRST invariance of the sewn vertex and shown that it has the correct ghost number.

  13. 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

  14. 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

  15. 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...

  16. 'Christmas tree' created by Skylab 4 crewmembers

    NASA Technical Reports Server (NTRS)

    1973-01-01

    This 'Christmas tree' was created by the three crewmen of the third manned Skylab mission aboard the space station in Earth orbit. Food cans were used to fashion the tree. This photograph was made from a television transmission made from a video tape recording on December 24, 1973.

  17. Water tree retardant XLPE cable using VLDPE

    SciTech Connect

    Asano, Akihiro ); Takahashi, Tohru; Maeda, Kazunori; Niwa, Toshio )

    1994-01-01

    Investigations were carried out on water tree retardant XLPE (XLVLDPE) cable using very low density polyethylene (VLDPE) which is a very recent new grade of polyethylene. To begin with, when the water tree retardant effects of various types of VLDPE being sold on the market were evaluated by using sheet specimens, extremely good water tree retardant effects were exhibited when the type of VLDPE was selected appropriately. Next, the above selected varieties of VLDPE were tested regarding the extruding into cables. The extrusion of VLDPE was found to be more difficult compared to conventional XLPE, and consequently required the modification of extrusion conditions and a crosslinking agent. The result of the water tree acceleration test of XLVLDPE cables indicated that the generation of bow-tie trees was suppressed to a larger extent than conventional XLPE cables. Although the AC initial breakdown voltage of XLVLDPE cables was lower than that of the conventional XLPE cables, there was almost no decrease in the breakdown voltage due to the water tree test and the breakdown voltage became higher than that of the conventional XLPE cables after the water tree tests. The superior water tree retardation characteristics of XLVLDPE described above was deduced to be due to the combined effect of the low crystallinity of the base polyethylene and the presence of the additive material (neutralizing agent and antioxidant).

  18. 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 ...

  19. Electrical signals in avocado trees

    PubMed Central

    Oyarce, Patricio

    2010-01-01

    Plant responses to environmental changes are associated with electrical excitability and signaling; automatic and continuous measurements of electrical potential differences (ΔEP) between plant tissues can be effectively used to study information transport mechanisms and physiological responses that result from external stimuli on plants. The generation and conduction of electrochemical impulses within plant different tissues and organs, resulting from abiotic and biotic changes in environmental conditions is reported. In this work, electrical potential differences are monitored continuously using Ag/AgCl microelectrodes, inserted 5 mm deep into sapwood at two positions in the trunks of several Avocado trees. Electrodes are referenced to a non polarisable Ag/AgCl microelectrode installed 20 cm deep in the soil. Systematic patterns of ΔEP during absolute darkness, day-night cycles and different conditions of soil water availability are discussed as alternative tools to assess early plant stress conditions. PMID:20592805

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Tree rings : timekeepers of the past

    USGS Publications Warehouse

    U.S. Geological Survey

    1973-01-01

    A casual look at the top of a tree stump reveals that it is composed of a series of concentric rings-tree rings -that become larger and larger in diameter outward from the center of the stump. Because a single tree ring is usually formed each year, the age of the tree at the time it was cut can be determined by simply counting the rings. If the year of cutting is known, the year during which each ring was formed can be determined by counting backwards from the outside ring. Such "dating" of rings may reveal that rings formed during certain extreme drought years are unusually narrow. This has led to speculation that tree ring characteristics may indicate a number of things about past water and climatic conditions.

  6. Fuzzy variable-branch decision tree

    NASA Astrophysics Data System (ADS)

    Yang, Shiueng-Bien

    2010-10-01

    Decision trees and their variants recently have been proposed. All trees used are fixed M-ary tree structured, such that the training samples in each node must be artificially divided into a fixed number of branches. This work proposes a fuzzy variable-branch decision tree (FVBDT) based on the fuzzy genetic algorithm (FGA). The FGA automatically searches for the proper number of branches of each node according to the classification error rate and the classification time of FVBDT. Therefore, FGA reduces both the classification error rate and classification time, and then optimizes the FVBDT. In our experiments, FVBDT outperforms the traditional C-fuzzy decision tree (CFDT) based on the fuzzy C-means (FCM) algorithm.

  7. Tree snubbing operation solves well control problem

    SciTech Connect

    Gebhardt, F.; Thompson, J.D.

    1987-09-01

    Wild Well Control, Inc. has used a unique method to remove a Christmas tree under high pressure and install BOPs without a rig. This allowed workover of a gas-condensate well with a shallow tubing break that could not be killed by surface pumping due to casing pressure limitations. The procedure eliminated the need for drilling a relief well. The tree-stripping procedure is applicable to wells with Christmas trees that are screwed to the tubing string and equipped with wrap-around tubing hangers. The method would not be required if the tree were provided with a mandrel hanger that could receive a back-pressure valve. The step-by-step procedure used to remove the tree under pressure is described.

  8. MTVis: tree exploration using a multitouch interface

    NASA Astrophysics Data System (ADS)

    Andrews, David; Teoh, Soon Tee

    2010-01-01

    We present MTVis, a multi-touch interactive tree visualization system. The multi-touch interface display hardware is built using the LED-LP technology, and the tree layout is based on RINGS, but enhanced with multitouch interactions. We describe the features of the system, and how the multi-touch interface enhances the user's experience in exploring the tree data structure. In particular, the multi-touch interface allows the user to simultaneously control two child nodes of the root, and rotate them so that some nodes are magnified, while preserving the layout of the tree. We also describe the other meaninful touch screen gestures the users can use to intuitively explore the tree.

  9. 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.

  10. Tapping tree rings for the environmental tales they tell

    SciTech Connect

    Amato, I.

    1988-10-01

    Elemental and chemical distributions in tree rings may be a record of the tree's chemical environment during its lifetime. This article examines spectroscopic techniques which are being used to analyze tree rings to obtain environmental clues.

  11. Benefits of tree mixes in carbon plantings

    NASA Astrophysics Data System (ADS)

    Hulvey, Kristin B.; Hobbs, Richard J.; Standish, Rachel J.; Lindenmayer, David B.; Lach, Lori; Perring, Michael P.

    2013-10-01

    Increasingly governments and the private sector are using planted forests to offset carbon emissions. Few studies, however, examine how tree diversity -- defined here as species richness and/or stand composition -- affects carbon storage in these plantings. Using aboveground tree biomass as a proxy for carbon storage, we used meta-analysis to compare carbon storage in tree mixtures with monoculture plantings. Tree mixes stored at least as much carbon as monocultures consisting of the mixture's most productive species and at times outperformed monoculture plantings. In mixed-species stands, individual species, and in particular nitrogen-fixing trees, increased stand biomass. Further motivations for incorporating tree richness into planted forests include the contribution of diversity to total forest carbon-pool development, carbon-pool stability and the provision of extra ecosystem services. Our findings suggest a two-pronged strategy for designing carbon plantings including: (1) increased tree species richness; and (2) the addition of species that contribute to carbon storage and other target functions.

  12. Temperature histories from tree rings and corals

    NASA Astrophysics Data System (ADS)

    Cook, Edward 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 Medieval Warm Period 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.

  13. Comparison of tree-child phylogenetic networks.

    PubMed

    Cardona, Gabriel; Rossell, Francesc; Valiente, Gabriel

    2009-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/. PMID:19875855

  14. ASTRID: Accurate Species TRees from Internode Distances

    PubMed Central

    2015-01-01

    Background Incomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets. Results We have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours. Conclusions ASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github. PMID:26449326

  15. 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

  16. 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

  17. 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

  18. 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

  19. The ghosts of trees past: savanna trees create enduring legacies in plant species composition.

    PubMed

    Stahlheber, Karen A; Crispin, Kimberly L; Anton, Cassidy; D'Antonio, Carla M

    2015-09-01

    Isolated trees in savannas worldwide are known to modify their local environment and interact directly with neighboring plants. Less is known about how related tree species differ in their impacts on surrounding communities, how the effects of trees vary between years, and how composition might change following loss of the tree. To address these knowledge gaps, we explored the following questions: How do savanna trees influence the surrounding composition of herbaceous plants? Is the influence of trees consistent across different species and years? How does this change following the death of the tree? We surveyed herbaceous species composition and environmental attributes surrounding living and dead evergreen and deciduous Quercus trees in California (USA) savannas across several years that differed in their total precipitation. Oak trees of all species created distinct, homogenous understory communities dominated by exotic grasses across several sites. The composition of the low-diversity understory communities showed less interannual variation than open grassland, despite a two-fold difference in precipitation between the driest and wettest year. Vegetation composition was correlated with variation in soil properties, which were strongly affected by trees. Oaks also influenced the communities beyond the edge of the crown, but this depended on site and oak species. Low-diversity understory communities persisted up to 43 years following the death of the tree. A gradual decline in the effect of trees on the physical, environment following death did not result in vegetation becoming more similar to open grassland over time. The presence of long-lasting legacies of past tree crowns highlights the difficulty of assigning control of the current distribution of herbaceous species in grassland to their contemporary environment. PMID:26594707

  20. Type I Error Control for Tree Classification

    PubMed Central

    Jung, Sin-Ho; Chen, Yong; Ahn, Hongshik

    2014-01-01

    Binary tree classification has been useful for classifying the whole population based on the levels of outcome variable that is associated with chosen predictors. Often we start a classification with a large number of candidate predictors, and each predictor takes a number of different cutoff values. Because of these types of multiplicity, binary tree classification method is subject to severe type I error probability. Nonetheless, there have not been many publications to address this issue. In this paper, we propose a binary tree classification method to control the probability to accept a predictor below certain level, say 5%. PMID:25452689

  1. 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.

  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. 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 generation routines are used to build classifiers. The test routines are used to evaluate classifiers and to classify data using a classifier. And the display routines are used to display classifiers in various formats. IND is written in C-language for Sun4 series computers. It consists of several programs with controlling shell scripts. Extensive UNIX man entries are included. IND is designed to be used on any UNIX system, although it has only been thoroughly tested on SUN platforms. The standard distribution medium for IND is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in PostScript format is included on the distribution medium. IND was developed in 1992.

  4. Chlorinated ethenes from groundwater in tree trunks

    USGS Publications Warehouse

    Vroblesky, D.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 Ioblolly 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.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.

  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. 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.

  7. 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

  8. Pendelluft in the bronchial tree

    PubMed Central

    Greenblatt, Elliot E.; Butler, James P.; Venegas, Jose G.

    2014-01-01

    Inhomogeneous inflation or deflation of the lungs can cause dynamic pressure differences between regions and lead to interregional airflows known as pendelluft. This work first uses analytical tools to clarify the theoretical limits of pendelluft at a single bifurcation. It then explores the global and regional pendelluft that may occur throughout the bronchial tree in a realistic example using an in silico model of bronchoconstriction. The theoretical limits of pendelluft volume exchanged at a local bifurcation driven by sinusoidal breathing range from 15.5% to 41.4% depending on the relative stiffness of the subtended regions. When nonsinusoidal flows are considered, pendelluft can be as high as 200% inlet tidal volume (Vin). At frequencies greater than 10 Hz, the inertia of the air in the airways becomes important, and the maximal local pendelluft is theoretically unbounded, even with sinusoidal breathing. In a single illustrative numerical simulation of bronchoconstriction with homogenous compliances, the overall magnitude of global pendelluft volume was <2% of the tidal volume. Despite the small overall magnitude, pendelluft volume exchange was concentrated in poorly ventilated regions of the lung, including local pendelluft at bifurcations of up to 13% Vin. This example suggests that pendelluft may be an important phenomena contributing to regional gas exchange, irreversible mixing, and aerosol deposition patterns inside poorly ventilated regions of the lung. The analytical results support the concept that pendelluft may be more prominent in diseases with significant heterogeneity in both resistance and compliance. PMID:25170072

  9. 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.

  10. Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics

    NASA Astrophysics Data System (ADS)

    Akutsu, Tatsuya

    Tree structured data often appear in bioinformatics. For example, glycans, RNA secondary structures and phylogenetic trees usually have tree structures. Comparison of trees is one of fundamental tasks in analysis of these data. Various distance measures have been proposed and utilized for comparison of trees, among which extensive studies have been done on tree edit distance. In this paper, we review key results and our recent results on the tree edit distance problem and related problems. In particular, we review polynomial time exact algorithms and more efficient approximation algorithms for the edit distance problem for ordered trees, and approximation algorithms for the largest common sub-tree problem for unordered trees. We also review applications of tree edit distance and its variants to bioinformatics with focusing on comparison of glycan structures.

  11. Heterogeneous Compression of Large Collections of Evolutionary Trees.

    PubMed

    Matthews, Suzanne J

    2015-01-01

    Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees. PMID:26357320

  12. 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.

  13. 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)

  14. 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.

  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. 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

  17. Decision tree helps select hydrotreating catalyst

    SciTech Connect

    Kellett, T.F.; Trevino, C.A.; Sartor, A.F.

    1980-01-01

    Decision tree helps select hydrotreating catalyst, as is shown by use of the decision tree to select between Shell 324, a second-generation nickel/molybdenum catalyst, and Shell 344, a second-generation cobalt/molybdenum catalyst, in a number of applications, including the desulfurization of a vacuum gas oil to 0.1% by wt product sulfur for a straight-run feedstock, desulfurization of a flashed distillate, denitrogenation, hydrotreating a gas oil for fluid catalytic cracker feed, and denitrogenation and H/sub 2/ uptake for cracked stocks. Operating data reported in the literature support the catalyst choices indicated by the decision tree. The decision tree does not indicate a preferred catalyst in cases involving desulfurization and denitrogenation of a straight run to given levels, and the hydrotreating for desulfurization of cracked stocks. Cracked stock processing difficulties, which sometimes require that a catalyst other than the preferred catalyst be used, are discussed.

  18. Systolic tree implementation of data structures

    SciTech Connect

    Chang, J.H.; Ibarra, O.H.; Chung, M.J.; Rao, K.K.

    1988-06-01

    The authors present systolic tree architectures for data structures such as stacks, queues, dequeues, priority queues, and dictionary machines. The stack, queue, and dequeue have a unit response time and a unit pipeline interval. The priority queue also has a unit response time, but the pipeline interval is 2. The response time and pipeline interval for the dictionary machine are O(log n) and O(1), respectively, where n is the number of data elements currently residing in the tree. In each node of the tree, the mechanism for controlling the transmission and distribution of data is finite state. This feature makes the designs presented here suitable for VLSI. If there are n data elements in the data structure, the depth of the tree is O(log n).

  19. Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy.

    PubMed

    Knowles, L Lacey; Lanier, Hayley C; Klimov, Pavel B; He, Qixin

    2012-11-01

    With the proliferation of species-tree methods, empiricists now have to confront the daunting task of method choice. Such decisions might be made based on theoretical considerations alone. However, the messiness of real data means that theoretical ideals may not hold in practice (e.g., with convergence of complicated MCMC algorithms and computational times that limit analyses to small data sets). On the other hand, simplifying assumptions made by some approaches may compromise the accuracy of species-tree estimates. Here we examine the purported tradeoff between accuracy and computational simplicity for species-tree analysis, focusing on the different ways the approaches treat gene-tree uncertainty. By considering a diversity of species trees, as well as different sampling designs and total sampling efforts, we not only compare the accuracy of species-tree estimates across methods, but we also partition the variation in accuracy across factors to identify their relative importance. This analysis shows that although the method of analysis affects accuracy, other factors - namely, the history of species divergence and aspects of the sampling design - have a larger impact. Despite a full modeling of gene tree uncertainty (e.g., using a Bayesian framework), species-tree estimates may not be accurate, particularly for recent diversification histories. Nevertheless, we demonstrate how factors within the control of the empirical investigator (e.g., decisions about sampling) improve the accuracy of species tree estimates, and more so than the method of analysis. Lastly, with much of the attention on species-tree analyses focused on the discord among loci arising from the coalescent, this work also highlights a previously overlooked key determinant of species-tree accuracy for recent divergences - the level of genetic variation at a locus, which has important implications for improving species-tree estimates in practice. PMID:22835380

  20. Trees and networks before and after Darwin

    PubMed Central

    2009-01-01

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

  1. 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.

  2. 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

  3. Predicting Gene Function using Predictive Clustering Trees

    NASA Astrophysics Data System (ADS)

    Vens, Celine; Schietgat, Leander; Struyf, Jan; Blockeel, Hendrik; Kocev, Dragi; Deroski, Sao

    In this chapter, we show how the predictive clustering tree framework can be used to predict the functions of genes. The gene function prediction task is an example of a hierarchical multi-label classification (HMC) task: genes may have multiple functions and these functions are organized in a hierarchy. The hierarchy of functions can be such that each function has at most one parent (tree structure) or such that functions may have multiple parents (DAG structure).

  4. 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.

  5. Fatal head trauma from tree related injuries.

    PubMed

    Escoffery, C T; Shirley, S E

    2001-10-01

    Two cases of death following tree related injuries are presented. Two females, an elderly woman and a child, suffered severe head trauma from falling objects from trees--a falling coconut and a falling branch respectively. Although this mode of injury has been previously documented, there have been no prior reports of in-hospital deaths in such patients. This uncommon cause of death is reviewed and recommendations made concerning its prevention. PMID:11693223

  6. 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.

  7. 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

  8. Microbes in tree swallow semen.

    PubMed

    Lombardo, M P; Thorpe, P A

    2000-07-01

    A frequently hypothesized but poorly studied cost of multiple mating in birds is that exposure to pathogenic sexually transmitted microbes (STM's) can lower reproductive success. Conversely, female birds may benefit from high frequencies of copulation and multiple copulation partners if they receive cloacal inoculations of beneficial STM's that can either protect them against future encounters with pathogens and/or serve as therapy against present infection. We examined the semen of 30 male tree swallows (Tachycineta bicolor) in 1998 to determine the presence and prevalence of potential pathogenic and beneficial STM's. Semen was collected directly from males after applying gentle pressure to the cloaca and we used standard microbiological techniques to identify microbes. We found that 19 of 30 samples contained one or more types of microbes. In these 19 positive samples, we isolated both pathogenic and beneficial microbes from 11, only pathogenic microbes from seven, and only beneficial microbes from one. This variation among males suggests that females would benefit from considering a particular male's potential as a donor of either pathogenic or beneficial STM's as a criterion for mate choice. There were few significant differences between males with pathogen-infected semen and those without pathogens in their semen in measures of size, morphology, and ectoparasite score and feather damage. Likewise, there were few significant differences between males with beneficial Lactobacilli spp. in their semen and those without Lactobacilli spp. in their semen in measures of size, morphology, and ectoparasite score and feather damage. We were unable to determine if there was a relationship between microbe presence and prevalence on reproductive performance. PMID:10941730

  9. Intraspecific scaling laws of vascular trees

    PubMed Central

    Huo, Yunlong; Kassab, Ghassan S.

    2012-01-01

    A fundamental physics-based derivation of intraspecific scaling laws of vascular trees has not been previously realized. Here, we provide such a theoretical derivation for the volumediameter and flowlength scaling laws of intraspecific vascular trees. In conjunction with the minimum energy hypothesis, this formulation also results in diameterlength, flowdiameter and flowvolume scaling laws. The intraspecific scaling predicts the volumediameter power relation with a theoretical exponent of 3, which is validated by the experimental measurements for the three major coronary arterial trees in swine (where a least-squares fit of these measurements has exponents of 2.96, 3 and 2.98 for the left anterior descending artery, left circumflex artery and right coronary artery trees, respectively). This scaling law as well as others agrees very well with the measured morphometric data of vascular trees in various other organs and species. This study is fundamental to the understanding of morphological and haemodynamic features in a biological vascular tree and has implications for vascular disease. PMID:21676970

  10. 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.

  11. 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.

  12. 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

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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…

  18. 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

  19. 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…

  20. Fault tree analysis for maintenance needs

    NASA Astrophysics Data System (ADS)

    Halme, Jari; Aikala, Antti

    2012-05-01

    One of the key issues in maintenance is to allocate focus and resources to those components and subsystems which are the most unreliable and prone to failures. In industrial systems, fault tree analysis technique can be used to study the reliability of the complex systems and their substructures. In this paper a fault tree application for analyzing online the current reliability and failure probability for maintenance purposes is presented. The analysis is utilizing data connected to the fault tree root causes and events. An indication of an anomaly case, service action, cumulative loading, etc., or just time passed or service hour counter level can trigger a new calculation of current probabilities of the fault tree events and subsystem interactions. In proposed approach real time, dynamic information from several available data sources and different measurement are interconnected to each fault tree event and root cause. There is also formulated an active, constantly updated link between the fault tree events and maintenance databases for the maintenance decision support, and to keep the analysis up to date. Typically top event probability is evaluated based on updated root cause probabilities and lower level events. At the industrial plant level an identification of a failure in a component event defined within a constructed and operatively existing fault tree explicitly means that the event's failure probability is one. By utilizing this indication, the most probable failure branches through the fault tree sub events to root causes can be identified and printed as a valid check list for maintenance purposes to focus service actions first to those fault tree branches most probable causing the failure. Respectively, during the checks, service actions, etc., components, especially those within the critical branches, detected as healthy can be a updated as having zero failure probability. This information can be used to further update the fault tree and produce online a new service order list. The added value of the proposed method with respect to developed software platform functions lies in its applicability to rationalize maintenance actions and in a case of a failure allocate resources where they are assumable mostly needed.

  1. 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...

  2. Efficient Exploration of the Space of Reconciled Gene Trees

    PubMed Central

    Szll?si, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

    2013-01-01

    Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene treespecies tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene treespecies tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szll?si et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

  3. 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.

  4. 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

  5. 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.

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

    PubMed

    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

  7. 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

  8. "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…

  9. Up in the Tree – The Overlooked Richness of Bryophytes and Lichens in Tree Crowns

    PubMed Central

    Boch, Steffen; Müller, Jörg; Prati, Daniel; Blaser, Stefan; Fischer, Markus

    2013-01-01

    Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m × 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments. PMID:24358373

  10. 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

  11. 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

  12. 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

  13. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

    PubMed Central

    Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A.; RoyChoudhury, Arindam

    2012-01-01

    The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

  14. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

    PubMed

    Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A; RoyChoudhury, Arindam

    2012-08-01

    The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

  15. 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.

  16. 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.

  17. Towards optimizing wood development in bioenergy trees.

    PubMed

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

    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

  18. 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.

  19. 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

  20. LocTree3 prediction of localization

    PubMed Central

    Goldberg, Tatyana; Hecht, Maximilian; Hamp, Tobias; Karl, Timothy; Yachdav, Guy; Ahmed, Nadeem; Altermann, Uwe; Angerer, Philipp; Ansorge, Sonja; Balasz, Kinga; Bernhofer, Michael; Betz, Alexander; Cizmadija, Laura; Do, Kieu Trinh; Gerke, Julia; Greil, Robert; Joerdens, Vadim; Hastreiter, Maximilian; Hembach, Katharina; Herzog, Max; Kalemanov, Maria; Kluge, Michael; Meier, Alice; Nasir, Hassan; Neumaier, Ulrich; Prade, Verena; Reeb, Jonas; Sorokoumov, Aleksandr; Troshani, Ilira; Vorberg, Susann; Waldraff, Sonja; Zierer, Jonas; Nielsen, Henrik; Rost, Burkhard

    2014-01-01

    The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18 = 80 3% for eukaryotes and a six-state accuracy Q6 = 89 4% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3. PMID:24848019

  1. 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.

  2. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    PubMed Central

    2008-01-01

    Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. Results We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Conclusion Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among orthologous genes are incomplete lineage sorting and functional restriction. PMID:18973688

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Optimal Branching Asymmetry of Hydrodynamic Pulsatile Trees

    NASA Astrophysics Data System (ADS)

    Florens, Magali; Sapoval, Bernard; Filoche, Marcel

    2011-04-01

    Most of the studies on optimal transport are done for steady state regime conditions. Yet, there exists numerous examples in living systems where supply tree networks have to deliver products in a limited time due to the pulsatile character of the flow, as it is the case for mammalian respiration. We report here that introducing a systematic branching asymmetry allows the tree to reduce the average delivery time of the products. It simultaneously increases its robustness against the inevitable variability of sizes related to morphogenesis. We then apply this approach to the human tracheobronchial tree. We show that in this case all extremities are supplied with fresh air, provided that the asymmetry is smaller than a critical threshold which happens to match the asymmetry measured in the human lung. This could indicate that the structure is tuned at the maximum asymmetry level that allows the lung to feed all terminal units with fresh air.

  9. 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.

  10. Rooting Gene Trees without Outgroups: EP Rooting

    PubMed Central

    Sinsheimer, Janet S.; Little, Roderick J. A.; Lake, James A.

    2012-01-01

    Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167–181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301–316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60–76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489–493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763–766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255–260). PMID:22593551

  11. 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.

  12. Phenology of temperate trees in tropical climates

    NASA Astrophysics Data System (ADS)

    Borchert, Rolf; Robertson, Kevin; Schwartz, Mark D.; Williams-Linera, Guadalupe

    2005-09-01

    Several North American broad-leaved tree species range from the northern United States at ˜47°N to moist tropical montane forests in Mexico and Central America at 15-20°N. Along this gradient the average minimum temperatures of the coldest month (T Jan), which characterize annual variation in temperature, increase from -10 to 12°C and tree phenology changes from deciduous to leaf-exchanging or evergreen in the southern range with a year-long growing season. Between 30 and 45°N, the time of bud break is highly correlated with T Jan and bud break can be reliably predicted for the week in which mean minimum temperature rises to 7°C. Temperature-dependent deciduous phenology—and hence the validity of temperature-driven phenology models—terminates in southern North America near 30°N, where T Jan>7°C enables growth of tropical trees and cultivation of frost-sensitive citrus fruits. In tropical climates most temperate broad-leaved species exchange old for new leaves within a few weeks in January-February, i.e., their phenology becomes similar to that of tropical leaf-exchanging species. Leaf buds of the southern ecotypes of these temperate species are therefore not winter-dormant and have no chilling requirement. As in many tropical trees, bud break of Celtis, Quercus and Fagus growing in warm climates is induced in early spring by increasing daylength. In tropical climates vegetative phenology is determined mainly by leaf longevity, seasonal variation in water stress and day length. As water stress during the dry season varies widely with soil water storage, climate-driven models cannot predict tree phenology in the tropics and tropical tree phenology does not constitute a useful indicator of global warming.

  13. Low Power Gated Clock Tree Driven Placement

    NASA Astrophysics Data System (ADS)

    Shen, Weixiang; Cai, Yici; Hong, Xianlong; Hu, Jiang

    As power consumption of the clock tree dominates over 40% of the total power in modem high performance VLSI designs, measures must be taken to keep it under control. One of the most effective methods is based on clock gating to shut off the clock when the modules are idle. However, previous works on gated clock tree power minimization are mostly focused on clock routing and the improvements are often limited by the given registers placement. The purpose of this work is to navigate the registers during placement to further reduce the clock tree power based on clock gating. Our method performs activity-aware register clustering that reduces the clock tree power not only by clumping the registers into a smaller area, but also by pulling the registers with the similar activity patterns closely to shut off the clock more time for the resultant subtrees. In order to reduce the impact of signal nets wirelength and power due to register clustering, we apply the timing and activity based net weighting in [14], which reduces the nets switching power by assigning a combination of activity and timing weights to the nets with higher switching rates or more critical timing. To tradeoff the power dissipated by the clock tree and the control signal, we extend the idea of local ungating in [6] and propose an algorithm of gate control signal optimization, which still sets the gate enable signal high if a register is active for a number of consecutive clock cycles. Experimental results on a set of MCNC benchmarks show that our approach is able to reduce the power and total wirelength of clock tree greatly with minimal overheads.

  14. 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

  15. Bayesian estimation of concordance among gene trees.

    PubMed

    An, Ccile; Larget, Bret; Baum, David A; Smith, Stacey D; Rokas, Antonis

    2007-02-01

    Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species. PMID:17095535

  16. Rooting gene trees without outgroups: EP rooting.

    PubMed

    Sinsheimer, Janet S; Little, Roderick J A; Lake, James A

    2012-01-01

    Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489-493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763-766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260). PMID:22593551

  17. Haplotype trees and modern human origins.

    PubMed

    Templeton, Alan R

    2005-01-01

    A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10(-17)). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans. PMID:16369961

  18. Efficient exploration of the space of reconciled gene trees.

    PubMed

    Szllsi, Gergely J; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

    2013-11-01

    Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szll?si et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. PMID:23925510

  19. 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

  20. 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

  1. Photoperiodic growth control in perennial trees.

    PubMed

    Azeez, Abdul; Sane, Aniruddha P

    2015-12-01

    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

  2. Probability distribution on the parse trees.

    PubMed

    Tepes, Bozidar; Hunjet, Dubravko; Elezović, Slobodan

    2005-12-01

    Paper describes probability distribution on the parse trees of natural language by using Bayesian networks. First parts of the paper describes probabilistic context-free grammar and parse trees. In the second part of the paper, Bayesian network was modelled and joint probability distribution on their vertex. On these theoretical ideas, in the third part, we describe our model tested on Database of grammatical sentences of Croatian language (http:/ /infoz.ffzg.hr / tepes /). At the end was presented a backward procedure and evaluation of our results. PMID:16417191

  3. Investigating how students communicate tree-thinking

    NASA Astrophysics Data System (ADS)

    Boyce, Carrie Jo

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

  4. 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.

  5. 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.

  6. 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.

  7. 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, Andr; 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

  8. Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement.

    PubMed

    Harfouche, Antoine; Meilan, Richard; Altman, Arie

    2014-11-01

    Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed. PMID:24695726

  9. 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

  10. 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

  11. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

    PubMed Central

    2012-01-01

    Background The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime. Results In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown. Conclusions Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships. PMID:22546066

  12. 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

  13. 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

  14. 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.

  15. 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 background of glacial deposits and crystalline rocks. The dead tree areas are located on the flanks of Mammoth Mountain (N:37 deg 37' 45" and W:119 deg 02' 05") at an elevation between 2600 and 3000 meters. The area is covered by an open type of Montane Forest. The dominant tree species are Lodgepole Pine (Pinus contorta), the Red Fir (Abies magnifica) and the Jeffrey Pine (Pinus jeffreyi). The soil surface near Horseshoe Lake is generally fairly bright. The surface is covered by glacial deposits (till) consisting mainly of weathered granitic rocks.

  16. Water, gravity and trees: Relationship of tree-ring widths and total water storage dynamics

    NASA Astrophysics Data System (ADS)

    Creutzfeldt, B.; Heinrich, I.; Merz, B.; Blume, T.; Gntner, A.

    2012-04-01

    Water stored in the subsurface as groundwater or soil moisture is the main fresh water source not only for drinking water and food production but also for the natural vegetation. In a changing environment water availability becomes a critical issue in many different regions. Long-term observations of the past are needed to improve the understanding of the hydrological system and the prediction of future developments. Tree ring data have repeatedly proved to be valuable sources for reconstructing long-term climate dynamics, e.g. temperature, precipitation and different hydrological variables. In water-limited environments, tree growth is primarily influenced by total water stored in the subsurface and hence, tree-ring records usually contain information about subsurface water storage. The challenge is to retrieve the information on total water storage from tree rings, because a training dataset of water stored in the sub-surface is required for calibration against the tree-ring series. However, measuring water stored in the subsurface is notoriously difficult. We here present high-precision temporal gravimeter measurements which allow for the depth-integrated quantification of total water storage dynamics at the field scale. In this study, we evaluate the relationship of total water storage change and tree ring growth also in the context of the complex interactions of other meteorological forcing factors. A tree-ring chronology was derived from a Norway spruce stand in the Bavarian Forest, Germany. Total water storage dynamics were measured directly by the superconducting gravimeter of the Geodetic Observatory Wettzell for a 9-years period. Time series were extended to 63-years period by a hydrological model using gravity data as the only calibration constrain. Finally, water storage changes were reconstructed based on the relationship between the hydrological model and the tree-ring chronology. Measurement results indicate that tree-ring growth is primarily controlled by total water storage in the subsurface. But high uncertainties intervals of the correlation coefficient urges for the extension of the measurement period. This multi-disciplinary study, combining hydrology, dendrochronology and geodesy shows that temporal gravimeter measurements may give us the unique opportunity to retrieve the information of total water storage contained in tree-ring records to reconstruct total water storage dynamics. Knowing the relationship of water storage and tree-ring growth can also support the reconstruction of other climate records based on tree-ring series, help with hydrological model testing and can improve our knowledge of long-term variations of water storage in the past.

  17. Autumn frost hardiness in Norway spruce plus tree progeny and trees of the local and transferred provenances in central Sweden.

    PubMed

    Hannerz, Mats; Westin, Johan

    2005-09-01

    Reforestation with provenances from locations remote from the planting site (transferred provenances) or the progeny of trees of local provenances selected for superior form and vigor (plus trees) offer alternative means to increase yield over that obtained by the use of seed from unselected trees of the local provenance. Under Swedish conditions, Norway spruce (Picea abies (L.) Karst.) of certain transferred provenances generally has an advantage in productivity relative to the local provenance comparable to that of progeny of plus trees. The aim of this study was to explore the extent to which productivity gains achieved by provenance transfer or the use of plus tree progeny are associated with reductions in autumn frost hardiness, relative to that of trees of the local provenance. In a field trial with 19-year-old trees in central Sweden, bud hardiness was tested on four occasions during the autumn of 2002. Trees of the local provenance were compared with trees of a south Swedish provenance originating 3 degrees of latitude to the south, a Belarusian provenance and the progeny of plus trees of local origin. The Belarusian provenance was the least hardy and the local provenance the most hardy, with plus tree progeny and the south Swedish provenance being intermediate in hardiness. Both the Belarusian provenance and the plus tree progeny were significantly taller than trees of the other populations. Within provenances, tree height was negatively correlated with autumn frost hardiness. Among the plus tree progeny, however, no such correlation between tree height and autumn frost hardiness was found. It is concluded that although the gain in productivity achieved by provenance transfer from Belarus was comparable to that achieved by using the progeny of plus trees of the local provenance, the use of trees of the Belarus provenance involved an increased risk of autumn frost damage because of later hardening. PMID:15996961

  18. 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.

  19. 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).…

  20. Understanding search trees via statistical physics

    NASA Astrophysics Data System (ADS)

    Majumdar, Satya N.; Dean, David S.; Krapivsky, P. L.

    2005-06-01

    We study the random m-ary search tree model (where m stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results. In particular, we show that the probability distributions of extreme observables associated with a random search tree such as the height and the balanced height of a tree have a travelling front structure. In addition, the variance of the number of nodes needed to store a data string of a given size N is shown to undergo a striking phase transition at a critical value of the branching ratio m_{c}=26. We identified the mechanism of this phase transition and showed that it is generic and occurs in various other problems as well. New results are obtained when each element of the data string is a D-dimensional vector. We show that this problem also has a phase transition at a critical dimension, D_{c}= pi/sin^{-1}left(1/sqrt{8}right)=8.69363ldots.

  1. Joshua Trees at Pierce Ferry, AZ

    USGS Multimedia Gallery

    This image, from April 2004, shows mortality of some adult Joshua trees resulting from years of hot-dry climate. During the prior year, this area received only 17 percent of its average precipitation and was 4 degrees F warmer than average -- conditions that are projected to become even more frequen...

  2. Saliency tree: a novel saliency detection framework.

    PubMed

    Liu, Zhi; Zou, Wenbin; Le Meur, Olivier

    2014-05-01

    This paper proposes a novel saliency detection framework termed as saliency tree. For effective saliency measurement, the original image is first simplified using adaptive color quantization and region segmentation to partition the image into a set of primitive regions. Then, three measures, i.e., global contrast, spatial sparsity, and object prior are integrated with regional similarities to generate the initial regional saliency for each primitive region. Next, a saliency-directed region merging approach with dynamic scale control scheme is proposed to generate the saliency tree, in which each leaf node represents a primitive region and each non-leaf node represents a non-primitive region generated during the region merging process. Finally, by exploiting a regional center-surround scheme based node selection criterion, a systematic saliency tree analysis including salient node selection, regional saliency adjustment and selection is performed to obtain final regional saliency measures and to derive the high-quality pixel-wise saliency map. Extensive experimental results on five datasets with pixel-wise ground truths demonstrate that the proposed saliency tree model consistently outperforms the state-of-the-art saliency models. PMID:24710397

  3. 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).

  4. Modeling huanglongbing transmission within a citrus tree

    PubMed Central

    Chiyaka, Christinah; Singer, Burton H.; Halbert, Susan E.; Morris, J. Glenn; van Bruggen, Ariena H. C.

    2012-01-01

    The citrus disease huanglongbing (HLB), associated with an uncultured bacterial pathogen, is threatening the citrus industry worldwide. A mathematical model of the transmission of HLB between its psyllid vector and citrus host has been developed to characterize the dynamics of the vector and disease development, focusing on the spread of the pathogen from flush to flush (a newly developing cluster of very young leaves on the expanding terminal end of a shoot) within a tree. This approach differs from that of prior models for vector-transmitted plant diseases where the entire plant is the unit of analysis. Dynamics of vector and host populations are simulated realistically as the flush population approaches complete infection. Model analysis indicates that vector activity is essential for initial infection but is not necessary for continued infection because infection can occur from flush to flush through internal movement in the tree. Flush production, within-tree spread, and latent period are the most important parameters influencing HLB development. The model shows that the effect of spraying of psyllids depends on time of initial spraying, frequency, and efficacy of the insecticides. Similarly, effects of removal of symptomatic flush depend on the frequency of removal and the time of initiation of this practice since the start of the epidemic. Within-tree resistance to spread, possibly affected by inherent or induced resistance, is a major factor affecting epidemic development, supporting the notion that alternate routes of transmission besides that by the vector can be important for epidemic development. PMID:22783015

  5. 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...

  6. 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…

  7. 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

  8. 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.

  9. POW Plus TREE Equals Powerful Opinion Essays.

    ERIC Educational Resources Information Center

    Harris, Karen R.; Graham, Steve; Mason, Linda

    2002-01-01

    The benefits of a self-regulated strategy development approach for teaching elementary school students with learning disabilities how to write opinion essays are discussed, and the steps of the POW plus TREE strategy of instruction are outlined: develop background knowledge, discuss, model, memorize, support it, and perform independently.

  10. 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 ...

  11. 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...

  12. 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...

  13. 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

  14. 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 ...

  15. 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 between candidate gene and disease outcome

  16. 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...

  17. 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...

  18. 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,

  19. 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

  20. 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.

  1. Household Products Could Harm Tree Swallows

    USGS Multimedia Gallery

    USGS scientists and partners have found that tree swallow eggs exposed to elevated levels of products known as perfluoroalkyl substances are associated with a decreased chance of hatching. PFASs are common environmental contaminants that have been used in products such as water and stain repell...

  2. 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...

  3. A Golden Eagle Perches in a Tree

    USGS Multimedia Gallery

    A golden eagle perches in a tree at the William L. Finley National Wildlife Refuge, Oregon. USGS researchers are conducting research that will help support the FWS’s and energy industry efforts to reduce impacts to golden eagles from wind energy operations, including, of course, collision with...

  4. 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...

  5. 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

  6. Constructal tree networks for heat transfer

    SciTech Connect

    Ledezma, G.A.; Bejan, A.; Errera, M.R.

    1997-07-01

    This paper addresses the fundamental problem of how to connect a heat generating volume to a point heat sink by using a finite amount of high-conductivity material that can be distributed through the volume. The problem is one of optimizing the access (or minimizing the thermal resistance) between a finite-size volume and one point. The solution is constructed by covering the volume with a sequence of building blocks, which proceeds toward larger sizes (assemblies), hence, the {open_quotes}constructal{close_quotes} name for this approach. Optimized numerically at each stage are geometric features such as the overall shape of the building block, its number of constituents, and the internal distribution of high-conductivity inserts. It is shown that in the optimal design, the high-conductivity material has a distribution with the shape of a tree. Every aspect of the tree architecture is deterministic: the shapes of the largest assembly and all its constituents, the number of branches at each level of assembly, the relative position of building blocks in each assembly, and the relative thicknesses of successive branches. The finer, innermost details of the tree architecture (e.g., the branching angle) have a negligible effect on the overall thermal resistance. The main conclusion is that the structure, working mechanism, and minimal resistance of the tree network can be obtained deterministically, and that the constrained optimization of access routes accounts for the macroscopic structure in nature. {copyright} {ital 1997 American Institute of Physics.}

  7. 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

  8. The DeepTree Exhibit: Visualizing the Tree of Life to Facilitate Informal Learning.

    PubMed

    Block, F; Horn, M S; Phillips, B C; Diamond, J; Evans, E M; Shen, Chia

    2012-12-01

    In this paper, we present the DeepTree exhibit, a multi-user, multi-touch interactive visualization of the Tree of Life. We developed DeepTree to facilitate collaborative learning of evolutionary concepts. We will describe an iterative process in which a team of computer scientists, learning scientists, biologists, and museum curators worked together throughout design, development, and evaluation. We present the importance of designing the interactions and the visualization hand-in-hand in order to facilitate active learning. The outcome of this process is a fractal-based tree layout that reduces visual complexity while being able to capture all life on earth; a custom rendering and navigation engine that prioritizes visual appeal and smooth fly-through; and a multi-user interface that encourages collaborative exploration while offering guided discovery. We present an evaluation showing that the large dataset encouraged free exploration, triggers emotional responses, and facilitates visitor engagement and informal learning. PMID:26357188

  9. 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.

  10. 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...

  11. Baldcypress Trees and Medina River at Bandera TX

    USGS Multimedia Gallery

    Baldcypress trees line the Medina River, as well as other rivers in the Texas Hill Country.  Many trees get uprooted or broken off from periodic catastrophic floods.  Photo taken in Bandera Park. ...

  12. 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

  13. 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

  14. 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)

  15. Health Tip: Take Precautions with Your Holiday Tree

    MedlinePLUS

    ... html Health Tip: Take Precautions With Your Holiday Tree And help protect children To use the sharing ... Thursday, December 10, 2015 (HealthDay News) -- A holiday tree is a festive decoration, but it's also a ...

  16. Absolutely continuous spectrum of a Schroedinger operator on a tree

    SciTech Connect

    Kupin, S.

    2008-11-15

    We give sufficient conditions for the presence of the absolutely continuous spectrum of a Schroedinger operator on a regular rooted tree without loops (also called regular Bethe lattice or Cayley tree)

  17. A different view of the fault tree forest

    SciTech Connect

    Daniel, S.L.; Kunsman, D.M.

    1992-01-01

    A different approach to obtaining an exact solution to a complex fault tree is presented. The fault tree is complex because it contains a large number of AND gates and many high-order multiple output gates.

  18. Geophysical Experim Ents At Tree Sites

    NASA Astrophysics Data System (ADS)

    Hagrey, S. A. Al; Ismaeil, A.; Meissner, R.

    In the scope of the EU-research project WATERUSE we are developing a hardware and software for an integrated high -resolution hydrogeophysical techniques for monitoring water content and flow in soils and tree trunk and roots. With 9 partners the project aims to provide tools for the evaluation of water fluxes and its governing processes in the drier regions of Europe, in order to develop guidelines for the sustainable use of water resources. In this work we present results of some geoelectrical measurements carried out at some tree sites (including Japanese Wingnut, Poplar, Pine, Peach and Cork Oak) within the vadose root zone and at a tree trunk at Kiel (Germany) and Atalaia and Rico Frico (Portugal). For the dc resistivity measurements, the applied electrode array include the classical dipole- dipole, Wenner and Schlumberger as well as the mise àla masse technique. With the tree at the centre of site, the electrodes were distributed at the ground surface along radial star profiles at equal angular interval and at grids at 10 cm interval. In the mise à la masse the current electrodes C1 and C2 are placed inside the tree root and at infinity and the potential difference was measured between all other adjacent pair of electrodes. The data are inverted using a 2D and 3D inversion program packages adopted for this type of application. The results show distinctively the heterogeneities in the vadose zone resulting from effects of the root zone and different moisture content. Also the ring structure and zones of different fluid concentration within the trunk can be mapped and compared with a dying stem section conserved directly after their cut.

  19. 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

  20. Tracing retinal vessel trees by transductive inference

    PubMed Central

    2014-01-01

    Background Structural study of retinal blood vessels provides an early indication of diseases such as diabetic retinopathy, glaucoma, and hypertensive retinopathy. These studies require accurate tracing of retinal vessel tree structure from fundus images in an automated manner. However, the existing work encounters great difficulties when dealing with the crossover issue commonly-seen in vessel networks. Results In this paper, we consider a novel graph-based approach to address this tracing with crossover problem: After initial steps of segmentation and skeleton extraction, its graph representation can be established, where each segment in the skeleton map becomes a node, and a direct contact between two adjacent segments is translated to an undirected edge of the two corresponding nodes. The segments in the skeleton map touching the optical disk area are considered as root nodes. This determines the number of trees to-be-found in the vessel network, which is always equal to the number of root nodes. Based on this undirected graph representation, the tracing problem is further connected to the well-studied transductive inference in machine learning, where the goal becomes that of properly propagating the tree labels from those known root nodes to the rest of the graph, such that the graph is partitioned into disjoint sub-graphs, or equivalently, each of the trees is traced and separated from the rest of the vessel network. This connection enables us to address the tracing problem by exploiting established development in transductive inference. Empirical experiments on public available fundus image datasets demonstrate the applicability of our approach. Conclusions We provide a novel and systematic approach to trace retinal vessel trees with the present of crossovers by solving a transductive learning problem on induced undirected graphs. PMID:24438151

  1. The relationship between tree growth patterns and likelihood of mortality: A study of two tree species in the Sierra Nevada

    USGS Publications Warehouse

    Das, A.J.; Battles, J.J.; Stephenson, N.L.; van Mantgem, P.J.

    2007-01-01

    We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ???20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk. ?? 2007 NRC.

  2. 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, ?, 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 consecutive voxels that filled the outer surface and the interior of the stem and large branches. From the model, the woody material volume of any part of the target tree can be directly calculated easily by counting the number of corresponding voxels and multiplying the result by the per-voxel volume.

  3. 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

  4. 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

  5. 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;9999:16. 2014 The Authors. Published 2014 SETAC PMID:25363584

  6. Machine Learning Through Signature Trees. Applications to Human Speech.

    ERIC Educational Resources Information Center

    White, George M.

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

  7. Joshua Trees in Inyo Mountains above Eureka Valley, CA

    USGS Multimedia Gallery

    Scattered mature Joshua trees in this northernmost stand of Joshua trees are surrounded by abundant seedlings and saplings. Recent climates, and General Circulation Model results of future climates, portray this area as being suitable for the survival and expansion of Joshua trees....

  8. 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...

  9. 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...

  10. 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...

  11. 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)

  12. 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...

  13. 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...

  14. Directional phytoscreening: contaminant gradients in trees for plume delineation.

    PubMed

    Limmer, Matt A; Shetty, Mikhil K; Markus, Samantha; Kroeker, Ryan; Parker, Beth L; Martinez, Camilo; Burken, Joel G

    2013-08-20

    Tree sampling methods have been used in phytoscreening applications to delineate contaminated soil and groundwater, augmenting traditional investigative methods that are time-consuming, resource-intensive, invasive, and costly. In the past decade, contaminant concentrations in tree tissues have been shown to reflect the extent and intensity of subsurface contamination. This paper investigates a new phytoscreening tool: directional tree coring, a concept originating from field data that indicated azimuthal concentrations in tree trunks reflected the concentration gradients in the groundwater around the tree. To experimentally test this hypothesis, large diameter trees were subjected to subsurface contaminant concentration gradients in a greenhouse study. These trees were then analyzed for azimuthal concentration gradients in aboveground tree tissues, revealing contaminant centroids located on the side of the tree nearest the most contaminated groundwater. Tree coring at three field sites revealed sufficiently steep contaminant gradients in trees reflected nearby groundwater contaminant gradients. In practice, trees possessing steep contaminant gradients are indicators of steep subsurface contaminant gradients, providing compass-like information about the contaminant gradient, pointing investigators toward higher concentration regions of the plume. PMID:23937095

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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.

  9. 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.

  10. 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...

  11. 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.

  12. 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...

  13. 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...

  14. 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,

  15. The Tree and Net Components of Prokaryote Evolution

    PubMed Central

    Puigbò, Pere; Wolf, Yuri I.; Koonin, Eugene V.

    2010-01-01

    Phylogenetic trees of individual genes of prokaryotes (archaea and bacteria) generally have different topologies, largely owing to extensive horizontal gene transfer (HGT), suggesting that the Tree of Life (TOL) should be replaced by a “net of life” as the paradigm of prokaryote evolution. However, trees remain the natural representation of the histories of individual genes given the fundamentally bifurcating process of gene replication. Therefore, although no single tree can fully represent the evolution of prokaryote genomes, the complete picture of evolution will necessarily combine trees and nets. A quantitative measure of the signals of tree and net evolution is derived from an analysis of all quartets of species in all trees of the “Forest of Life” (FOL), which consists of approximately 7,000 phylogenetic trees for prokaryote genes including approximately 100 nearly universal trees (NUTs). Although diverse routes of net-like evolution collectively dominate the FOL, the pattern of tree-like evolution that reflects the consistent topologies of the NUTs is the most prominent coherent trend. We show that the contributions of tree-like and net-like evolutionary processes substantially differ across bacterial and archaeal lineages and between functional classes of genes. Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT. PMID:20889655

  16. 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 vegetation opacity and single scattering albedo. One goal of our current research is to determine whether the tau-omega model can work for tree canopies given the increased scatter from trees compared to grasses and crops, and. if so, what are effective values for tau and omega for trees.

  17. Investigating the Underlying Causes of Tree Mortality with Carbon and Oxygen Isotopes in Tree-rings

    NASA Astrophysics Data System (ADS)

    English, N. B.; McDowell, N.; Allen, C. D.; Das, A. J.; Mora, C. I.; Stephenson, N. L.

    2010-12-01

    Increasing rates of tree mortality in the western United States have potentially profound effects on native biodiversity and ecosystem structure and function. Regional drought and insect or pathogen outbreaks have been implicated; however, the underlying cause(s) of recent tree mortality remain unclear. Hypotheses include 1) hydraulic failure; 2) carbon starvation; or 3) increased susceptibility to pests due to (1) and/or (2). We examined evidence for and against these hypotheses by measuring patterns in the ?13C and ?18O of tree-rings from the last 50 years in eight species of isohydric and anisohydric trees, both living and dead, from across the western United States. We compared isotopic compositions of ?13C and ?18O between living and dead trees with models of expected isotope responses to hydraulic failure, carbon starvation and pest infestation to eliminate or support specific mechanisms of tree mortality. Our data thus far show that Pinaceae (including Abies, Picea, Pinus, and Psuedotsuga) respond isohydrically to drought, while Cupressaceae (including Calocedrus, Juniperus, and Sequoiadendron) respond anisohydrically to drought. We expect that in water-limited forests, Pinaceae will exhibit more rapid and pronounced increases in ?13C and ?18O, attributable to water stress, than in Cupressaceae. However, we observe variable results within Pinaceae and between live and dead trees within a given species. For example, in Pion from various sites in New Mexico, dead trees had either higher or lower ?13C in the years preceding their death than living trees at the same site. The isotopic patterns associated with mortality varied between energy-limited (Oregon, Washington, high-elevation Colorado and California) and water-limited (low-elevation Colorado and New Mexico) forests in a predictable manner. We expect dying trees in energy-limited systems to show changes in ?13C but not in ?18O. Our preliminary conclusions are that either: 1) multiple mechanisms of mortality occur across the western United States; or 2) similar mechanisms may result in differing isotopic patterns between sites and species.

  18. Unifying constructal theory of tree roots, canopies and forests.

    PubMed

    Bejan, A; Lorente, S; Lee, J

    2008-10-01

    Here, we show that the most basic features of tree and forest architecture can be put on a unifying theoretical basis, which is provided by the constructal law. Key is the integrative approach to understanding the emergence of "designedness" in nature. Trees and forests are viewed as integral components (along with dendritic river basins, aerodynamic raindrops, and atmospheric and oceanic circulation) of the much greater global architecture that facilitates the cyclical flow of water in nature (Fig. 1) and the flow of stresses between wind and ground. Theoretical features derived in this paper are: the tapered shape of the root and longitudinally uniform diameter and density of internal flow tubes, the near-conical shape of tree trunks and branches, the proportionality between tree length and wood mass raised to 1/3, the proportionality between total water mass flow rate and tree length, the proportionality between the tree flow conductance and the tree length scale raised to a power between 1 and 2, the existence of forest floor plans that maximize ground-air flow access, the proportionality between the length scale of the tree and its rank raised to a power between -1 and -1/2, and the inverse proportionality between the tree size and number of trees of the same size. This paper further shows that there exists an optimal ratio of leaf volume divided by total tree volume, trees of the same size must have a larger wood volume fraction in windy climates, and larger trees must pack more wood per unit of tree volume than smaller trees. Comparisons with empirical correlations and formulas based on ad hoc models are provided. This theory predicts classical notions such as Leonardo's rule, Huber's rule, Zipf's distribution, and the Fibonacci sequence. The difference between modeling (description) and theory (prediction) is brought into evidence. PMID:18647610

  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. Tree species diversity in commercially logged bornean rainforest

    PubMed

    Cannon; Peart; Leighton

    1998-08-28

    The effects of commercial logging on tree diversity in tropical rainforest are largely unknown. In this study, selectively logged tropical rainforest in Indonesian Borneo is shown to contain high tree species richness, despite severe structural damage. Plots logged 8 years before sampling contained fewer species of trees greater than 20 centimeters in diameter than did similar-sized unlogged plots. However, in samples of the same numbers of trees (requiring a 50 percent larger area), logged forest contained as many tree species as unlogged forest. These findings warrant reassessment of the conservation potential of large tracts of commercially logged tropical rainforest. PMID:9721105

  5. 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.

  6. An Electronic Tree Inventory for Arboriculture Management

    NASA Astrophysics Data System (ADS)

    Tait, Roger J.; Allen, Tony J.; Sherkat, Nasser; Bellett-Travers, Marcus D.

    The integration of Global Positioning System (GPS) technology into mobile devices provides them with an awareness of their physical location. This geospatial context can be employed in a wide range of applications including locating nearby places of interest as well as guiding emergency services to incidents. In this research, a GPS-enabled Personal Digital Assistant (PDA) is used to create a computerised tree inventory for the management of arboriculture. Using the General Packet Radio Service (GPRS), GPS information and arboreal image data are sent to a web-server. An office-based PC running customised Geographical Information Software (GIS) then automatically retrieves the GPS tagged image data for display and analysis purposes. The resulting application allows an expert user to view the condition of individual trees in greater detail than is possible using remotely sensed imagery.

  7. Inferring evolutionary trees from ordinal data

    SciTech Connect

    Kearney, P.E.; Hayward, R.B.; Meijer, H.

    1997-06-01

    In this paper we present four results on the inference of evolutionary trees from ordinal information. An evolutionary tree T, or phylogeny, is an ordinal representation of a distance matrix , for all species a, b, c and d under consideration. In particular, we show that (1) Ordinal representations of distance matrices can be found in O(n{sup 2}log{sup 2} n) time where n is the number of species. Ordinal representations are shown to be unique, when they exist. (3) Determining if there is an ordinal representation for an incomplete distance matrix, a situation which arises in evolutionary studies, is NP-complete. (3) Finding a phylogeny that best fits a distance matrix containing ordinal errors is NP-complete. (4) Under reasonable conditions, a weighted ordinal representation of a distance matrix can be obtained in polynomial time.

  8. 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.

  9. 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

  10. Tree-inspired Piezoelectric Energy Harvesting

    NASA Astrophysics Data System (ADS)

    Hobbs, William; Hu, David

    2009-11-01

    We design and build a tabletop wind energy harvester inspired by the swaying of trees. The device consists of cantilevered cylinders (``tree trunks'') arranged linearly downwind. The bases of the cylinders contain piezoelectric transducers that capture energy from vibration of the cylinder transverse to the flow. For a particular Reynolds number, and ratio of vortex shedding frequency to cylinder natural frequency, we experimentally measure the power generated ( 1 micro-watt) as a function of cylinder arrangement. We report optimal spacings for generating peak power. We also report the distribution of power down the array. We qualitatively account for these trends using flow visualizations of vortex shedding using a flowing soap film dynamically matched with our piezoelectric system.

  11. Falsifying tree level string motivated bouncing cosmologies

    SciTech Connect

    Constantinidis, C.P.; Fabris, J.C.; Furtado, R.G.; Pinto-Neto, N.; Gonzalez, D.

    2006-06-15

    The string effective action at tree level contains, in its bosonic sector, the Einstein-Hilbert term, the dilaton, and the axion, besides scalar and gauge fields coming from the Ramond-Ramond sector. The reduction to four dimensions brings to scene moduli fields. We generalize this effective action by introducing two arbitrary parameters, {omega} and m, connected with the dilaton and axion couplings. In this way, more general frameworks can be analyzed. Regular solutions with a bounce can be obtained for a range of (negative) values of the parameter {omega} which, however, exclude the pure string configuration ({omega}=-1). We study the evolution of scalar perturbations in such cosmological scenarios. The predicted primordial power spectrum decreases with the wave number with spectral index n{sub s}=-2, in contradiction with the results of the Wilkinson microwave anisotropy probe (WMAP). Hence, all such effective string motivated cosmological bouncing models seem to be ruled out, at least at the tree level approximation.

  12. Fault tree analysis of refinery utility systems

    SciTech Connect

    Arendt, J.S.

    1983-01-01

    This paper presents a reliability analysis of selected petroleum refinery utility systems. Fault tree analysis is used to identify system design and operation contributions to refinery unavailability. Recommendations to utility systems that will increase refinery productivity are also discussed. High plant productivity is an objective of process plant design and operation. Availability is often used to measure plant productivity. Plant availability can be improved by reducing the number of process shutdowns or minimizing the duration of shutdowns. One method to improve availability is to determine the systems that contribute most to plant unavailability and then use fault tree analysis to determine system design and operating weaknesses. Then, resources can be allocated for cost-effective improvements to those systems that contribute most to plant unavailability. This study indicates the need for developing emergency procedures to mitigate the effects of utility system failures on refinery availability. Concise, well-designed emergency procedures can significantly improve plant productivity without major capital expense.

  13. 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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  16. 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.

  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 Raumur 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 phenology of temperate trees should improve phenological models, and help to design more realistic warming experiments. It should equally encourage physiological research to reappraise knowledge on temperature sensors in plants.

  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. Tree Height and Tropical Forest Biomass Estimation

    NASA Technical Reports Server (NTRS)

    Hunter, M. O.; Keller, M.; Victoria, D.; Morton, D. C.

    2013-01-01

    Tropical forests account for approximately half of above-ground carbon stored in global vegetation. However, uncertainties in tropical forest carbon stocks remain high because it is costly and laborious to quantify standing carbon stocks. Carbon stocks of tropical forests are determined using allometric relations between tree stem diameter and height and biomass. Previous work has shown that the inclusion of height in biomass allometries, compared to the sole use of diameter, significantly improves biomass estimation accuracy. Here, we evaluate the effect of height measurement error on biomass estimation and we evaluate the accuracy of recently published diameter-height allometries at four areas within the Brazilian Amazon. As no destructive sample of biomass was available at these sites, reference biomass values were based on allometries. We found that the precision of individual tree height measurements ranged from 3 to 20% of total height. This imprecision resulted in a 5-6% uncertainty in biomass when scaled to 1 ha transects. Individual height measurement may be replaced with existing regional and global height allometries. However, we recommend caution when applying these relations. At Tapajos National Forest in the Brazilian state of Pará, using the pantropical and regional allometric relations for height resulted in site biomass 21% and 25% less than reference values. At the other three study sites, the pantropical equation resulted in errors of less that 2 %, and the regional allometry produced errors of less than 12 %. As an alternative to measuring all tree heights or to using regional and pantropical relations, we recommend measuring height for a well-distributed sample of about 100 trees per site. Following this methodology, 95% confidence intervals of transect biomass were constrained to within 4.5% on average when compared to reference values.

  20. Quantum Accelerator Modes from the Farey Tree

    NASA Astrophysics Data System (ADS)

    Buchleitner, A.; D'Arcy, M. B.; Fishman, S.; Gardiner, S. A.; Guarneri, I.; Ma, Z.-Y.; Rebuzzini, L.; Summy, G. S.

    2006-04-01

    We show that mode locking finds a purely quantum nondissipative counterpart in atom-optical quantum accelerator modes. These modes are formed by exposing cold atoms to periodic kicks in the direction of the gravitational field. They are anchored to generalized Arnold tongues, parameter regions where driven nonlinear classical systems exhibit mode locking. A hierarchy for the rational numbers known as the Farey tree provides an ordering of the Arnold tongues and hence of experimentally observed accelerator modes.

  1. Computer storage and retrieval of coronary trees

    NASA Technical Reports Server (NTRS)

    Starmer, C. F.; Smith, W. M.

    1975-01-01

    Coronary cineangiography is a routine procedure for evaluation of the coronary circulation. From the biplane cineangiograms a visual representation of coronary perfusion was obtained. A collection of simple ideas and procedures to aid in the collection is described. The uses to which the tree data will be put include the evaluation of myocardial function and the formation of a library sufficiently large to enable some taxonomic classification of coronary artery patterns to be made.

  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. 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.

  4. 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.

  5. 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

  6. General aspects of tree level gauge mediation

    NASA Astrophysics Data System (ADS)

    Nardecchia, Marco; Romanino, Andrea; Ziegler, Robert

    2010-03-01

    Tree level gauge mediation (TGM) may be considered as the simplest way to communicate supersymmetry breaking: through the tree level renormalizable exchange of heavy gauge messengers. We study its general structure, in particular the general form of tree level sfermion masses and of one loop, but enhanced, gaugino masses. This allows us to set up general guidelines for model building and to identify the hypotheses underlying the phenomenological predictions. In the context of models based on the minimal gauge group SO(10), we show that only two pure embeddings of the MSSM fields are possible using d < 120 representations, each of them leading to specific predictions for the ratios of family universal sfermion masses at the GUT scale, m {5/2} = 2 m {10/2} or m {5/2} = (3/4) m {10/2} (in SU(5) notation). These ratios are determined by group factors and are peculiar enough to make this scheme testable at the LHC. We also discuss three possible approaches to the ?-problem, one of them distinctive of TGM.

  7. Potential sources of methylmercury in tree foliage.

    PubMed

    Tabatchnick, Melissa D; Nogaro, Graldine; Hammerschmidt, Chad R

    2012-01-01

    Litterfall is a major source of mercury (Hg) and toxic methylmercury (MeHg) to forest soils and influences exposures of wildlife in terrestrial and aquatic ecosystems. However, the origin of MeHg associated with tree foliage is largely unknown. We tested the hypothesis that leaf MeHg is influenced by root uptake and thereby related to MeHg levels in soils. Concentrations of MeHg and total Hg in deciduous and coniferous foliage were unrelated to those in soil at 30 urban and rural forested locations in southwest Ohio. In contrast, tree genera and trunk diameter were significant variables influencing Hg in leaves. The fraction of total Hg as MeHg averaged 0.4% and did not differ among tree genera. Given that uptake of atmospheric Hg(0) appears to be the dominant source of total Hg in foliage, we infer that MeHg is formed by in vivo transformation of Hg in proportion to the amount accumulated. PMID:22035929

  8. Giant leucaena (koa haole) energy tree farm

    SciTech Connect

    Brewbaker, J.L.

    1980-09-01

    Giant leucaena is a tall arboreal form of the common koa haole of the tropics that is known for its wide adaptability, hardiness, and rapid growth. Wood yields of the giant leucaena equal or exceed those of other tropical trees and can be the equivalent annually of 30 barrels of oil per acre. In addition, the tree is a legume that produces a marketable co-product, a nutritious, high-nitrogen leaf meal. A thorough assessment is provided of the known yield capability of giant leucaena, its soil and fertilizer needs, its impact on the environment, its water and irrigation needs, its handling from nursery through establishment, its wood properties and combustion characteristics, and methods of harvesting suitable for the comparatively small trees to be grown. Analyses are also given of capital equipment and operating expenses, labor needs, effects of tax incentives, and economic considerations of application to various scenarios and market conditions in Hawaii. This study suggests that giant leucaena could be grown profitably in Molokai as a source of fuel wood and co-product animal feed.

  9. Pesticide bioconcentration modelling for fruit trees.

    PubMed

    Paraíba, Lourival Costa

    2007-01-01

    The model presented allows simulating the pesticide concentration evolution in fruit trees and estimating the pesticide bioconcentration factor in fruits. Pesticides are non-ionic organic compounds that are degraded in soils cropped with woody species, fruit trees and other perennials. The model allows estimating the pesticide uptake by plants through the water transpiration stream and also the time in which maximum pesticide concentration occur in the fruits. The equation proposed presents the relationships between bioconcentration factor (BCF) and the following variables: plant water transpiration volume (Q), pesticide transpiration stream concentration factor (TSCF), pesticide stem-water partition coefficient (K(Wood,W)), stem dry biomass (M) and pesticide dissipation rate in the soil-plant system (k(EGS)). The modeling started and was developed from a previous model "Fruit Tree Model" (FTM), reported by Trapp and collaborators in 2003, to which was added the hypothesis that the pesticide degradation in the soil follows a first order kinetic equation. The FTM model for pesticides (FTM-p) was applied to a hypothetic mango plant cropping (Mangifera indica) treated with paclobutrazol (growth regulator) added to the soil. The model fitness was evaluated through the sensitivity analysis of the pesticide BCF values in fruits with respect to the model entry data variability. PMID:17092536

  10. Monozygotic cleavage polyembryogenesis and conifer tree improvement.

    PubMed

    Durzan, Don J

    2008-01-01

    The mass cloning of elite genotypes of commercially important conifers has led to the establishment of an industrial forest of two of the most important softwood species in the USA. Embryonal-suspensor masses, produced by monozygotic cleavage polyembryony (MCP), are rescued from controlled-pollinated seeds in tree breeding orchards. MCP is scaled up as cell suspensions and grown into mature somatic embryos. The embryos serve as a source for the production of various artificial and manufactured seeds used in replicated field trials to test genotype x environmental interactions. For the capture of genetic gains, early selections are based on correlations with known traits. This reduces the costs of years of tree improvement. Mass cloning and genotype cryopreservation enables field testing under a wider range of sites. Process-controlled bioreactors are proposed as artificial ovules to impose nutritional variables from the mother tree, and to simulate environmental factors that are known to affect the performance of the new generation. Comparisons among extant and modern conifer genotypes would provide new insights regarding their latent potentials for apomixis, the alternation of generations, and adaptive plasticity. PMID:18822861

  11. 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

  12. 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

  13. Potential transgenic routes to increase tree biomass.

    PubMed

    Dubouzet, Joseph G; Strabala, Timothy J; Wagner, Armin

    2013-11-01

    Biomass is a prime target for genetic engineering in forestry because increased biomass yield will benefit most downstream applications such as timber, fiber, pulp, paper, and bioenergy production. Transgenesis can increase biomass by improving resource acquisition and product utilization and by enhancing competitive ability for solar energy, water, and mineral nutrients. Transgenes that affect juvenility, winter dormancy, and flowering have been shown to influence biomass as well. Transgenic approaches have increased yield potential by mitigating the adverse effects of prevailing stress factors in the environment. Simultaneous introduction of multiple genes for resistance to various stress factors into trees may help forest trees cope with multiple or changing environments. We propose multi-trait engineering for tree crops, simultaneously deploying multiple independent genes to address a set of genetically uncorrelated traits that are important for crop improvement. This strategy increases the probability of unpredictable (synergistic or detrimental) interactions that may substantially affect the overall phenotype and its long-term performance. The very limited ability to predict the physiological processes that may be impacted by such a strategy requires vigilance and care during implementation. Hence, we recommend close monitoring of the resultant transgenic genotypes in multi-year, multi-location field trials. PMID:24094056

  14. 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.

  15. 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

  16. Embedding of tree networks into hypercubes

    SciTech Connect

    Wu, A.Y.

    1985-08-01

    The hypercube is a good host graph for the embedding of networks of processors because of its low degree and low diameter. Graphs such as trees and arrays can be embedded into a hypercube with small costs. The design of the embedding mappings makes use of the structures of these graphs. In general, there is a trade-off between the dilation cost and the expansion cost. Rosenberg illustrates how one of these costs can be minimized only at the expense of a dramatic increase in the other cost in three situations where binary trees are the host graphs. This paper shows that there is no embedding of a complete binary tree into a hypercube with dilation cost of 1 and expansion cost less than 2. But there is an embedding with dilation cost 1 and expansion cost approximately 2, and there is an embedding with dilation cost 2 and expansion cost approximately 1. For embedding of general graphs, if the size of the hypercube is minimal, then the dilation cost of the embedding may be as large as log (number of nodes in the graph). On the other hand, there is always an embedding of an n node graph into a degree n - 1 hypercube (very high expansion cost) with a dilation cost of 2. We have also shown that there are classes of graphs which cannot have adjacency-preserving (dilation cost = 1) embeddings into hypercubes of any size.

  17. State variable method of fault tree analysis

    SciTech Connect

    Bartholomew, R.J.; Knudsen, H.K.; Whan, G.A.

    1984-01-01

    The current technique of Fault Tree Analysis (FTA) generally employs computer codes that calculate the minimal cut sets of the Boolean function, where each cut set comprises basic initiator events (roots) whose intersection implies the occurrence of a TOP (system failure) event. Because the number of calculations can be very large for typical fault trees, the importance of any given cut set is assessed by qualitative algorithms that may include the number of basic events in the cut set, and quantitative importance algorithms that involve probabilistic upper and lower bound estimates, and the sets are culled before quantitative probability calculations are made. The assumption of statistical independence of all events is often imposed as a requirement for quantititative analysis. The question addressed in this paper is: can a tractable mathematical model be found that can perform quantitative calculations without the need of upper or lower bound simplifications and include within its structure the capability of handling common cause/common mode statistical dependence, failure mode coupling interdependence, and sequential failure time dependence. The Failure Mode State Variable (FMSV) model developed here is the affirmative answer to this question. The model is applied to simplified fault trees representing some nuclear power system components and subsystems considered for space electric power generation.

  18. 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

  19. Common allometric response of open-grown leader shoots to tree height in co-occurring deciduous broadleaved trees

    PubMed Central

    Miyata, Rie; Kubo, Takuya; Nabeshima, Eri; Kohyama, Takashi S.

    2011-01-01

    Background and Aims Morphology of crown shoots changes with tree height. The height of forest trees is usually correlated with the light environment and this makes it difficult to separate the effects of tree size and of light conditions on the morphological plasticity of crown shoots. This paper addresses the tree-height dependence of shoot traits under full-light conditions where a tree crown is not shaded by other crowns. Methods Focus is given to relationships between tree height and top-shoot traits, which include the shoot's leaf-blades and non-leafy mass, its total leaf-blade area and the length and basal diameter of the shoot's stem. We examine the allometric characteristics of open-grown current-year leader shoots at the tops of forest tree crowns up to 24 m high and quantify their responses to tree height in 13 co-occurring deciduous hardwood species in a cool-temperate forest in northern Japan. Key Results Dry mass allocated to leaf blades in a leader shoot increased with tree height in all 13 species. Specific leaf area decreased with tree height. Stem basal area was almost proportional to total leaf area in a leader shoot, where the proportionality constant did not depend on tree height, irrespective of species. Stem length for a given stem diameter decreased with tree height. Conclusions In the 13 species observed, height-dependent changes in allometry of leader shoots were convergent. This finding suggests that there is a common functional constraint in tree-height development. Under full-light conditions, leader shoots of tall trees naturally experience more severe water stress than those of short trees. We hypothesize that the height dependence of shoot allometry detected reflects an integrated response to height-associated water stress, which contributes to successful crown expansion and height gain. PMID:21914698

  20. [Seed germination of four tree species from the tropical dry forest of Valle del Cauca, Colombia].

    PubMed

    Vargas Figueroa, Jhon Alexander; Duque Palacio, Olga Luca; Torres Gonzlez, Alba Marina

    2015-03-01

    The ecological restoration strategies for highly threatened ecosystems such as the tropical dry forest, depend on the knowledge of limiting factors of biological processes for the different species. Some of these include aspects such as germination and seed longevity of typical species present in those forests. In this study, we evaluated the effect of light and temperature on seed germination of two Fabaceae (Samanea saman and Jacaranda caucana) and two Bignoniaceae (Pithecellobium dulce and Tabebuia rosea) species having potential use in restoration, and we analyzed the seed storage behavior of these species for a three months period. To study the light effect, four levels of light quality on seeds were used (photoperiod of 12 hours of white light, darkness and light enriched in red and far-red, both for an hour each day), and we combined them with three levels of alternated temperatures (20/25, 20/30 and 25/30*C-16/8h). For the storage behavior, two levels of seed moisture content particular for each species were used (low: 3.5-6.1% and high: 8.3-13.8%), with three storage temperatures (20, 5 and -20 degrees C) and two storage times (one and three months). The criterion for germination was radicle emergence which was measured in four replicates per treatment, and was expressed as percentage of germination (PG). There were significant differences in germination of Samanea saman and Jacaranda caucana among light and temperature treatments, with the lowest value in darkness treatments, whereas germination of Pithecellobium dulce and Tabebuia rosea did not differ between treatments (PG>90%). The most suitable temperature regime to promote germination in all species was 25/30 degrees C. These four species showed an orthodox seed storage behavior. We concluded that seeds of R dulce, J. caucana and T. rosea did not have an apparent influence of all light conditions tested in their germination response, which might confer advantages in colonization and establishment processes, while S. saman did not germinate well in darkness. We suggest the use of seeds of P dulce, J. caucana and T rosea in ecological restoration processes, due to their tolerance and germination under a wide range of temperature and light conditions. Futhermore, seeds of S. saman might be used in open areas such as forest gaps. PMID:26299129

  1. 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 low elevation in Hawaii compared with continental tree lines, which can be up to 1500 m higher. If the elevation of tree line is influenced by the inability of M. polymorpha leaves to supercool to lower subzero temperatures, then it will be the first example that freezing damage resulting from limited supercooling capacity can be a factor in tree line formation. PMID:10817972

  2. 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.

  3. 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.

  4. 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.; Njd, 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.

  5. Weighing trees: Measuring interception and evaporation dynamics by monitoring sub- micrometer tree trunk compaction

    NASA Astrophysics Data System (ADS)

    Friesen, J.; van de Giesen, N.; Savenije, H.; Oguntunde, P.; Selker, J.

    2007-12-01

    Interception of rain and snow by tree crowns can be a significant part of the water balance. Rain, intercepted by leaves, that evaporates directly back into the atmosphere may make up 10% to 60% of total precipitation. In most forests, 2 mm or more is intercepted per rainfall event. Measuring interception and its subsequent evaporation is difficult. Measuring rain above and below the canopy is prone to noise. Radiometric measurements are difficult to calibrate. Here, we make use of the fact that water or snow intercepted by the crown compacts the trunk, simply following Hooke's law. By measuring the compaction, the amount of water stored in the crown can be measured. In practice, many problems have to be overcome before a good weight signal is obtained. For starters, 1 kg of water stored in a small tree causes a compaction of only 100 nm over a stretch of 1 m. Such small displacements can actually be measured relatively easily with special potentiometers. We used such displacement sensors together with quartz rods of 1m length, that were bolted to the trunk. Quartz was chosen to reduce the effect of temperature changes. In addition, the trees were insulated and kept at a constant temperature with heating wire. The main source of noise is bending by wind. By radially installing three sensors, wind effects could accounted for as well. Final measurement accuracies of 1 kg to 5g were obtained, depending on tree size. Tree weighing results from Europe and Africa will be presented.

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

    NASA Astrophysics Data System (ADS)

    Kaneta, Yusaku; Arimura, Hiroki

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

  7. 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 20102012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 2050 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

  8. 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

  9. Screening for antimicrobial activity of ten medicinal plants used in Colombian folkloric medicine: A possible alternative in the treatment of non-nosocomial infections

    PubMed Central

    Rojas, Jhon J; Ochoa, Veronica J; Ocampo, Saul A; Muoz, John F

    2006-01-01

    Background The antimicrobial activity and Minimal Inhibitory Concentration (MIC) of the extracts of Bidens pilosa L., Bixa orellana L., Cecropia peltata L., Cinchona officinalis L., Gliricidia sepium H.B. & K, Jacaranda mimosifolia D.Don, Justicia secunda Vahl., Piper pulchrum C.DC, P. paniculata L. and Spilanthes americana Hieron were evaluated against five bacteria (Staphylococcus aureus, Streptococcus ? hemoltic, Bacillus cereus, Pseudomonas aeruginosa, and Escherichia coli), and one yeast (Candida albicans). These plants are used in Colombian folk medicine to treat infections of microbial origin. Methods Plants were collected by farmers and traditional healers. The ethanol, hexane and water extracts were obtained by standard methods. The antimicrobial activity was found by using a modified agar well diffusion method. All microorganisms were obtained from the American Type Culture Collection (ATCC). MIC was determined in the plant extracts that showed some efficacy against the tested microorganisms. Gentamycin sulfate (1.0 ?g/ml), clindamycin (0.3 ?g/ml) and nystatin (1.0 ?g/ml) were used as positive controls. Results The water extracts of Bidens pilosa L., Jacaranda mimosifolia D.Don, and Piper pulchrum C.DC showed a higher activity against Bacillus cereus and Escherichia coli than gentamycin sulfate. Similarly, the ethanol extracts of all species were active against Staphylococcus aureus except for Justicia secunda. Furthermore, Bixa orellana L, Justicia secunda Vahl. and Piper pulchrum C.DC presented the lowest MICs against Escherichia coli (0.8, 0.6 and 0.6 ?g/ml, respectively) compared to gentamycin sulfate (0.9 8g/ml). Likewise, Justicia secunda and Piper pulchrum C.DC showed an analogous MIC against Candida albicans (0.5 and 0.6 ?g/ml, respectively) compared to nystatin (0.6 ?g/ml). Bixa orellana L, exhibited a better MIC against Bacillus cereus (0.2 ?g/ml) than gentamycin sulfate (0.5 ?g/ml). Conclusion This in vitro study corroborated the antimicrobial activity of the selected plants used in folkloric medicine. All these plants were effective against three or more of the pathogenic microorganisms. However, they were ineffective against Streptococcus ? hemolytic and Pseudomonas aeruginosa. Their medicinal use in infections associated with these two species is not recommended. This study also showed that Bixa orellana L, Justicia secunda Vahl. and Piper pulchrum C.DC could be potential sources of new antimicrobial agents. PMID:16483385

  10. Rubber Tree (Hevea brasiliensis Muell. Arg).

    PubMed

    Venkatachalam, Perumal; Jayashree, Radha; Rekha, Karumamkandathil; Sushmakumari, Sreedharannair; Sobha, Sankaren; Kumari Jayasree, Parukkuttyamma; Kala, Radha Gopikkuttanunithan; Thulaseedharan, Arjunan

    2006-01-01

    Rubber tree (Hevea brasiliensis Muell. Arg.) is an important industrial crop for natural rubber production. At present, more than 9.5 million hectares in about 40 countries are devoted to rubber tree cultivation with a production about 6.5 million tons of dry rubber each year. The world supply of natural rubber is barely keeping up with a global demand for 12 million tons of natural rubber in 2020. Tapping panel dryness (TPD) is a complex physiological syndrome widely found in rubber tree plantations, which causes severe yield and crop losses in natural rubber producing countries. Currently, there is no effective prevention or treatment for this serious malady. As it is a perennial tree crop, the integration of specific desired traits through conventional breeding is both time-consuming and labour-intensive. Genetic transformation with conventional breeding is certainly a more promising tool for incorporation of agronomically important genes that could improve existing Hevea genotype. This chapter provides an Agrobacterium-mediated transformation protocol for rubber tree using immature anther-derived calli as initial explants. We have applied this protocol to generate genetically engineered plants from a high yielding Indian clone RRII 105 of Hevea brasiliensis (Hb). Calli were co-cultured with Agrobacterium tumefaciens harboring a plasmid vector containing the Hb superoxide dismutase (SOD) gene and the reporter gene used was beta-glucuronidase (GUS) gene (uidA). The selectable marker gene used was neomycin phosphotransferase (nptII) and kanamycin was used as selection agent. We found that a suitable transformation protocol for Hevea consists of a 3-d co-cultivation with Agrobacterium in the presence of 20 mM acetosyringone, 15 mM betaine HCl, and 11.55 mM proline followed by selection on medium containing 300 mg/L kanamycin. Transformed calli surviving on medium containing 300 mg/L kanamycin showed a strong GUS-positive reaction. Upon subsequent subculture into fresh media, we obtained somatic embryogenesis and germinated plantlets, which were found to be GUS positive. The integration of uidA, nptII, and HbSOD transgenes into Hevea genome was confirmed by polymerase chain reaction (PCR) as well as Southern blot analysis. PMID:17033060

  11. Local analysis and modeling of tree competition and growth

    NASA Astrophysics Data System (ADS)

    Shi, Haijin

    2003-10-01

    This study focuses on local analysis of tree competition and local modeling of tree growth. First, relationships between the Local Indicator of Spatial Association (LISA) and traditional tree competition indices and individual tree growth are investigated. The results show that like most of the competition indices, LISA has moderate correlations with tree basal area growth. For predicting the tree basal area growth, one of LISA, the local Gi, performs better than many (73%) competition indices at a plot aggregation level, and has higher explanatory power than most (91%) competition indices at an individual plot level. The LISA also has strong linear relationships with some traditional competition indices, e.g. Lorimer index. The relationships are stronger ( r? > 0.90) at an individual plot level than for all plots combined ( r? > 0.75). The LISA can be statistically tested to identify local clusters of trees of similar sizes ("hot spots") or dissimilar sizes ("cold spots"), even though without discernible spatial pattern. These significant "hot spots" or "cold spots" indicate the subareas in a forest stand where the competition among trees may be more severe than the average. Therefore, the LISA can replace the traditional competition indices for exploring the competitive status of neighboring trees, investigating the relationships between tree competition and growth, and estimating individual tree growth. The hot spots or cold spots identified by the LISA provide useful information for the design of silvicultural and management treatments. Second, the spatial heterogeneity of multivariate relationships between tree growth and diameter is explored using Geographically Weighted Regression (GWR). GWR attempts to capture spatial variation by calibrating a multiple regression model fitted at each tree in a sample plot, weighting all neighboring trees by a function of distance from the subject tree. GWR produces a set of parameter estimates and model statistics (e.g., model R2) for each tree in the sample plot. It is evident that the GWR model not only predicts individual tree growth better than the traditional OLS model, but also provides useful information on the nature of the growth variation caused by neighboring competitors and surrounding environmental factors. The parameter estimates and model statistics of the GWR model can be mapped using visualization tools such as Geographical Information System (GIS) to illustrate local spatial variation in the regression relationship under study. The influence of micro-site variation, competition status, growth potential, and the impacts of management activities on trees can be evaluated, tested, modeled, and readily visualized by GWR. This study indicates that LISA and GWR are useful to provide us much more information on spatial relationships in aid to both model development and better understanding of spatial processes.

  12. Effects of memory on the shapes of simple outbreak trees

    PubMed Central

    Plazzotta, Giacomo; Kwan, Christopher; Boyd, Michael; Colijn, Caroline

    2016-01-01

    Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset. PMID:26888437

  13. Tree structure and cavity microclimate: implications for bats and birds

    NASA Astrophysics Data System (ADS)

    Clement, Matthew J.; Castleberry, Steven B.

    2013-05-01

    It is widely assumed that tree cavity structure and microclimate affect cavity selection and use in cavity-dwelling bats and birds. Despite the interest in tree structure and microclimate, the relationship between the two has rarely been quantified. Currently available data often comes from artificial structures that may not accurately represent conditions in natural cavities. We collected data on tree cavity structure and microclimate from 45 trees in five cypress-gum swamps in the Coastal Plain of Georgia in the United States in 2008. We used hierarchical linear models to predict cavity microclimate from tree structure and ambient temperature and humidity, and used Aikaike's information criterion to select the most parsimonious models. We found large differences in microclimate among trees, but tree structure variables explained <28 % of the variation, while ambient conditions explained >80 % of variation common to all trees. We argue that the determinants of microclimate are complex and multidimensional, and therefore cavity microclimate cannot be deduced easily from simple tree structures. Furthermore, we found that daily fluctuations in ambient conditions strongly affect microclimate, indicating that greater weather fluctuations will cause greater differences among tree cavities.

  14. Tree Testing of Hierarchical Menu Structures for Health Applications

    PubMed Central

    Le, Thai; Chaudhuri, Shomir; Chung, Jane; Thompson, Hilaire J; Demiris, George

    2014-01-01

    To address the need for greater evidence-based evaluation of Health Information Technology (HIT) systems we introduce a method of usability testing termed tree testing. In a tree test, participants are presented with an abstract hierarchical tree of the system taxonomy and asked to navigate through the tree in completing representative tasks. We apply tree testing to a commercially available health application, demonstrating a use case and providing a comparison with more traditional in-person usability testing methods. Online tree tests (N=54) and in-person usability tests (N=15) were conducted from August to September 2013. Tree testing provided a method to quantitatively evaluate the information structure of a system using various navigational metrics including completion time, task accuracy, and path length. The results of the analyses compared favorably to the results seen from the traditional usability test. Tree testing provides a flexible, evidence-based approach for researchers to evaluate the information structure of HITs. In addition, remote tree testing provides a quick, flexible, and high volume method of acquiring feedback in a structured format that allows for quantitative comparisons. With the diverse nature and often large quantities of health information available, addressing issues of terminology and concept classifications during the early development process of a health information system will improve navigation through the system and save future resources. Tree testing is a usability method that can be used to quickly and easily assess information hierarchy of health information systems. PMID:24582924

  15. Identifying a species tree subject to random lateral gene transfer.

    PubMed

    Steel, Mike; Linz, Simone; Huson, Daniel H; Sanderson, Michael J

    2013-04-01

    A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favor gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency when majority-rule three-taxon gene trees are used to reconstruct species trees under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets. PMID:23340439

  16. Tree decline and the future of Australian farmland biodiversity.

    PubMed

    Fischer, Joern; Zerger, Andre; Gibbons, Phil; Stott, Jenny; Law, Bradley S

    2010-11-01

    Farmland biodiversity is greatly enhanced by the presence of trees. However, farmland trees are declining worldwide, including in North America, Central America, and parts of southern Europe. We show that tree decline and its likely consequences are particularly severe in Australia's temperate agricultural zone, which is a threatened ecoregion. Using field data on trees, remotely sensed imagery, and a demographic model for trees, we predict that by 2100, the number of trees on an average farm will contract to two-thirds of its present level. Statistical habitat models suggest that this tree decline will negatively affect many currently common animal species, with predicted declines in birds and bats of up to 50% by 2100. Declines were predicted for 24 of 32 bird species modeled and for all of six bat species modeled. Widespread declines in trees, birds, and bats may lead to a reduction in economically important ecosystem services such as shade provision for livestock and pest control. Moreover, many other species for which we have no empirical data also depend on trees, suggesting that fundamental changes in ecosystem functioning are likely. We conclude that Australia's temperate agricultural zone has crossed a threshold and no longer functions as a self-sustaining woodland ecosystem. A regime shift is occurring, with a woodland system deteriorating into a treeless pasture system. Management options exist to reverse tree decline, but new policy settings are required to encourage their widespread adoption. PMID:20974946

  17. Grass competition suppresses savanna tree growth across multiple demographic stages.

    PubMed

    Riginos, Corinna

    2009-02-01

    Savanna ecosystems, defined by the codominance of trees and grasses, cover one-fifth of the world's land surface and are of great socioeconomic and biological importance. Yet, the fundamental question of how trees and grasses coexist to maintain the savanna state remains poorly understood. Many models have been put forward to explain tree-grass coexistence, but nearly all have assumed that grasses do not limit tree growth and demography beyond the sapling stage. This assumption, however, has rarely been tested. Here I show that grass can strongly suppress the growth of trees. I removed grass around trees of three size classes in an Acacia drepanolobium savanna in Laikipia, Kenya. For even the largest trees, grass removal led to a doubling in growth and a doubling in the probability of transitioning to the next size class over two years. These results suggest that grass competition in productive (nutrient-rich) savannas may limit tree growth as much as herbivory and fire (the main factors thought to determine tree demography within a rainfall region) and should be incorporated into savanna models if tree-grass coexistence and savanna dynamics are to be understood. PMID:19323216

  18. The development of seasonal tree water deficit in Callitris intratropica.

    PubMed

    Drew, David M; Richards, Anna E; Downes, Geoffrey M; Cook, Garry D; Baker, Patrick

    2011-09-01

    The tropical conifer Callitris intratropica (Cupressaceae) produces clear annual growth rings, and has been shown to be potentially useful for understanding past climate variability in northern Australia. As climate patterns in this region become less predictable, an understanding of plant responses to different weather patterns is of importance. In this paper, we examine tree water relations using a parameter here called tree water deficit (?D), determined from de-trended stem size variability in densely grown ('grove') and isolated trees. This parameter provides an integrated measure of the trees' response to water supply and demand under constantly changing environmental conditions. The work, conducted over 12 months, found that daily variation in tree water deficit was determined mainly by soil water availability, but temperature and relative humidity contributed more to the variability over some periods. Isolated and grove trees exhibited quite distinct patterns of ?D development during the year, but particularly during the transition between the dry and wet seasons. The results of this work suggest that the dendrochronological interpretation of tree rings in the context of strongly seasonal water availability should incorporate an understanding of the development of seasonal drought in isolated trees compared with trees experiencing strong intra-specific competition. Different responses based on the ecological situations of the trees will affect their patterns of stem growth, and ultimately the climatic information that is incorporated in ring width variability. PMID:21558386

  19. Tree decline and the future of Australian farmland biodiversity

    PubMed Central

    Fischer, Joern; Zerger, Andre; Gibbons, Phil; Stott, Jenny; Law, Bradley S.

    2010-01-01

    Farmland biodiversity is greatly enhanced by the presence of trees. However, farmland trees are declining worldwide, including in North America, Central America, and parts of southern Europe. We show that tree decline and its likely consequences are particularly severe in Australia's temperate agricultural zone, which is a threatened ecoregion. Using field data on trees, remotely sensed imagery, and a demographic model for trees, we predict that by 2100, the number of trees on an average farm will contract to two-thirds of its present level. Statistical habitat models suggest that this tree decline will negatively affect many currently common animal species, with predicted declines in birds and bats of up to 50% by 2100. Declines were predicted for 24 of 32 bird species modeled and for all of six bat species modeled. Widespread declines in trees, birds, and bats may lead to a reduction in economically important ecosystem services such as shade provision for livestock and pest control. Moreover, many other species for which we have no empirical data also depend on trees, suggesting that fundamental changes in ecosystem functioning are likely. We conclude that Australia's temperate agricultural zone has crossed a threshold and no longer functions as a self-sustaining woodland ecosystem. A regime shift is occurring, with a woodland system deteriorating into a treeless pasture system. Management options exist to reverse tree decline, but new policy settings are required to encourage their widespread adoption. PMID:20974946

  20. Dendroscope: An interactive viewer for large phylogenetic trees

    PubMed Central

    Huson, Daniel H; Richter, Daniel C; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula

    2007-01-01

    Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. PMID:18034891