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Recursive algorithms for phylogenetic tree counting.

Science.gov (United States)

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.
[Prediction of the total Japanese cedar pollen counts based on male flower-setting conditions of standard trees].

Science.gov (United States)

Yuta, Atsushi; Ukai, Kotaro; Sakakura, Yasuo; Tani, Hideshi; Matsuda, Fukiko; Yang, Tian-qun; Majima, Yuichi

2002-07-01

We made a prediction of the Japanese cedar (Cryptomeria japonica) pollen counts at Tsu city based on male flower-setting conditions of standard trees. The 69 standard trees from 23 kinds of clones, planted at Mie Prefecture Science and Technology Promotion Center (Hakusan, Mie) in 1964, were selected. Male flower-setting conditions for 276 faces (69 trees x 4 points of the compass) were scored from 0 to 3. The average of scores and total pollen counts from 1988 to 2000 was analyzed. As the results, the average scores from standard trees and total pollen counts except two mass pollen-scattered years in 1995 and 2000 had a positive correlation (r = 0.914) by linear function. On the mass pollen-scattered years, pollen counts were influenced from the previous year. Therefore, the score of the present year minus that of the previous year were used for analysis. The average scores from male flower-setting conditions and pollen counts had a strong positive correlation (r = 0.994) when positive scores by taking account of the previous year were analyzed. We conclude that prediction of pollen counts are possible based on the male flower-setting conditions of standard trees.
Tests with VHR images for the identification of olive trees and other fruit trees in the European Union

Science.gov (United States)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

In the context of the Common Agricultural Policy (CAP) there is a strong interest of the European Commission for counting and individually locating fruit trees. An automatic counting algorithm developed by the JRC (OLICOUNT) was used in the past for olive trees only, on 1m black and white orthophotos but with limits in case of young trees or irregular groves. This study investigates the improvement of fruit tree identification using VHR images on a large set of data in three test sites, one in Creta (Greece; one in the south-east of France with a majority of olive trees and associated fruit trees, and the last one in Florida on citrus trees. OLICOUNT was compared with two other automatic tree counting, applications, one using the CRISP software on citrus trees and the other completely automatic based on regional minima (morphological image analysis). Additional investigation was undertaken to refine the methods. This paper describes the automatic methods and presents the results derived from the tests.
A recursive algorithm for trees and forests

OpenAIRE

Guo, Song; Guo, Victor J. W.

2017-01-01

Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\\{1,2,\\ldots,n\\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.
Detection and Counting of Orchard Trees from Vhr Images Using a Geometrical-Optical Model and Marked Template Matching

Science.gov (United States)

Maillard, Philippe; Gomes, Marília F.

2016-06-01

This article presents an original algorithm created to detect and count trees in orchards using very high resolution images. The algorithm is based on an adaptation of the "template matching" image processing approach, in which the template is based on a "geometricaloptical" model created from a series of parameters, such as illumination angles, maximum and ambient radiance, and tree size specifications. The algorithm is tested on four images from different regions of the world and different crop types. These images all have the GoogleEarth application. Results show that the algorithm is very efficient at detecting and counting trees as long as their spectral and spatial characteristics are relatively constant. For walnut, mango and orange trees, the overall accuracy was clearly above 90%. However, the overall success rate for apple trees fell under 75%. It appears that the openness of the apple tree crown is most probably responsible for this poorer result. The algorithm is fully explained with a step-by-step description. At this stage, the algorithm still requires quite a bit of user interaction. The automatic determination of most of the required parameters is under development.
Why count trees? Volunteer motivations and experiences with tree monitoring in New York City

Science.gov (United States)

Michelle L. Johnson; Lindsay K. Campbell; Erika S. Svendsen; Philip. Silva

2018-01-01

Volunteer programs can benefit from a deeper understanding of the motivations and experiences of people engaged in citizen science. Research to date has studied motivations of citizen scientists and tree-planting volunteers. Less work has focused on tree-monitoring volunteers, a role that is rapidly increasing as more cities involve the public in monitoring the urban...
Type extension trees

DEFF Research Database (Denmark)

Jaeger, Manfred

2006-01-01

We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....
On the Shapley Value of Unrooted Phylogenetic Trees.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-01-17

The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows for the calculation of the Shapley value from the edge lengths of a tree. We show that non-isomorphic trees may have permutation-equivalent Shapley transformation matrices and permutation-equivalent null spaces. This implies that estimating the split counts associated with a tree or the Shapley values of its leaves does not suffice to reconstruct the correct tree topology. We then turn to the use of the Shapley value as a prioritization criterion in biodiversity conservation and compare it to a greedy solution concept. Here, we show that for certain phylogenetic trees, the Shapley value may fail as a prioritization criterion, meaning that the diversity spanned by the top k species (ranked by their Shapley values) cannot approximate the total diversity of all n species.
Single Polygon Counting on Cayley Tree of Order 3

Science.gov (United States)

Pah, Chin Hee

2010-07-01

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

International Nuclear Information System (INIS)

O'Loughlin, M.; Joshi, G.

1989-01-01

After reviewing p-adic numbers, their relationship to trees, and some recent proposals for actions of a p-adic string theory with a tree-like world sheet, the possibility of constructing p-adic vertex operators in a similar way to the Frenkel-Kac construction of Kac-Moody algebras, is investigated. 25 refs., 5 figs
Categorizing ideas about trees: a tree of trees.

Science.gov (United States)

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.
Totally optimal decision trees for Boolean functions

KAUST Repository

Chikalov, Igor

2016-07-28

We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters characterizing both time (in the worst- and average-case) and space complexity of decision trees, i.e., depth, total path length (average depth), and number of nodes. We have created tools based on extensions of dynamic programming to study totally optimal trees. These tools are applicable to both exact and approximate decision trees, and allow us to make multi-stage optimization of decision trees relative to different parameters and to count the number of optimal trees. Based on the experimental results we have formulated the following hypotheses (and subsequently proved): for almost all Boolean functions there exist totally optimal decision trees (i) relative to the depth and number of nodes, and (ii) relative to the depth and average depth.
Initial development of passion fruit trees (Passiflora edulis f. flavicarpa, P. edulis f. edulis and P. alata grafted onto Passiflora cincinnata

Directory of Open Access Journals (Sweden)

Valdir Zucareli

2014-10-01

Full Text Available The present work aimed to evaluate the initial growth and leaf mineral levels in passion fruit trees (Passiflora edulis f. flavicarpa Deg., P. edulis f. edulis Sims. and P. alata Dryander grafted onto Passiflora cincinnata. To obtain seedlings, seeds were sown in plastic bags (500 mL and hypocotyl grafting was performed when seedlings reached the stage of two fully expanded leaves. Fifteen days after grafting, plants were transplanted to 10L pots filled with previously limed and fertilized soil. Each pot contained two plants and corresponded to one plot. For each commercial species studied as rootstock, experimental design was completely randomized, in 3x5 (plant type x time of harvest factorial arrangement, with four replicates of two plants per plot and five destructive harvests. Plant types were ungrafted P. cincinnata, ungrafted commercial passion fruit tree and commercial passion fruit tree grafted onto P. cincinnata. The first harvest was performed at 15 days after transplanting and the remaining ones at 14-day intervals (60, 74, 88, 102 and 116 DAS. At each harvest, the number of leaves per plant was counted, and leaf area, stem length, and stem, root, leaf and total dry matter were estimated. At the last harvest, the mineral composition (macro and micronutrients of plants was analyzed. In general, it was observed that grafting onto P. cincinnata did not interfere negatively with the initial development and mineral levels of commercial passion fruit trees, and this interference varied according to the used canopy.
P{owering 'Trees

Indian Academy of Sciences (India)

Melia dubia Cav. of Meliaceae is a large deciduous tree. Leaves are compound with toothed leaflets. Flowers are small, greenish-yellow in much-branched inflorescences. Fruits are green, ellipsoidal with a single seed covered by hard portion ( as in a mango fruit) and surrounded by fleshy pulp outside. The bark is bitter ...
Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

Science.gov (United States)

Gregg, W C Thomas; Ather, S Hussain; Hahn, Matthew W

2017-11-01

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Root activity patterns of some tree crops. Results of a five-year co-ordinated research programme of the Joint FAO/IAEA Division of Atomic Energy in Food and Agriculture. [32p; injection into banana trees, orange trees, cacao trees, coffee trees, and oil palms

Energy Technology Data Exchange (ETDEWEB)

1975-01-01

A coordinated research program was followed using a soil injection method which employed /sup 32/P-labelled superphosphate solution. The technique was applied for determining the root activity distribution of various crops. Field experiments were carried out in Uganda on bananas, Spain and Taiwan on citrus, Ghana on cocoa, Columbia and Kenya on coffee, and Ivory Coast and Malaysia on oil palms, to study the patterns of root activity as a function of depth and distance from the tree base, soil type, tree age and season. A few weeks after injection, leaf samples of similar age were taken from well-defined morphological positions on the tree and analyzed for /sup 32/P. The activity of the label in the sample reflects the root activity at the various positions in the soil. Some preliminary experiments were also carried out using /sup 32/P-superphosphate to evaluate the efficiency of different methods of fertilizer placement in relation to phosphate uptake by the plantation as a whole.
Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2013-01-01

We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...
Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2015-01-01

We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...
Generalising tree traversals and tree transformations to DAGs

DEFF Research Database (Denmark)

Bahr, Patrick; Axelsson, Emil

2017-01-01

We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....
Surface tree languages and parallel derivation trees

NARCIS (Netherlands)

Engelfriet, Joost

1976-01-01

The surface tree languages obtained by top-down finite state transformation of monadic trees are exactly the frontier-preserving homomorphic images of sets of derivation trees of ETOL systems. The corresponding class of tree transformation languages is therefore equal to the class of ETOL languages.

TreePics: visualizing trees with pictures

Directory of Open Access Journals (Sweden)

Nicolas Puillandre

2017-09-01

Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.
Mercury and other element exposure in tree swallows nesting at low pH and neutral pH lakes in northern Wisconsin USA

International Nuclear Information System (INIS)

Custer, Thomas W.; Custer, Christine M.; Thogmartin, Wayne E.; Dummer, Paul M.; Rossmann, Ronald; Kenow, Kevin P.; Meyer, Michael W.

2012-01-01

The primary objective of this study was to determine whether tree swallows (Tachycineta bicolor) demonstrate similar responses to lake pH and mercury (Hg) contamination in northern Wisconsin as do common loons (Gavia immer). Similar to common loons, Hg concentrations in the blood of tree swallow nestlings were higher, Hg concentrations in eggs tended to be higher, and egg size tended to be smaller at low (<6.2) pH lakes. In contrast to common loons, tree swallow nestling production was not lower at low pH lakes. Based on modeling associations, Hg concentrations in tree swallow eggs and nestling blood can be used to predict Hg concentrations in common loons without the invasive or destructive sampling of loons. Mean concentrations of cadmium, manganese, and mercury in nestling livers were higher at low pH lakes than neutral pH lakes. Concentrations of cadmium, chromium, mercury, selenium, and zinc were not at toxic levels. - Highlights: ► Mercury concentrations in tree swallow nestling livers were higher in low than neutral pH lakes. ► Tree swallow eggs were smaller at low than neutral pH lakes. ► Tree swallow hatching success was not correlated with mercury concentrations in eggs. ► Mercury concentrations in tree swallows can be used to predict common loon exposure. - Mercury concentrations in tree swallows were higher at low pH lakes.
Rattle tree (Albizia lebbeck Benth. effects on potato (Solanum tuberosum L. productivity on the Jos Plateau, Nigeria

Directory of Open Access Journals (Sweden)

Kareem Alasi Ibraheem

2014-01-01

Full Text Available Field experiment was conducted in the biotite-granite area (Alfisol of the Jos Plateau, Nigeria, consisting of five cropping seasons to determine the effects of the tree rows (under alley cropping and green manure of Albizia lebbeck Benth. (rattle tree on the yield / productivity of Solanum tuberosum L. (Irish potato. The experiment was a randomized complete block design comprising five treatments and three replicates. An early maturing potato variety (Bertita was employed, its pre-sprouted tubers were planted in the alleys (spaces between the tree rows of A. lebbeck two weeks after green manure was applied (5 and 10 t ha-1, pre and post experimental soil sample analyses and cultivation operations were carried out. Results indicated that the rattle tree had profound effect on the potato growth parameters (plant height, leaf count, collar girth (at P < 0.01 and yield indices (tuber count (P < 0.05 and tuber weight (P < 0.01 due to nutrients from the green manure and nitrogen fixation activities of the rattle tree. A. lebbeck green manure application at 10 t ha-1 in the alleys of A. lebbeck hedgerows emerged as the most effective treatment in terms of growth performance and optimal yield. Collar girth and leaf count of the potato accounted for 80.4 - 91.3% of the variation in yield (R2 = 0.804 - 0.913 with collar girth having the highest value (R2 =0.910 in rainy season (rain fed cropping, while leaf count had the highest value (R2=0.913 during the dry season (irrigated cropping.
ColorTree: a batch customization tool for phylogenic trees.

Science.gov (United States)

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.
Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

Science.gov (United States)

Brienen, Roel J W; Zuidema, Pieter A

2005-11-01

Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate-growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines.
Tree Colors: Color Schemes for Tree-Structured Data.

Science.gov (United States)

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

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

Science.gov (United States)

Muhlbacher, Thomas; Linhardt, Lorenz; Moller, Torsten; Piringer, Harald

2018-01-01

Balancing accuracy gains with other objectives such as interpretability is a key challenge when building decision trees. However, this process is difficult to automate because it involves know-how about the domain as well as the purpose of the model. This paper presents TreePOD, a new approach for sensitivity-aware model selection along trade-offs. TreePOD is based on exploring a large set of candidate trees generated by sampling the parameters of tree construction algorithms. Based on this set, visualizations of quantitative and qualitative tree aspects provide a comprehensive overview of possible tree characteristics. Along trade-offs between two objectives, TreePOD provides efficient selection guidance by focusing on Pareto-optimal tree candidates. TreePOD also conveys the sensitivities of tree characteristics on variations of selected parameters by extending the tree generation process with a full-factorial sampling. We demonstrate how TreePOD supports a variety of tasks involved in decision tree selection and describe its integration in a holistic workflow for building and selecting decision trees. For evaluation, we illustrate a case study for predicting critical power grid states, and we report qualitative feedback from domain experts in the energy sector. This feedback suggests that TreePOD enables users with and without statistical background a confident and efficient identification of suitable decision trees.
Colourings of (k-r,k-trees

Directory of Open Access Journals (Sweden)

M. Borowiecki

2017-01-01

Full Text Available Trees are generalized to a special kind of higher dimensional complexes known as \\((j,k\\-trees ([L. W. Beineke, R. E. Pippert, On the structure of \\((m,n\\-trees, Proc. 8th S-E Conf. Combinatorics, Graph Theory and Computing, 1977, 75-80], and which are a natural extension of \\(k\\-trees for \\(j=k-1\\. The aim of this paper is to study\\((k-r,k\\-trees ([H. P. Patil, Studies on \\(k\\-trees and some related topics, PhD Thesis, University of Warsaw, Poland, 1984], which are a generalization of \\(k\\-trees (or usual trees when \\(k=1\\. We obtain the chromatic polynomial of \\((k-r,k\\-trees and show that any two \\((k-r,k\\-trees of the same order are chromatically equivalent. However, if \\(r\
Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

Science.gov (United States)

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.
Prevalence and Persistence of Misconceptions in Tree Thinking.

Science.gov (United States)

Kummer, Tyler A; Whipple, Clinton J; Jensen, Jamie L

2016-12-01

Darwin described evolution as "descent with modification." Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as "tree thinking." We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic ( reading the tips and node counting ) were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory ( ladder thinking and similarity equals relatedness ) proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses.
Prevalence and Persistence of Misconceptions in Tree Thinking†

Science.gov (United States)

Kummer, Tyler A.; Whipple, Clinton J.; Jensen, Jamie L.

2016-01-01

Darwin described evolution as “descent with modification.” Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as “tree thinking.” We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic (reading the tips and node counting) were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory (ladder thinking and similarity equals relatedness) proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses. PMID:28101265
Prevalence and Persistence of Misconceptions in Tree Thinking

Directory of Open Access Journals (Sweden)

Tyler A. Kummer

2016-12-01

Full Text Available Darwin described evolution as “descent with modification.” Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as “tree thinking.” We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic (reading the tips and node counting were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory (ladder thinking and similarity equals relatedness proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses.
Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera.

Science.gov (United States)

Nguyen, Thuy Tuong; Slaughter, David C; Hanson, Bradley D; Barber, Andrew; Freitas, Amy; Robles, Daniel; Whelan, Erin

2015-07-28

This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera) and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration) required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1) an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2) a plant counting method based on projection histograms; and (3) a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images.
Effect of Tree Leaves on Rumen Fermentation, Microbial Count and Blood Urea Nitrogen of West African Dwarf Goats

Directory of Open Access Journals (Sweden)

Adelusi, O. O.

2016-12-01

Full Text Available This experiment was carried out to assess the effect of Azadirachta indica, Newbouldia laevis and Spondias mombin leaves on rumen fermentation, microbial count and blood urea nitrogen (BUN of West African Dwarf (WAD goats. Sixteen WAD bucks (11.6 ? 0.9 kg in body weight were allocated to 4 treatments: 1 Control and 2 40 g/day of Azadirachta indica, 3 40 g/day of Newbouldia laevis and 4 40 g/day of Spondias mombin leaves arranged in a completely randomised design. The ground leaves were included in concentrate diets served on dry matter basis at 2% of body weight while Panicum maximum was fed ad libitum. The control diet had no tree leaves. Data were collected on chemical composition, rumen fermentation and microbial ecology, and BUN. Saponin was highest (P < 0.05 in S. mombin (8.14% while A. indica and N. laevis had 5.78% and 1.56%, respectively. Rumen ammonia nitrogen was least (P < 0.05 in goats fed A. indica (8.35 mg/dL while the highest (P < 0.05 total volatile fatty acid (TVFA was obtained from goats fed S. mombin with 125.51 mM. Goats fed N. laevis yielded the highest (P < 0.05 acetate with 70.65 mol/100 mol while propionate production was highest (P < 0.05 in the rumen of goats fed S. mombin (27.15 mol/100 mol. Viable bacteria count was lowest (P < 0.05 in rumen of goats fed A. indica (3.95?1012 cfu/ml while the least (P < 0.05 protozoa population was obtained from the rumen of bucks fed S. mombin (4.18?109 cfu/ml. All goats in the treatments containing tree leaves had higher (P < 0.05 and a rapid increase in BUN between 0 and 6 h post feeding when compared with the Control. It is concluded that feeding ground leaves of S. mombin to goats increases rumen total volatile fatty acid and propionate production and reduces the protozoa population.
Tree Nut Allergies

Science.gov (United States)

... Blog Vision Awards Common Allergens Tree Nut Allergy Tree Nut Allergy Learn about tree nut allergy, how ... a Tree Nut Label card . Allergic Reactions to Tree Nuts Tree nuts can cause a severe and ...
On P-adic λ-model on the Cayley tree

International Nuclear Information System (INIS)

Khamaraev, M.; Mukhamedov, F.

2004-04-01

We consider a nearest-neighbour p-adic A-model with spin values ±1 on the Cayley tree of order k ≥ 1. We prove that a p-adic Gibbs measure is unique for p≥ 3. If p 2 then we find a condition which guarantees uniqueness of p-adic Gibbs measure. Besides, the results are applied to the p-adic Ising model. (author)
Decision trees with minimum average depth for sorting eight elements

KAUST Repository

AbouEisha, Hassan M.

2015-11-19

We prove that the minimum average depth of a decision tree for sorting 8 pairwise different elements is equal to 620160/8!. We show also that each decision tree for sorting 8 elements, which has minimum average depth (the number of such trees is approximately equal to 8.548×10^326365), has also minimum depth. Both problems were considered by Knuth (1998). To obtain these results, we use tools based on extensions of dynamic programming which allow us to make sequential optimization of decision trees relative to depth and average depth, and to count the number of decision trees with minimum average depth.
Matching Subsequences in Trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li

2009-01-01

Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...
Big trees, old trees, and growth factor tables

Science.gov (United States)

Kevin T. Smith

2018-01-01

The potential for a tree to reach a great size and to live a long life frequently captures the public's imagination. Sometimes the desire to know the age of an impressively large tree is simple curiosity. For others, the date-of-tree establishment can make a big diff erence for management, particularly for trees at historic sites or those mentioned in property...
A Suffix Tree Or Not a Suffix Tree?

DEFF Research Database (Denmark)

Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

2015-01-01

In this paper we study the structure of suffix trees. Given an unlabeled tree r on n nodes and suffix links of its internal nodes, we ask the question “Is r a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as r? We place no restrictions on S, in part...

Tree-growth analyses to estimate tree species' drought tolerance

NARCIS (Netherlands)

Eilmann, B.; Rigling, A.

2012-01-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree
A P2P Botnet detection scheme based on decision tree and adaptive multilayer neural networks.

Science.gov (United States)

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

2018-01-01

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

Science.gov (United States)

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

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

Directory of Open Access Journals (Sweden)

Thuy Tuong Nguyen

2015-07-01

Full Text Available This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1 an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2 a plant counting method based on projection histograms; and (3 a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images.
TREE SELECTING AND TREE RING MEASURING IN DENDROCHRONOLOGICAL INVESTIGATIONS

Directory of Open Access Journals (Sweden)

Sefa Akbulut

2004-04-01

Full Text Available Dendrochronology is a method of dating which makes use of the annual nature of tree growth. Dendrochronology may be divided into a number of subfields, each of which covers one or more aspects of the use of tree ring data: dendroclimatology, dendrogeomorphology, dendrohydrology, dendroecology, dendroarchaelogy, and dendrogylaciology. Basic of all form the analysis of the tree rings. The wood or tree rings can aid to dating past events about climatology, ecology, geology, hydrology. Dendrochronological studies are conducted either on increment cores or on discs. It may be seen abnormalities on tree rings during the measurement like that false rings, missing rings, reaction wood. Like that situation, increment cores must be extracted from four different sides of each tree and be studied as more as on tree.
Visualizing Individual Tree Differences in Tree-Ring Studies

Directory of Open Access Journals (Sweden)

Mario Trouillier

2018-04-01

Full Text Available Averaging tree-ring measurements from multiple individuals is one of the most common procedures in dendrochronology. It serves to filter out noise from individual differences between trees, such as competition, height, and micro-site effects, which ideally results in a site chronology sensitive to regional scale factors such as climate. However, the climate sensitivity of individual trees can be modulated by factors like competition, height, and nitrogen deposition, calling attention to whether average chronologies adequately assess climatic growth-control. In this study, we demonstrate four simple but effective methods to visually assess differences between individual trees. Using individual tree climate-correlations we: (1 employed jitter plots with superimposed metadata to assess potential causes for these differences; (2 plotted the frequency distributions of climate correlations over time as heat maps; (3 mapped the spatial distribution of climate sensitivity over time to assess spatio-temporal dynamics; and (4 used t-distributed Stochastic Neighborhood Embedding (t-SNE to assess which trees were generally more similar in terms of their tree-ring pattern and their correlation with climate variables. This suite of exploratory methods can indicate if individuals in tree-ring datasets respond differently to climate variability, and therefore, should not solely be explored with climate correlations of the mean population chronology.
"Growing trees backwards": Description of a stand reconstruction model (P-53)

Science.gov (United States)

Jonathan D. Bakker; Andrew J. Sanchez Meador; Peter Z. Fule; David W. Huffman; Margaret M. Moore

2008-01-01

We describe an individual-tree model that uses contemporary measurements to "grow trees backward" and reconstruct past tree diameters and stand structure in ponderosa pine dominated stands of the Southwest. Model inputs are contemporary structural measurements of all snags, logs, stumps, and living trees, and radial growth measurements, if available. Key...
Nodal distances for rooted phylogenetic trees.

Science.gov (United States)

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).
Fault tree handbook

International Nuclear Information System (INIS)

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

1981-01-01

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

International Nuclear Information System (INIS)

Hordijk, Wim; Fontanari, Jose F; Stadler, Peter F

2003-01-01

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure - a barrier tree - the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their 'depth' in the tree
Modular tree automata

DEFF Research Database (Denmark)

Bahr, Patrick

2012-01-01

Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular...
Rate of tree carbon accumulation increases continuously with tree size.

Science.gov (United States)

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

2014-03-06

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

OpenAIRE

Prodinger, Helmut

2017-01-01

Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the respective representations a 2-partitions and trapezoidal words.
A support vector machine based test for incongruence between sets of trees in tree space

Science.gov (United States)

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The
Animals and trees: food for thought

Energy Technology Data Exchange (ETDEWEB)

Openshaw, K.

1979-01-01

In many areas of Africa, combining tree-growing with animal rearing is advantageous, as the trees provide shade, animal fodder and timber for fuel and building, while grazing animals reduce the fire hazard from ground vegetation and improve soil fertility through droppings. Acacia albida, Prosopis cineraria, P. chilensis, leucaena leucocephala and Ailanthus excelsa are discussed as promising fodder trees, and an appendix is included with notes on 21 other trees for fodder or the production of medicines.
Rate of tree carbon accumulation increases continuously with tree size

Science.gov (United States)

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

2014-01-01

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

KAUST Repository

Hussain, Shahid

2016-01-01

This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining

KAUST Repository

Hussain, Shahid

2016-07-10

This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

Science.gov (United States)

Vaughan, Timothy G

2017-08-01

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

Science.gov (United States)

Huang, Wen; Zhou, Guifang; Marchand, Melissa; Ash, Jeremy R; Morris, David; Van Dooren, Paul; Brown, Jeremy M; Gallivan, Kyle A; Wilgenbusch, Jim C

2016-12-01

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Is bark pH more important than tree species in determining the composition of nitrophytic or acidophytic lichen floras?

Energy Technology Data Exchange (ETDEWEB)

Spier, L. [Alterra, Landscape Center, POB 47, 6700 AA Wageningen (Netherlands); Dobben, H. van, E-mail: han.vandobben@wur.n [Alterra, Landscape Center, POB 47, 6700 AA Wageningen (Netherlands); Dort, K. van [Alterra, Landscape Center, POB 47, 6700 AA Wageningen (Netherlands)

2010-12-15

To study the pH preference of epiphytic lichens, the bark pH of Fraxinus, Tilia, Quercus and Ulmus trees in an urban environment was measured using a flat surface electrode. The total number of trees was 253. A survey was made of the lichens in a 40 x 40 cm quadrat surrounding the pH measurement point. Our data analysis using multivariate and univariate statistical techniques indicates that the tree species is the most important factor influencing lichen colonisation, and that bark pH alone is of less importance. We hypothesize that the changed pollution climate, with strong decreases in both sulphur dioxide and ammonia concentrations over the past two decades and a concomitant general increase in bark pH, has made epiphytes less sensitive to pH. - Tree species, rather than bark pH determines the occurrence of acidophytes and nitrophytes on trees.
Flowering Trees

Indian Academy of Sciences (India)

IAS Admin

Flowering Trees. Ailanthus excelsa Roxb. (INDIAN TREE OF. HEAVEN) of Simaroubaceae is a lofty tree with large pinnately compound alternate leaves, which are ... inflorescences, unisexual and greenish-yellow. Fruits are winged, wings many-nerved. Wood is used in making match sticks. 1. Male flower; 2. Female flower.
DLRS: gene tree evolution in light of a species tree.

Science.gov (United States)

Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

2012-11-15

PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).
Why do trees die? Characterizing the drivers of background tree mortality

Science.gov (United States)

Das, Adrian J.; Stephenson, Nathan L.; Davis, Kristin P.

2016-01-01

The drivers of background tree mortality rates—the typical low rates of tree mortality found in forests in the absence of acute stresses like drought—are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the “ambient” or “random” background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from
Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Gyrocarpus americanus Jacq. (Helicopter Tree) of Hernandiaceae is a moderate size deciduous tree that grows to about 12 m in height with a smooth, shining, greenish-white bark. The leaves are ovate, rarely irregularly ... flowers which are unpleasant smelling. Fruit is a woody nut with two long thin wings.
Cache-Oblivious Search Trees via Binary Trees of Small Height

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Jacob, R.

2002-01-01

We propose a version of cache oblivious search trees which is simpler than the previous proposal of Bender, Demaine and Farach-Colton and has the same complexity bounds. In particular, our data structure avoids the use of weight balanced B-trees, and can be implemented as just a single array......, and range queries in worst case O(logB n + k/B) memory transfers, where k is the size of the output.The basic idea of our data structure is to maintain a dynamic binary tree of height log n+O(1) using existing methods, embed this tree in a static binary tree, which in turn is embedded in an array in a cache...... oblivious fashion, using the van Emde Boas layout of Prokop.We also investigate the practicality of cache obliviousness in the area of search trees, by providing an empirical comparison of different methods for laying out a search tree in memory....
Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Boswellia serrata Roxb. ex Colebr. (Indian Frankincense tree) of Burseraceae is a large-sized deciduous tree that is native to India. Bark is thin, greenish-ash-coloured that exfoliates into smooth papery flakes. Stem exudes pinkish resin ... Fruit is a three-valved capsule. A green gum-resin exudes from the ...
Systolic trees and systolic language recognition by tree automata

Energy Technology Data Exchange (ETDEWEB)

Steinby, M

1983-01-01

K. Culik II, J. Gruska, A. Salomaa and D. Wood have studied the language recognition capabilities of certain types of systolically operating networks of processors (see research reports Cs-81-32, Cs-81-36 and Cs-82-01, Univ. of Waterloo, Ontario, Canada). In this paper, their model for systolic VLSI trees is formalised in terms of standard tree automaton theory, and the way in which some known facts about recognisable forests and tree transductions can be applied in VLSI tree theory is demonstrated. 13 references.
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

Science.gov (United States)

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree
Flowering Trees

Indian Academy of Sciences (India)

More Details Fulltext PDF. Volume 8 Issue 8 August 2003 pp 112-112 Flowering Trees. Zizyphus jujuba Lam. of Rhamnaceae · More Details Fulltext PDF. Volume 8 Issue 9 September 2003 pp 97-97 Flowering Trees. Moringa oleifera · More Details Fulltext PDF. Volume 8 Issue 10 October 2003 pp 100-100 Flowering Trees.
Embedding complete ternary tree in hypercubes using AVL trees

NARCIS (Netherlands)

S.A. Choudum; I. Raman (Indhumathi)

2008-01-01

htmlabstractA complete ternary tree is a tree in which every non-leaf vertex has exactly three children. We prove that a complete ternary tree of height h, TTh, is embeddable in a hypercube of dimension . This result coincides with the result of [2]. However, in this paper, the embedding utilizes
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Science.gov (United States)

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

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non
Trees are good, but…

Science.gov (United States)

E.G. McPherson; F. Ferrini

2010-01-01

We know that âtrees are good,â and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individualâs attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...
Detection of Citrus Trees from Uav Dsms

Science.gov (United States)

Ok, A. O.; Ozdarici-Ok, A.

2017-05-01

This paper presents an automated approach to detect citrus trees from digitals surface models (DSMs) as a single source. The DSMs in this study are generated from Unmanned Aerial Vehicles (UAVs), and the proposed approach first considers the symmetric nature of the citrus trees, and it computes the orientation-based radial symmetry in an efficient way. The approach also takes into account the local maxima (LM) information to verify the output of the radial symmetry. Our contributions in this study are twofold: (i) Such an integrated approach (symmetry + LM) has not been tested to detect (citrus) trees (in orchards), and (ii) the validity of such an integrated approach has not been experienced for an input, e.g. a single DSM. Experiments are performed on five test patches. The results reveal that our approach is capable of counting most of the citrus trees without manual intervention. Comparison to the state-of-the-art reveals that the proposed approach provides notable detection performance by providing the best balance between precision and recall measures.
Multiple-purpose trees for pastoral farming in New Zealand: with emphasis on tree legumes. [Lucerne Tree: Medick Tree

Energy Technology Data Exchange (ETDEWEB)

Davies, D J.G.; Macfarlane, R P

1979-01-01

The potential for soil conservation and agroforestry of several native and exotic legumes is discussed. Flowering period, chemical composition of leaves/pods, hardiness to frost and drought, timber value, forage potential for livestock and bees, ornamental value and other products are tabulated with information on up to 38 species. Two low-growing species that have proved useful for slope stabilization as well as forage are tree lucerne (Cytisus palmensis) and tree medick (Medicago arborea), the latter being shrubby and more suitable for cold districts. Gleditsia triacanthos is recommended as a shade and fodder tree for farm pasture.
Annual tree rings in Piptadenia gonoacantha (Mart. J.F.Macbr. in a restoration experiment in the Atlantic Forest: potential for dendroecological research

Directory of Open Access Journals (Sweden)

Arno Fritz das Neves Brandes

2016-01-01

Full Text Available ABSTRACT The tree Piptadenia gonoachantha is widely used in forestry and in forest restoration projects, which require methods for evaluating tree growth. Long-term studies are necessary to determine patterns and detect changes in species growth rhythms. Tree ring analysis provides a precise method for determining age and documenting long-term growth trends in tropical tree species. The present study evaluated the periodicity of tree ring formation and radial growth dynamics of P. gonoachantha from a population of known age in the Poço das Antas Biological Reserve. Two radii from six trees were sampled using non-destructive methods. Tree rings were counted and measured to estimate age and to calculate diametric increment. All samples had 16 tree rings, which matched the known plantation age and confirmed the annual formation of rings. The individuals sampled had a mean annual diametric increment of 9.5 mm / year. Results showed a trend towards decreasing growth rate with increasing age. Individuals of P. gonoachantha in Ombrophilous Dense Forest produce annual tree rings, which holds potential for future dendroecological studies.
Shedding light on tree growth : ring analysis of juvenile tropical trees

NARCIS (Netherlands)

Soliz Gamboa, C.C.

2010-01-01

In the understory of tropical forests light is believed to be the main limiting growth factor for the newly established trees. Trees growing in shade of the understory may experience periods of slow radial growth. It is expected that gaps created by tree or branch fall will provoke tree growth
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

Science.gov (United States)

2013-01-01

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

Science.gov (United States)

Nidzgorski, Daniel A; Hobbie, Sarah E

2016-07-01

Many urban waterways suffer from excess nitrogen (N) and phosphorus (P), feeding algal blooms, which cause lower water clarity and oxygen levels, bad odor and taste, and the loss of desirable species. Nutrient movement from land to water is likely to be influenced by urban vegetation, but there are few empirical studies addressing this. In this study, we examined whether or not urban trees can reduce nutrient leaching to groundwater, an important nutrient export pathway that has received less attention than stormwater. We characterized leaching beneath 33 trees of 14 species, and seven open turfgrass areas, across three city parks in Saint Paul, Minnesota, USA. We installed lysimeters at 60 cm depth to collect soil water approximately biweekly from July 2011 through October 2013, except during winter and drought periods, measured dissolved organic carbon (C), N, and P in soil water, and modeled water fluxes using the BROOK90 hydrologic model. We also measured soil nutrient pools (bulk C and N, KCl-extractable inorganic N, Brays-P), tree tissue nutrient concentrations (C, N, and P of green leaves, leaf litter, and roots), and canopy size parameters (leaf biomass, leaf area index) to explore correlations with nutrient leaching. Trees had similar or lower N leaching than turfgrass in 2012 but higher N leaching in 2013; trees reduced P leaching compared with turfgrass in both 2012 and 2013, with lower leaching under deciduous than evergreen trees. Scaling up our measurements to an urban subwatershed of the Mississippi River (~17 400 ha, containing ~1.5 million trees), we estimated that trees reduced P leaching to groundwater by 533 kg in 2012 (0.031 kg/ha or 3.1 kg/km 2 ) and 1201 kg in 2013 (0.069 kg/ha or 6.9 kg/km 2 ). Removing these same amounts of P using stormwater infrastructure would cost $2.2 million and $5.0 million per year (2012 and 2013 removal amounts, respectively). © 2016 by the Ecological Society of America.
Trees

Science.gov (United States)

Al-Khaja, Nawal

2007-01-01

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

Spectra of chemical trees

International Nuclear Information System (INIS)

Balasubramanian, K.

1982-01-01

A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees
MeshTree: A Delay optimised Overlay Multicast Tree Building Protocol

OpenAIRE

Tan, Su-Wei; Waters, A. Gill; Crawford, John

2005-01-01

We study decentralised low delay degree-constrained overlay multicast tree construction for single source real-time applications. This optimisation problem is NP-hard even if computed centrally. We identify two problems in traditional distributed solutions, namely the greedy problem and delay-cost trade-off. By offering solutions to these problems, we propose a new self-organising distributed tree building protocol called MeshTree. The main idea is to embed the delivery tree in a degree-bound...
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

Science.gov (United States)

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.
A tree girdling beetle in Korogwe District: its potential risk to ...

African Journals Online (AJOL)

A study was conducted to identify and assess damage of an insect pest girdling young Eucalypts in Korogwe Forest Plantation, Tanga. Purposive sampling was employed to establish 10 plots of 10m by 10m. A total of 90 trees were sampled. Insect pest specimens were collected and girdled trees counted in each plot. The
TreePlus: interactive exploration of networks with enhanced tree layouts.

Science.gov (United States)

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

2006-01-01

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

Science.gov (United States)

Górecki, Pawel; Eulenstein, Oliver

2014-01-01

Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.
Radiocarbon dating of a pine tree (Pinus densiflora) from Yeongwol, Korea

International Nuclear Information System (INIS)

Kim, C.H.; Lee, J.H.; Kang, J.; Song, S.; Yun, M.H.; Kim, J.C.

2015-01-01

We report the results of the dating of a pine tree (Pinus densiflora) from Yeongwol, Korea. The age of the tree was estimated to be in the range of hundreds of years, however, the tree had been broken by a strong wind in March 2010 and now only the stump of the tree is left. At the time of sampling in 2014, there were several decayed parts in the stump, so using the usual dendrochronological method (i.e. ring counting) for dating was difficult. However, we found a small wood sample with tree rings near the center of the stump that could be used for radiocarbon wiggle-match dating. Radiocarbon dates were determined using Accelerator mass spectrometry (AMS). The IntCal13 curve was used to calibrate the radiocarbon dates, and the wiggle matching technique was used to reduce the error of the calibrated ages. Based on the dating results, we suggest that the pine tree is approximately 300 years or older.
Radiocarbon dating of a pine tree (Pinus densiflora) from Yeongwol, Korea

Energy Technology Data Exchange (ETDEWEB)

Kim, C.H.; Lee, J.H.; Kang, J.; Song, S.; Yun, M.H. [AMS Lab., NCIRF, Seoul National University, Seoul 151-742 (Korea, Republic of); Kim, J.C. [Dept. of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of)

2015-10-15

We report the results of the dating of a pine tree (Pinus densiflora) from Yeongwol, Korea. The age of the tree was estimated to be in the range of hundreds of years, however, the tree had been broken by a strong wind in March 2010 and now only the stump of the tree is left. At the time of sampling in 2014, there were several decayed parts in the stump, so using the usual dendrochronological method (i.e. ring counting) for dating was difficult. However, we found a small wood sample with tree rings near the center of the stump that could be used for radiocarbon wiggle-match dating. Radiocarbon dates were determined using Accelerator mass spectrometry (AMS). The IntCal13 curve was used to calibrate the radiocarbon dates, and the wiggle matching technique was used to reduce the error of the calibrated ages. Based on the dating results, we suggest that the pine tree is approximately 300 years or older.
Radiocarbon dating of a pine tree (Pinus densiflora) from Yeongwol, Korea

Science.gov (United States)

Kim, C. H.; Lee, J. H.; Kang, J.; Song, S.; Yun, M. H.; Kim, J. C.

2015-10-01

We report the results of the dating of a pine tree (Pinus densiflora) from Yeongwol, Korea. The age of the tree was estimated to be in the range of hundreds of years, however, the tree had been broken by a strong wind in March 2010 and now only the stump of the tree is left. At the time of sampling in 2014, there were several decayed parts in the stump, so using the usual dendrochronological method (i.e. ring counting) for dating was difficult. However, we found a small wood sample with tree rings near the center of the stump that could be used for radiocarbon wiggle-match dating. Radiocarbon dates were determined using Accelerator mass spectrometry (AMS). The IntCal13 curve was used to calibrate the radiocarbon dates, and the wiggle matching technique was used to reduce the error of the calibrated ages. Based on the dating results, we suggest that the pine tree is approximately 300 years or older.
Maximum parsimony, substitution model, and probability phylogenetic trees.

Science.gov (United States)

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

2011-01-01

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

Science.gov (United States)

David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

2015-01-01

Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...
TreeFam: a curated database of phylogenetic trees of animal gene families

DEFF Research Database (Denmark)

Li, Heng; Coghlan, Avril; Ruan, Jue

2006-01-01

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively......, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins...
Tree-space statistics and approximations for large-scale analysis of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Owen, Megan; Petersen, Jens

2013-01-01

parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than...
Increased tree establishment in Lithuanian peat bogs--insights from field and remotely sensed approaches.

Science.gov (United States)

Edvardsson, Johannes; Šimanauskienė, Rasa; Taminskas, Julius; Baužienė, Ieva; Stoffel, Markus

2015-02-01

Over the past century an ongoing establishment of Scots pine (Pinus sylvestris L.), sometimes at accelerating rates, is noted at three studied Lithuanian peat bogs, namely Kerėplis, Rėkyva and Aukštumala, all representing different degrees of tree coverage and geographic settings. Present establishment rates seem to depend on tree density on the bog surface and are most significant at sparsely covered sites where about three-fourth of the trees have established since the mid-1990s, whereas the initial establishment in general was during the early to mid-19th century. Three methods were used to detect, compare and describe tree establishment: (1) tree counts in small plots, (2) dendrochronological dating of bog pine trees, and (3) interpretation of aerial photographs and historical maps of the study areas. In combination, the different approaches provide complimentary information but also weigh up each other's drawbacks. Tree counts in plots provided a reasonable overview of age class distributions and enabled capturing of the most recently established trees with ages less than 50 years. The dendrochronological analysis yielded accurate tree ages and a good temporal resolution of long-term changes. Tree establishment and spread interpreted from aerial photographs and historical maps provided a good overview of tree spread and total affected area. It also helped to verify the results obtained with the other methods and an upscaling of findings to the entire peat bogs. The ongoing spread of trees in predominantly undisturbed peat bogs is related to warmer and/or drier climatic conditions, and to a minor degree to land-use changes. Our results therefore provide valuable insights into vegetation changes in peat bogs, also with respect to bog response to ongoing and future climatic changes. Copyright © 2014 Elsevier B.V. All rights reserved.
Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

Science.gov (United States)

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.
Decision-Tree Program

Science.gov (United States)

Buntine, Wray

1994-01-01

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

Science.gov (United States)

Eilmann, Britta; Rigling, Andreas

2012-02-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.
Are trees long-lived?

Science.gov (United States)

Kevin T. Smith

2009-01-01

Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...
Measurement of radioactive contamination and decontamination on wooden exteriors and garden trees in Northern Fukushima Prefecture

International Nuclear Information System (INIS)

Sugiura, Hiroyuki; Kawano, Keisuke; Kayama, Yukihiko

2012-01-01

Measurement and decontamination of surface of trees and surrounding wooden structures contaminated by radioactive substance were studied in the gardens and public parks of Northern Fukushima Prefecture which experienced radioactive contamination due to the accident at the TEPCO's Fukushima Daiichi Nuclear Power Plant. The counts per minute (CPM) above the centre surface of wooden garden tables in open air were 1.5 times higher than those of garden benches and 9 times higher than that of a garden bench in the square gazebo. Decontamination of wooden garden benches by high-pressure washing was more effective than planing. The counts per minute (CPM) above the soil around garden trees increased by 1.2 times after high-pressure washing. Radioactivity counting rate did not decrease when the leaves fallen from zelocova trees were removed; however, they decreased by about half when soil cover was installed at the base of the trees. Clearly, the upper surfaces of garden trees and wooden surrounding structures were strongly contaminated by radioactive substances, and they should be decontaminated by high-pressure washing before removing the surface soil. (author)
Analysis of electrical tree propagation in XLPE power cable insulation

International Nuclear Information System (INIS)

Bao Minghui; Yin Xiaogen; He Junjia

2011-01-01

Electrical treeing is one of the major breakdown mechanisms for solid dielectrics subjected to high electrical stress. In this paper, the characteristics of electrical tree growth in XLPE samples have been investigated. XLPE samples are obtained from a commercial XLPE power cable, in which electrical trees have been grown from pin to plane in the frequency range of 4000-10,000 Hz, voltage range of 4-10 kV, and the distances between electrodes of 1 and 2 mm. Images of trees and their growing processes were taken by a CCD camera. The fractal dimensions of electric trees were obtained by using a simple box-counting technique. The results show that the tree growth rate and fractal dimension was bigger when the frequency or voltage was higher, or the distance between electrodes was smaller. Contrary to our expectation, it has been found that when the distance between electrodes changed from 1 to 2 mm, the required voltage of the similar electrical trees decreased only 1or 2 kV. In order to evaluate the difficulties of electrical tree propagation in different conditions, a simple energy threshold analysis method has been proposed. The threshold energy, which presents the minimum energy that a charge carrier in the well at the top of the tree should have to make the tree grow, has been computed considering the length of electrical tree, the fractal dimension, and the growth time. The computed results indicate that when one of the three parameters of voltage, frequency, and local electric field increase, the trends of energy threshold can be split into 3 regions.

Phosphorus absorption (32P) by apple trees under drip irrigation as influenced by the physical properties of the soil

International Nuclear Information System (INIS)

Habib, R.

1983-01-01

P absorption by apple tree roots (Golden delicious/M2) is studied using carrier-free 32 P. A qualitative model of the influence of some physical properties of the soil is proposed combining individual tree responses to 32 P injection. (orig.)
There's Life in Hazard Trees

Science.gov (United States)

Mary Torsello; Toni McLellan

The goals of hazard tree management programs are to maximize public safety and maintain a healthy sustainable tree resource. Although hazard tree management frequently targets removal of trees or parts of trees that attract wildlife, it can take into account a diversity of tree values. With just a little extra planning, hazard tree management can be highly beneficial...
Tree island pattern formation in the Florida Everglades

Science.gov (United States)

Carr, Joel; D'Odorico, P.; Engel, Victor C.; Redwine, Jed

2016-01-01

The Florida Everglades freshwater landscape exhibits a distribution of islands covered by woody vegetation and bordered by marshes and wet prairies. Known as “tree islands”, these ecogeomorphic features can be found in few other low gradient, nutrient limited freshwater wetlands. In the last few decades, however, a large percentage of tree islands have either shrank or disappeared in apparent response to altered water depths and other stressors associated with human impacts on the Everglades. Because the processes determining the formation and spatial organization of tree islands remain poorly understood, it is still unclear what controls the sensitivity of these landscapes to altered conditions. We hypothesize that positive feedbacks between woody plants and soil accretion are crucial to emergence and decline of tree islands. Likewise, positive feedbacks between phosphorus (P) accumulation and trees explain the P enrichment commonly observed in tree island soils. Here, we develop a spatially-explicit model of tree island formation and evolution, which accounts for these positive feedbacks (facilitation) as well as for long range competition and fire dynamics. It is found that tree island patterns form within a range of parameter values consistent with field data. Simulated impacts of reduced water levels, increased intensity of drought, and increased frequency of dry season/soil consuming fires on these feedback mechanisms result in the decline and disappearance of tree islands on the landscape.
Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Energy Technology Data Exchange (ETDEWEB)

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

Directory of Open Access Journals (Sweden)

Hughes Joseph

2011-05-01

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

Directory of Open Access Journals (Sweden)

Shu-Chuan Chen

Full Text Available 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.
On Determining if Tree-based Networks Contain Fixed Trees.

Science.gov (United States)

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

2016-05-01

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

Science.gov (United States)

Smith, Merryn G; Miller, Rebecca E; Arndt, Stefan K; Kasel, Sabine; Bennett, Lauren T

2018-04-01

Non-structural carbohydrates (NSCs) form a fundamental yet poorly quantified carbon pool in trees. Studies of NSC seasonality in forest trees have seldom measured whole-tree NSC stocks and allocation among organs, and are not representative of all tree functional types. Non-structural carbohydrate research has primarily focussed on broadleaf deciduous and coniferous evergreen trees with distinct growing seasons, while broadleaf evergreen trees remain under-studied despite their different growth phenology. We measured whole-tree NSC allocation and temporal variation in Eucalyptus obliqua L'Hér., a broadleaf evergreen tree species typically occurring in mixed-age temperate forests, which has year-round growth and the capacity to resprout after fire. Our overarching objective was to improve the empirical basis for understanding the functional importance of NSC allocation and stock changes at the tree- and organ-level in this tree functional type. Starch was the principal storage carbohydrate and was primarily stored in the stem and roots of young (14-year-old) trees rather than the lignotuber, which did not appear to be a specialized starch storage organ. Whole-tree NSC stocks were depleted during spring and summer due to significant decreases in starch mass in the roots and stem, seemingly to support root and crown growth but potentially exacerbated by water stress in summer. Seasonality of stem NSCs differed between young and mature trees, and was not synchronized with stem basal area increments in mature trees. Our results suggest that the relative magnitude of seasonal NSC stock changes could vary with tree growth stage, and that the main drivers of NSC fluctuations in broadleaf evergreen trees in temperate biomes could be periodic disturbances such as summer drought and fire, rather than growth phenology. These results have implications for understanding post-fire tree recovery via resprouting, and for incorporating NSC pools into carbon models of mixed
The effect of contaminated groundwater on tree growth: A tree-ring analysis

International Nuclear Information System (INIS)

LeBlanc, D.C.; Loehle, C.

1990-10-01

A study was conducted on the effect of contaminated groundwater seepage on tree growth downslope from F- and H-Area seepage basins of the Savannah River Site. Trees in wetlands along Four Mile Creek began to show localized stress and mortality in the late 1970s. Extreme winter temperatures and high rainfall were ruled out as potential causal factors of tree stress. Drought was shown to affect trees in both contaminated and uncontaminated zones, but trees in uncontaminated areas exhibit better recovery after drought than trees in contaminated areas. Pollution-mediated alteration of soil acidity and aluminum, sodium, and heavy metal concentrations likely acted to predispose trees to decline, with severe drought acting as the trigger for decline initiation and tree death. Thus, a moderate pollution loading, not sufficient to cause visible damage of itself, may create conditions in which sudden, severe decline could result from natural stresses. This mechanism of forest decline is common, and should be considered in evaluations of the impact of pollution on wetland forest systems. 28 refs., 4 figs., 6 tabs
SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Science.gov (United States)

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-09-30

Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.
D2-tree

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

2015-01-01

We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers...
Tree felling 2014

CERN Multimedia

2014-01-01

With a view to creating new landscapes and making its population of trees safer and healthier, this winter CERN will complete the tree-felling campaign started in 2010. Tree felling will take place between 15 and 22 November on the Swiss part of the Meyrin site. This work is being carried out above all for safety reasons. The trees to be cut down are at risk of falling as they are too old and too tall to withstand the wind. In addition, the roots of poplar trees are very powerful and spread widely, potentially damaging underground networks, pavements and roadways. Compensatory tree planting campaigns will take place in the future, subject to the availability of funding, with the aim of creating coherent landscapes while also respecting the functional constraints of the site. These matters are being considered in close collaboration with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP). GS-SE Group
Phylogenetic trees

OpenAIRE

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

2016-01-01

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.
The Effect of Nitrogen Form on pH and Petunia Growth in a WholeTree Substrate

Science.gov (United States)

The objective of our research was to investigate the effect of nitrogen form and proportion on peat-lite (PL) and WholeTree (WT) substrate pH and petunia growth. Chipped whole pine trees (consisting of needles, limbs, bark, wood and cones) were obtained from a commercial fuel wood chipping operation...
Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

Science.gov (United States)

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.
Dependencies in event trees analyzed by Petri nets

International Nuclear Information System (INIS)

Nývlt, Ondřej; Rausand, Marvin

2012-01-01

This paper discusses how non-marked Petri nets can be used to model and analyze event trees where the pivotal (branching) events are dependent and modeled by fault trees. The dependencies may, for example, be caused by shared utilities, shared components, or general common cause failures that are modeled by beta-factor models. These dependencies are cumbersome to take into account when using standard event-/fault tree modeling techniques, and may lead to significant errors in the calculated end-state probabilities of the event tree if they are not properly analyzed. A new approach is proposed in this paper, where the whole event tree is modeled by a non-marked Petri net and where P-invariants, representing the structural properties of the Petri net, are used to obtain the frequency of each end-state of the event tree with dependencies. The new approach is applied to a real example of an event tree analysis of the Strahov highway tunnel in Prague, Czech Republic, including two types of dependencies (shared Programmable Logic Controllers and Common Cause Failures). - Highlights: ► In this paper, we model and analyze event trees (ET) using Petri nets. ► The pivotal events of the modeled event trees are dependent (e.g., shared PLCs, CCF). ► A new method based on P-invariants to obtain probabilities of end states is proposed. ► Method is shown in the case study of the Stahov tunnel in the Czech Republic.
Covering tree with stars

DEFF Research Database (Denmark)

Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

2015-01-01

We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...
Trees in the city: valuing street trees in Portland, Oregon

Science.gov (United States)

G.H. Donovan; D.T. Butry

2010-01-01

We use a hedonic price model to simultaneously estimate the effects of street trees on the sales price and the time-on-market (TOM) of houses in Portland. Oregon. On average, street trees add $8,870 to sales price and reduce TOM by 1.7 days. In addition, we found that the benefits of street trees spill over to neighboring houses. Because the provision and maintenance...
Urban tree growth modeling

Science.gov (United States)

E. Gregory McPherson; Paula J. Peper

2012-01-01

This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...
Electron Tree

DEFF Research Database (Denmark)

Appelt, Ane L; Rønde, Heidi S

2013-01-01

The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

Classification and regression trees

CERN Document Server

Breiman, Leo; Olshen, Richard A; Stone, Charles J

1984-01-01

The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.
Low-level liquid scitillation counting for quantification of annual {sup 3}H and {sup 14}C concentrations in tree disks

Energy Technology Data Exchange (ETDEWEB)

Kopka, B [Goettingen Univ. (Germany). Isotopenlaboratorium fuer Biologische und Medizinische Forschung; Schikowski, J [Goettingen Univ. (Germany). Isotopenlaboratorium fuer Biologische und Medizinische Forschung; Porstendoerfer, J [Goettingen Univ. (Germany). Isotopenlaboratorium fuer Biologische und Medizinische Forschung

1997-03-01

The government of Schleswig Holstein funded a study to perform the retrospective determination of airborne {sup 3}H and {sup 14}C concentrations. It is well known, that in tree rings most of the hydrogen and cabron is fixed after insertion in the matrix of wood and that the radionuclide concentration correlates with former airborne activity concentrations. For the retrospective study wood disks of trees located in the region near the nuclear power plant of Kruemmel and control disks of unsuspected areas were selected. The hydrogen of the wood was transformed to water and the carbon to carbondioxide by classical oxidation processes (combustion in a furnace). The contents of {sup 3}H in the water and {sup 14}C of the carbondioxide (solved in scintillation liquid) were determined by liquid scintillation counting, using a low-level counter (type Quantulus 1220, Wallac). (orig.)
FB-Tree: A B+-Tree for Flash-Based SSDs

DEFF Research Database (Denmark)

Jørgensen, Martin V.; Rasmussen, René B.; Saltenis, Simonas

2011-01-01

Due to their many advantages, flash-based SSDs (Solid-State Drives) have become a mainstream alternative to magnetic disks for database servers. Nevertheless, database systems, designed and optimized for magnetic disks, still do not fully exploit all the benefits of the new technology. We propose....... As a consequence, the FB-tree outperforms a regular B+-tree in all scenarios tested. For instance, the throughput of a random workload of 75% updates increases by a factor of three using only two times the space of the B+-tree....
Benefit-based tree valuation

Science.gov (United States)

E.G. McPherson

2007-01-01

Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...
Fragmentation of random trees

International Nuclear Information System (INIS)

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→∞. We obtain analytically the size density ϕ s of trees of size s. The size density has power-law tail ϕ s ∼s −α with exponent α=1+(1/m). Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α 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. (paper)
FTAP, Minimal Cut Sets of Arbitrary Fault Trees. FRTPLT, Fault Tree Structure and Logical Gates Plot for Program FTAP. FRTGEN, Fault Trees by Sub-tree Generator from Parent Tree for Program FTAP

International Nuclear Information System (INIS)

Willie, Randall R.; Rabien, U.

1997-01-01

1 - Description of problem or function: FTAP is a general-purpose program for deriving minimal reliability cut and path set families from the fault tree for a complex system. The program has a number of useful features that make it well-suited to nearly all fault tree applications. An input fault tree may specify the system state as any logical function of subsystem or component state variables or complements of these variables; thus, for instance, 'exclusive-or' type relations may be formed. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. The program offers the flexibility of several distinct methods of generating cut set families. FTAP can also identify certain subsystems as system modules and provide a collection of minimal cut set families that essentially expresses the system state as a function of these module state variables. Another feature allows a useful subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily may consist of only those sets not containing more than some fixed number of elements or only those sets 'interesting' to the analyst in some special sense. Finally, the analyst can modify the input fault tree in various ways by declaring state variables identically true or false. 2 - Method of solution: Fault tree methods are based on the observation that the system state, either working or failed, can usually be expressed as a Boolean relation between states of several large, readily identifiable subsystems. The state of each subsystem in turn depends on states of simpler subsystems and components which compose it, so that the state of the system itself is determined by a hierarchy of logical relationships between states of subsystems. A fault tree is a graphical representation of these relationships. 3 - Restrictions on the
Winter Birch Trees

Science.gov (United States)

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

Science.gov (United States)

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 or...
How many trees are enough? Tree death and the urban canopy

Science.gov (United States)

Lara A. Roman

2014-01-01

Massive city tree planting campaigns have invigorated the urban forestry movement, and engaged politicians, planners, and the public in urban greening. Million tree initiatives have been launched in Los Angeles, CA; Denver, CO; New York City, NY; Philadelphia, PA, and other cities. Sacramento, CA even has a five million tree program. These...
Keeping trees as assets

Science.gov (United States)

Kevin T. Smith

2009-01-01

Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...
Visualization of Uncertain Contour Trees

DEFF Research Database (Denmark)

Kraus, Martin

2010-01-01

Contour trees can represent the topology of large volume data sets in a relatively compact, discrete data structure. However, the resulting trees often contain many thousands of nodes; thus, many graph drawing techniques fail to produce satisfactory results. Therefore, several visualization methods...... were proposed recently for the visualization of contour trees. Unfortunately, none of these techniques is able to handle uncertain contour trees although any uncertainty of the volume data inevitably results in partially uncertain contour trees. In this work, we visualize uncertain contour trees...... by combining the contour trees of two morphologically filtered versions of a volume data set, which represent the range of uncertainty. These two contour trees are combined and visualized within a single image such that a range of potential contour trees is represented by the resulting visualization. Thus...
Safety validation of decision trees for hepatocellular carcinoma.

Science.gov (United States)

Wang, Xian-Qiang; Liu, Zhe; Lv, Wen-Ping; Luo, Ying; Yang, Guang-Yun; Li, Chong-Hui; Meng, Xiang-Fei; Liu, Yang; Xu, Ke-Sen; Dong, Jia-Hong

2015-08-21

To evaluate a different decision tree for safe liver resection and verify its efficiency. A total of 2457 patients underwent hepatic resection between January 2004 and December 2010 at the Chinese PLA General Hospital, and 634 hepatocellular carcinoma (HCC) patients were eligible for the final analyses. Post-hepatectomy liver failure (PHLF) was identified by the association of prothrombin time 50 μmol/L (the "50-50" criteria), which were assessed at day 5 postoperatively or later. The Swiss-Clavien decision tree, Tokyo University-Makuuchi decision tree, and Chinese consensus decision tree were adopted to divide patients into two groups based on those decision trees in sequence, and the PHLF rates were recorded. The overall mortality and PHLF rate were 0.16% and 3.0%. A total of 19 patients experienced PHLF. The numbers of patients to whom the Swiss-Clavien, Tokyo University-Makuuchi, and Chinese consensus decision trees were applied were 581, 573, and 622, and the PHLF rates were 2.75%, 2.62%, and 2.73%, respectively. Significantly more cases satisfied the Chinese consensus decision tree than the Swiss-Clavien decision tree and Tokyo University-Makuuchi decision tree (P decision trees. The Chinese consensus decision tree expands the indications for hepatic resection for HCC patients and does not increase the PHLF rate compared to the Swiss-Clavien and Tokyo University-Makuuchi decision trees. It would be a safe and effective algorithm for hepatectomy in patients with hepatocellular carcinoma.
Forest FIRE and FIRE wood : tools for tree automata and tree algorithms

NARCIS (Netherlands)

Cleophas, L.G.W.A.; Piskorski, J.; Watson, B.W.; Yli-Jyrä, A.

2009-01-01

Pattern matching, acceptance, and parsing algorithms on node-labeled, ordered, ranked trees ('tree algorithms') are important for applications such as instruction selection and tree transformation/term rewriting. Many such algorithms have been developed. They often are based on results from such
Monitoring Million Trees LA: Tree performance during the early years and future benefits

Science.gov (United States)

E. Gregory McPherson

2014-01-01

Million Trees LA (MTLA) is one of several large-scale mayoral tree planting initiatives striving to create more livable cities through urban forestry. This study combined field sampling of tree survival and growth with numerical modeling of future benefits to assess performance of MTLA plantings. From 2006 to 2010 MTLA planted a diverse mix of 91,786 trees....
Skewed Binary Search Trees

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Moruz, Gabriel

2006-01-01

It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...
The ghosts of trees past: savanna trees create enduring legacies in plant species composition.

Science.gov (United States)

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.
Barking up the wrong tree: injuries due to falls from trees in Solomon Islands.

Science.gov (United States)

Negin, Joel; Vizintin, Pavle; Houasia, Patrick; Martiniuk, Alexandra L C

2014-12-11

To investigate tree-related injuries in Solomon Islands by the types of trees involved, who is affected and the types of injuries caused. Descriptive case series of all cases of injuries related to trees presenting to the National Referral Hospital in Honiara from 1994 to 2011. Data were collected by the attending clinician using a Trauma Epidemiology form, which provides information on age, sex, cause of injury and type of fracture. Number of injuries by tree type, sex and age. Of the 7651 injuries in the database, 1107 (14%) were caused by falls from trees. Falls from coconut trees led to the highest number of injuries, followed by falls from mango, guava, apple and nut trees. Overall, 85% of injuries occurred in individuals aged trees, 77% of patients were aged tree types. Overall, 71% of injuries occurred among males. Of all injuries, 92% were fractures, 3% were dislocations and 5% were non-fracture, non-dislocation injuries. The arm (including wrist, elbow and hand) was the most common location of injury across all tree types. Distal radius fractures in the forearm were particularly common, as were ulna fractures. While mangos and guavas are undeniably delicious, the quest for their flesh can be hazardous. Children will always climb trees, but the search for food among children in lower-income settings may lead to higher rates of injury.
Recursive Trees for Practical ORAM

Directory of Open Access Journals (Sweden)

Moataz Tarik

2015-06-01

Full Text Available We present a new, general data structure that reduces the communication cost of recent tree-based ORAMs. Contrary to ORAM trees with constant height and path lengths, our new construction r-ORAM allows for trees with varying shorter path length. Accessing an element in the ORAM tree results in different communication costs depending on the location of the element. The main idea behind r-ORAM is a recursive ORAM tree structure, where nodes in the tree are roots of other trees. While this approach results in a worst-case access cost (tree height at most as any recent tree-based ORAM, we show that the average cost saving is around 35% for recent binary tree ORAMs. Besides reducing communication cost, r-ORAM also reduces storage overhead on the server by 4% to 20% depending on the ORAM’s client memory type. To prove r-ORAM’s soundness, we conduct a detailed overflow analysis. r-ORAM’s recursive approach is general in that it can be applied to all recent tree ORAMs, both constant and poly-log client memory ORAMs. Finally, we implement and benchmark r-ORAM in a practical setting to back up our theoretical claims.
A parallel buffer tree

DEFF Research Database (Denmark)

Sitchinava, Nodar; Zeh, Norbert

2012-01-01

We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number of...... in the optimal OhOf(psortN + K/PB) parallel I/O complexity, where K is the size of the output reported in the process and psortN is the parallel I/O complexity of sorting N elements using P processors....
Tree Transduction Tools for Cdec

Directory of Open Access Journals (Sweden)

Austin Matthews

2014-09-01

Full Text Available We describe a collection of open source tools for learning tree-to-string and tree-to-tree transducers and the extensions to the cdec decoder that enable translation with these. Our modular, easy-to-extend tools extract rules from trees or forests aligned to strings and trees subject to different structural constraints. A fast, multithreaded implementation of the Cohn and Blunsom (2009 model for extracting compact tree-to-string rules is also included. The implementation of the tree composition algorithm used by cdec is described, and translation quality and decoding time results are presented. Our experimental results add to the body of evidence suggesting that tree transducers are a compelling option for translation, particularly when decoding speed and translation model size are important.

City of Pittsburgh Trees

Data.gov (United States)

Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...
Flowering Trees

Indian Academy of Sciences (India)

user

Flowering Trees. Gliricidia sepium(Jacq.) Kunta ex Walp. (Quickstick) of Fabaceae is a small deciduous tree with. Pinnately compound leaves. Flower are prroduced in large number in early summer on terminal racemes. They are attractive, pinkish-white and typically like bean flowers. Fruit is a few-seeded flat pod.
Drawing Trees

DEFF Research Database (Denmark)

Halkjær From, Andreas; Schlichtkrull, Anders; Villadsen, Jørgen

2018-01-01

We formally prove in Isabelle/HOL two properties of an algorithm for laying out trees visually. The first property states that removing layout annotations recovers the original tree. The second property states that nodes are placed at least a unit of distance apart. We have yet to formalize three...
Interspecific variation in tree seedlings establishment in canopy gaps in relation to tree density

Energy Technology Data Exchange (ETDEWEB)

Reader, R.J.; Bonser, S.P.; Duralia, T.E.; Bricker, B.D. [Guelph Univ., ON (Canada). Dept. of Botany

1995-10-01

We tested whether interspecific variation in tree seedling establishment in canopy gaps was significantly related to interspecific variation in tree density, for seven deciduous forest tree species (Quercus alba, Hamamelis virginiana, Acer rubrum, Sassafras albidum, Quercus rubra, Prunus serotina, Ostrya virginiana). For each species, seedling establishment was calculated as the difference in seedling density before experimental gap creation versus three years after gap creation. In each of the six experimentally-created gap types (33% or 66% removal of tree basal area from 0.01ha, 0.05ha or 0.20ha patches), differences in seedling establishment among species were significantly related to differences in their density in the tree canopy. A regression model with log{sub e} tree density as the independent variable accounted for between 93% and 98% of interspecific variation in seedling establishment. Our results provide empirical support for models of tree dynamics in gaps that assume seedling establishment depends on canopy tree density. 17 refs, 1 fig, 3 tabs
Phylogenetic trees in bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Burr, Tom L [Los Alamos National Laboratory

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

OpenAIRE

N. Price, Morgan

2009-01-01

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 i...
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

OpenAIRE

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

2009-01-01

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 in...
Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.
On Tree-Based Phylogenetic Networks.

Science.gov (United States)

Zhang, Louxin

2016-07-01

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

Science.gov (United States)

Colijn, C; Plazzotta, G

2018-01-01

The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
Visualizing phylogenetic tree landscapes.

Science.gov (United States)

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D
Human decision error (HUMDEE) trees

International Nuclear Information System (INIS)

Ostrom, L.T.

1993-01-01

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
Tree felling: a necessary evil

CERN Multimedia

CERN Bulletin

2013-01-01

CERN started a campaign of tree felling in 2010 for safety reasons, and it will continue this year in various parts of the Meyrin site. As in previous years, the trees cut down in 2013 will be recycled and some will be replaced. Diseased tree that had to be cut down on the Meyrin site. In association with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP), CERN commissioned the Geneva school of landscaping, engineering and architecture (Haute école du paysage, d’ingénierie et d’architecture, HEPIA) to compile an inventory of the trees on the Meyrin site. In total, 1285 trees (excluding poplars) were recorded. 75.5% of these trees were declared to be in a good state of health (i.e. 971 trees), 21.5% in a moderate state of health (276 trees) and 3% in a poor state of health (38 trees). As for the poplars, the 236 specimens recorded on the Meyrin site were judged to be too old, to...
Per tree estimates with n-tree distance sampling: an application to increment core data

Science.gov (United States)

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

Science.gov (United States)

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.
Maximum Gene-Support Tree

Directory of Open Access Journals (Sweden)

Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the ﬁnding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reﬂects the phylogenetic relationship among species in comparison.
Tree Rings: Timekeepers of the Past.

Science.gov (United States)

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…
Flowering Trees

Indian Academy of Sciences (India)

Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February. Fruit is ...
Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Cerbera manghasL. (SEA MANGO) of Apocynaceae is a medium-sized evergreen coastal tree with milky latex. The bark is grey-brown, thick and ... Fruit is large. (5–10 cm long), oval containing two flattened seeds and resembles a mango, hence the name Mangas or. Manghas. Leaves and fruits contain ...
Talking Trees

Science.gov (United States)

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…

Is Tree Species Diversity or Species Identity the More Important Driver of Soil Carbon Stocks, C/N Ratio, and pH?

DEFF Research Database (Denmark)

Dawud, Seid Muhie; Raulund-Rasmussen, Karsten; Domisch, Timo

2016-01-01

We explored tree species diversity effects on soil C stock, C/N ratio, and pH as compared with effects of tree species identity. We sampled forest floors and mineral soil (0–40 cm) in a diversity gradient of 1–5 tree species composed of conifers and broadleaves in Białowieża Forest, Poland...... mechanism for higher root carbon input and in turn a deeper distribution of C in diverse forests. Diversity and identity affected soil pH in topsoil with positive and negative impacts, respectively. More diverse forests would lead to higher soil nutrient status as reflected by higher topsoil p......H, but there was a slight negative effect on N status as indicated by higher C/N ratios in the deeper layers. We conclude that tree species diversity increases soil C stocks and nutrient status to some extent, but tree species identity is a stronger driver of the studied soil properties, particularly in the topsoil....
ELB-trees an efficient and lock-free B-tree derivative

DEFF Research Database (Denmark)

Bonnichsen, Lars Frydendal; Karlsson, Sven; Probst, Christian W.

2013-01-01

overhead. All lock-free data structures are based on simple atomic operations that, though supported by modern processors, are expensive in execution time. We present a lock-free data structure, ELB-trees, which under certain assumptions can be used as multimaps as well as priority queues. Specifically...... it cannot store duplicate key-value pairs, and it is not linearizable. Compared to existing data structures, ELB-trees require fewer atomic operations leading to improved performance. We measure the parallel performance of ELB-trees using a set of benchmarks and observe that ELB-trees are up to almost 30......As computer systems scale in the number of processors, scalable data structures with good parallel performance become increasingly important. Lock-free data structures promise such improved parallel performance at the expense of higher algorithmic complexity and higher sequential execution time...
Atlas of United States Trees, Volume 2: Alaska Trees and Common Shrubs.

Science.gov (United States)

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…
The valuative tree

CERN Document Server

Favre, Charles

2004-01-01

This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.
Understanding recruitment failure in tropical tree species: Insights from a tree ring study

NARCIS (Netherlands)

Vlam, M.; Baker, P.J.; Bunyavejchewin, S.; Mohren, G.M.J.; Zuidema, P.A.

2014-01-01

Many tropical tree species have population structures that exhibit strong recruitment failure. While the presence of adult trees indicates that appropriate regeneration conditions occurred in the past, it is often unclear why small individuals are absent. Knowing how, when and where these tree
Attack Trees with Sequential Conjunction

NARCIS (Netherlands)

Jhawar, Ravi; Kordy, Barbara; Mauw, Sjouke; Radomirović, Sasa; Trujillo-Rasua, Rolando

2015-01-01

We provide the first formal foundation of SAND attack trees which are a popular extension of the well-known attack trees. The SAND at- tack tree formalism increases the expressivity of attack trees by intro- ducing the sequential conjunctive operator SAND. This operator enables the modeling of
Tree Size Comparison of Some Important Street Trees Growing at ...

African Journals Online (AJOL)

PROF HORSFALL

More research is needed on these trees for healthy environment of city. The present ..... use and CO2 emissions from power plants. Environ. Poll. .... Anna. Bot., 65:567-574. Kozlowski, T.T., 1971. Growth and Development of. Trees. Vol. 1.
Flowering Trees

Indian Academy of Sciences (India)

medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends. Flowers are large, white, attractive, and fragrant. Corolla is funnel-shaped. Fruit is an ...
Flowering Trees

Indian Academy of Sciences (India)

Srimath

Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.
Mathematical foundations of event trees

International Nuclear Information System (INIS)

Papazoglou, Ioannis A.

1998-01-01

A mathematical foundation from first principles of event trees is presented. The main objective of this formulation is to offer a formal basis for developing automated computer assisted construction techniques for event trees. The mathematical theory of event trees is based on the correspondence between the paths of the tree and the elements of the outcome space of a joint event. The concept of a basic cylinder set is introduced to describe joint event outcomes conditional on specific outcomes of basic events or unconditional on the outcome of basic events. The concept of outcome space partition is used to describe the minimum amount of information intended to be preserved by the event tree representation. These concepts form the basis for an algorithm for systematic search for and generation of the most compact (reduced) form of an event tree consistent with the minimum amount of information the tree should preserve. This mathematical foundation allows for the development of techniques for automated generation of event trees corresponding to joint events which are formally described through other types of graphical models. Such a technique has been developed for complex systems described by functional blocks and it is reported elsewhere. On the quantification issue of event trees, a formal definition of a probability space corresponding to the event tree outcomes is provided. Finally, a short discussion is offered on the relationship of the presented mathematical theory with the more general use of event trees in reliability analysis of dynamic systems
Stand conditions and tree characteristics affect quality of longleaf pine for red-cockaded woodpecker cavity trees

Science.gov (United States)

W.G. Ross; D.L. Kulhavy; R.N. Conner

1997-01-01

We measured resin flow of longleaf (Pinus palustris Mill.) pines in red-cockaded woodpecker (Picoides borealis Vieillot) clusters in the Angelina National Forest in Texas, and the Apalachicola National Forest in Florida. Sample trees were categorized as active cavity trees, inactive cavity trees and control trees. Sample trees were further...
Making CSB + -Trees Processor Conscious

DEFF Research Database (Denmark)

Samuel, Michael; Pedersen, Anders Uhl; Bonnet, Philippe

2005-01-01

of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose......Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... a systematic method for adapting CSB+-tree to new platforms. This work is a first step towards integrating CSB+-tree in MySQL’s heap storage manager....
Tree architecture and life-history strategies across 200 co-occurring tropical tree species

NARCIS (Netherlands)

Iida, Y.; Kohyama, T.S.; Kubo, T.; Kassim, A.R.; Poorter, L.; Sterck, F.J.; Potts, M.D.

2011-01-01

1. Tree architecture is thought to allow species to partition horizontal and vertical light gradients in the forest canopy. Tree architecture is closely related to light capture, carbon gain and the efficiency with which trees reach the canopy. Previous studies that investigated how light gradients
Total well dominated trees

DEFF Research Database (Denmark)

Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....
Reconstruction of tritium release history from contaminated groundwater using tree ring analysis

International Nuclear Information System (INIS)

Kalin, R.M.; Murphy, C.E. Jr.; Hall, G.

1995-01-01

The history of tritium releases to the groundwater from buried waste was reconstructed through dendrochronology. Wood from dated tree rings was sectioned from a cross-section of a tree that was thought to tap the groundwater. Cellulose was chemically separated from the wood. The cellulose was combusted and the water of combustion collected for liquid scintillation counting. The tritium concentration in the rings rose rapidly after 1972 which was prior to the first measurements made in this area. Trends in the tritium concentration of water outcropping to the surface are similar to the trends in tritium concentration in tree rings. 14 refs., 3 figs
New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning.

Science.gov (United States)

Malhi, Yadvinder; Jackson, Tobias; Patrick Bentley, Lisa; Lau, Alvaro; Shenkin, Alexander; Herold, Martin; Calders, Kim; Bartholomeus, Harm; Disney, Mathias I

2018-04-06

Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.
Tree manipulation experiment

Science.gov (United States)

Nishina, K.; Takenaka, C.; Ishizuka, S.; Hashimoto, S.; Yagai, Y.

2012-12-01

Some forest operations such as thinning and harvesting management could cause changes in N cycling and N2O emission from soils, since thinning and harvesting managements are accompanied with changes in aboveground environments such as an increase of slash falling and solar radiation on the forest floor. However, a considerable uncertainty exists in effects of thinning and harvesting on N2O fluxes regarding changes in belowground environments by cutting trees. To focus on the effect of changes in belowground environments on the N2O emissions from soils, we conducted a tree manipulation experiment in Japanese cedar (Cryptomeria japonica) stand without soil compaction and slash falling near the chambers and measured N2O flux at 50 cm and 150 cm distances from the tree trunk (stump) before and after cutting. We targeted 5 trees for the manipulation and established the measurement chambers to the 4 directions around each targeted tree relative to upper slope (upper, left, right, lower positions). We evaluated the effect of logging on the emission by using hierarchical Bayesian model. HB model can evaluate the variability in observed data and their uncertainties in the estimation with various probability distributions. Moreover, the HB model can easily accommodate the non-linear relationship among the N2O emissions and the environmental factors, and explicitly take non-independent data (nested structure of data) for the estimation into account by using random effects in the model. Our results showed tree cutting stimulated N2O emission from soils, and also that the increase of N2O flux depended on the distance from the trunk (stump): the increase of N2O flux at 50 cm from the trunk (stump) was greater than that of 150 cm from the trunk. The posterior simulation of the HB model indicated that the stimulation of N2O emission by tree cut- ting could reach up to 200 cm in our experimental plot. By tree cutting, the estimated N2O emission at 0-40 cm from the trunk doubled
The Re-Think Tree.

Science.gov (United States)

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)
Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

Science.gov (United States)

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.
Coded Splitting Tree Protocols

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

2013-01-01

This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

Estimation of the number of aphids carrying Citrus tristeza virus that visit adult citrus trees.

Science.gov (United States)

Marroquín, Carlos; Olmos, Antonio; Teresa Gorris, María; Bertolini, Edson; Carmen Martínez, M; Carbonell, Emilio A; Hermoso de Mendoza, Alfonso; Cambra, Mariano

2004-03-01

Aphid species were counted on citrus trees in orchards in Valencia, Spain, in the spring and autumn of 1997, 1998 and 1999. Moericke yellow water traps, the 'sticky shoot' method and counts of established colonies were used in extensive surveys in which 29,502 aphids were recorded and identified. Aphis spiraecola and Aphis gossypii were the most abundant aphid species. The numbers of aphid species landing on mature trees of grapefruit, sweet orange, lemon and clementine and satsuma mandarins, were estimated by counting the numbers of young shoots/tree and aphids trapped on sticky shoots. The proportions of the different aphid species captured were: A. gossypii (53%), A. spiraecola (32%), Toxoptera aurantii (11%), Myzus persicae (1%), Aphis craccivora (1%) and other species (2%). Clementine was the most visited species with 266,700 aphids landing/tree in spring 2000, followed by lemon (147,000), sweet orange (129,150), grapefruit (103,200), and satsuma (92,400). The numbers and relative percentages of aphids carrying Citrus tristeza virus (CTV) were assessed by nested RT-PCR in single closed tubes and analysed by extraction of RNA-CTV targets from trapped aphids. An average of 37,190 CTV-carrying aphids visited each tree in spring 2000 (29 per shoot). The percentage detection of viral RNA in the aphid species that landed were 27% for A. gossypii, 23% for A. spiraecola and 19% for T. aurantii. This high incidence of aphids carrying CTV is consistent with the high prevalence and rapid spread of CTV in sweet orange, clementine, and satsuma mandarins in recent years in the region. The infection rate was proportional to the number of aphids landing/tree.
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf.

Science.gov (United States)

Cardona, Gabriel; Mir, Arnau; Rosselló, Francesc; Rotger, Lucía; Sánchez, David

2013-01-16

Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to measure quantitatively the difference between a pair of phylogenetic trees by first encoding them by means of their half-matrices of cophenetic values, and then comparing these matrices. This idea has been used several times since then to define dissimilarity measures between phylogenetic trees but, to our knowledge, no proper metric on weighted phylogenetic trees with nested taxa based on this idea has been formally defined and studied yet. Actually, the cophenetic values of pairs of different taxa alone are not enough to single out phylogenetic trees with weighted arcs or nested taxa. For every (rooted) phylogenetic tree T, let its cophenetic vectorφ(T) consist of all pairs of cophenetic values between pairs of taxa in T and all depths of taxa in T. It turns out that these cophenetic vectors single out weighted phylogenetic trees with nested taxa. We then define a family of cophenetic metrics dφ,p by comparing these cophenetic vectors by means of Lp norms, and we study, either analytically or numerically, some of their basic properties: neighbors, diameter, distribution, and their rank correlation with each other and with other metrics. The cophenetic metrics can be safely used on weighted phylogenetic trees with nested taxa and no restriction on degrees, and they can be computed in O(n2) time, where n stands for the number of taxa. The metrics dφ,1 and dφ,2 have positive skewed distributions, and they show a low rank correlation with the Robinson-Foulds metric and the nodal metrics, and a very high correlation with each other and with the splitted nodal metrics. The diameter of dφ,p, for p⩾1 , is in O(n(p+2)/p), and thus for low p they are more discriminative, having a wider range of values.
Drawing Contour Trees in the Plane.

Science.gov (United States)

Heine, C; Schneider, D; Carr, Hamish; Scheuermann, G

2011-11-01

The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Applying known techniques to convey this information proves hard and sometimes even impossible. We present several adaptions of popular graph drawing approaches to the problem of contour tree drawing and evaluate them. We identify five esthetic criteria for drawing contour trees and present a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria. Our implementation is fast and effective for contour tree sizes usually used in interactive systems (around 100 branches) and also produces readable pictures for larger trees, as is shown for an 800 branch example.
Minnesota's Forest Trees. Revised.

Science.gov (United States)

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…
Covering tree with stars

DEFF Research Database (Denmark)

Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

2013-01-01

We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting ...
DIF Trees: Using Classification Trees to Detect Differential Item Functioning

Science.gov (United States)

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…
Picking a tree: habitat use by the tree agama, Acanthocercus ...

African Journals Online (AJOL)

We studied tree agama (Acanthocercus a. atricollis) habitat use in the Magaliesberg mountain range in northern South Africa using sightings of marked individuals, and in a few cases, radio-telemetry. Acanthocercus a. atricollis preferentially selected thorn trees (46%; Acacia karroo), followed by common sugarbush (10%; ...
Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.

Science.gov (United States)

Blair, Jaime E; Coffey, Michael D; Martin, Frank N

2012-01-01

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.
Street trees reduce the negative effects of urbanization on birds.

Science.gov (United States)

Pena, João Carlos de Castro; Martello, Felipe; Ribeiro, Milton Cezar; Armitage, Richard A; Young, Robert J; Rodrigues, Marcos

2017-01-01

The effects of streets on biodiversity is an important aspect of urban ecology, but it has been neglected worldwide. Several vegetation attributes (e.g. street tree density and diversity) have important effects on biodiversity and ecological processes. In this study, we evaluated the influences of urban vegetation-represented by characteristics of street trees (canopy size, proportion of native tree species and tree species richness)-and characteristics of the landscape (distance to parks and vegetation quantity), and human impacts (human population size and exposure to noise) on taxonomic data and functional diversity indices of the bird community inhabiting streets. The study area was the southern region of Belo Horizonte (Minas Gerais, Brazil), a largely urbanized city in the understudied Neotropical region. Bird data were collected on 60 point count locations distributed across the streets of the landscape. We used a series of competing GLM models (using Akaike's information criterion for small sample sizes) to assess the relative contribution of the different sets of variables to explain the observed patterns. Seventy-three bird species were observed exploiting the streets: native species were the most abundant and frequent throughout this landscape. The bird community's functional richness and Rao's Quadratic Entropy presented values lower than 0.5. Therefore, this landscape was favoring few functional traits. Exposure to noise was the most limiting factor for this bird community. However, the average size of arboreal patches and, especially the characteristics of street trees, were able to reduce the negative effects of noise on the bird community. These results show the importance of adequately planning the urban afforestation process: increasing tree species richness, preserving large trees and planting more native trees species in the streets are management practices that will increase bird species richness, abundance and community functional aspects and
Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

Science.gov (United States)

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

2012-02-01

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

Directory of Open Access Journals (Sweden)

J. Bussières

2008-12-01

Full Text Available Four major tree-planting trials on cut-over peatlands in eastern Canada were surveyed in 2002, in order to evaluate the potential use of trees in rehabilitation following horticultural peat extraction. At one of the sites, an experiment to determine the appropriate fertilisation rate for trees planted on cut-over peatlands was also conducted over several years. Tree performance was assessed by measuring survival, total height and annual growth of red maple (Acer rubrum L., tamarack (Larix laricina (Du Roi Koch., black spruce (Picea mariana (Mill. B.S.P., jack pine (Pinus banksiana Lamb. and hybrid poplar (Populus spp.. Establishment and growth of tamarack and black spruce in cut-over peatlands showed good potential when compared to performance in conventional forestry plantations. Red maple and jack pine gave poor productivity but promising survival, whilst hybrid poplar plantings failed. Adding nutrients was essential for growth but dosages above 122.5 g of 3.4N-8.3P-24.2K per tree gave no further improvement. Therefore, several different tree species can be planted to reclaim cut-over peatlands in eastern Canada, so long as the appropriate species are chosen and nutrients are provided.
The national tree-list layer

Science.gov (United States)

Stacy A. Drury; Jason M. Herynk

2011-01-01

The National Tree-List Layer (NTLL) project used LANDFIRE map products to produce the first national tree-list map layer that represents tree populations at stand and regional levels. The NTLL was produced in a short time frame to address the needs of Fire and Aviation Management for a map layer that could be used as input for simulating fire-caused tree mortality...
Beyond Tree Throw: Wind, Water, Rock and the Mechanics of Tree-Driven Bedrock Physical Weathering

Science.gov (United States)

Marshall, J. A.; Anderson, R. S.; Dawson, T. E.; Dietrich, W. E.; Minear, J. T.

2017-12-01

Tree throw is often invoked as the dominant process in converting bedrock to soil and thus helping to build the Critical Zone (CZ). In addition, observations of tree roots lifting sidewalk slabs, occupying cracks, and prying slabs of rock from cliff faces have led to a general belief in the power of plant growth forces. These common observations have led to conceptual models with trees at the center of the soil genesis process. This is despite the observation that tree throw is rare in many forested settings, and a dearth of field measurements that quantify the magnitude of growth forces. While few trees blow down, every tree grows roots, inserting many tens of percent of its mass below ground. Yet we lack data quantifying the role of trees in both damaging bedrock and detaching it (and thus producing soil). By combing force measurements at the tree-bedrock interface with precipitation, solar radiation, wind speed, and wind-driven tree sway data we quantified the magnitude and frequency of tree-driven soil-production mechanisms from two contrasting climatic and lithologic regimes (Boulder and Eel Creek CZ Observatories). Preliminary data suggests that in settings with relatively thin soils, trees can damage and detach rock due to diurnal fluctuations, wind response and rainfall events. Surprisingly, our data suggests that forces from roots and trunks growing against bedrock are insufficient to pry rock apart or damage bedrock although much more work is needed in this area. The frequency, magnitude and style of wind-driven tree forces at the bedrock interface varies considerably from one to another species. This suggests that tree properties such as mass, elasticity, stiffness and branch structure determine whether trees respond to gusts big or small, move at the same frequency as large wind gusts, or are able to self-dampen near-ground sway response to extended wind forces. Our measurements of precipitation-driven and daily fluctuations in root pressures exerted on
Nonbinary Tree-Based Phylogenetic Networks.

Science.gov (United States)

Jetten, Laura; van Iersel, Leo

2018-01-01

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

DEFF Research Database (Denmark)

Adamaszek, Anna Maria; Chalermsook, Parinya; Ene, Alina

2016-01-01

We study the Unsplittable Flow problem (UFP) on trees with a submodular objective function. The input to this problem is a tree with edge capacities and a collection of tasks, each characterized by a source node, a sink node, and a demand. A subset of the tasks is feasible if the tasks can...... simultaneously send their demands from the source to the sink without violating the edge capacities. The goal is to select a feasible subset of the tasks that maximizes a submodular objective function. Our main result is an O(k log n)-approximation algorithm for Submodular UFP on trees where k denotes...... the pathwidth of the given tree. Since every tree has pathwidth O(log n), we obtain an O(log2 n) approximation for arbitrary trees. This is the first non-trivial approximation guarantee for the problem and it matches the best approximation known for UFP on trees with a linear objective function. Our main...
Tree Mortality Undercuts Ability of Tree-Planting Programs to Provide Benefits: Results of a Three-City Study

Directory of Open Access Journals (Sweden)

Sarah Widney

2016-03-01

Full Text Available Trees provide numerous benefits for urban residents, including reduced energy usage, improved air quality, stormwater management, carbon sequestration, and increased property values. Quantifying these benefits can help justify the costs of planting trees. In this paper, we use i-Tree Streets to quantify the benefits of street trees planted by nonprofits in three U.S. cities (Detroit, Michigan; Indianapolis, Indiana, and Philadelphia, Pennsylvania from 2009 to 2011. We also use both measured and modeled survival and growth rates to “grow” the tree populations 5 and 10 years into the future to project the future benefits of the trees under different survival and growth scenarios. The 4059 re-inventoried trees (2864 of which are living currently provide almost $40,000 (USD in estimated annual benefits ($9–$20/tree depending on the city, the majority (75% of which are increased property values. The trees can be expected to provide increasing annual benefits during the 10 years after planting if the annual survival rate is higher than the 93% annual survival measured during the establishment period. However, our projections show that with continued 93% or lower annual survival, the increase in annual benefits from tree growth will not be able to make up for the loss of benefits as trees die. This means that estimated total annual benefits from a cohort of planted trees will decrease between the 5-year projection and the 10-year projection. The results of this study indicate that without early intervention to ensure survival of planted street trees, tree mortality may be significantly undercutting the ability of tree-planting programs to provide benefits to neighborhood residents.
Coalescent methods for estimating phylogenetic trees.

Science.gov (United States)

Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

2009-10-01

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.
Decision trees in epidemiological research.

Science.gov (United States)

Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

2017-01-01

In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.
Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.

Directory of Open Access Journals (Sweden)

Jaime E Blair

Full Text Available To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.
Retrospective evaluation of tritium fallout by tree-ring analysis

International Nuclear Information System (INIS)

Kozak, K.; Biro, T.; Golder, F.; Rank, D.; Rajner, V.; Staudner, F.

1993-01-01

Tritium analyses of tree-ring cellulose were made to test its suitability for retrospective evaluation of a local tritium fallout. Several spruce trees were taken from an Austrian alpine area where tritium contamination of May 1974 precipitation had been detected. Wood from the annual growth rings of 1973, 1974 and 1975 was separated and the cellulose extracted. After isotopic equilibration with dead water, cellulose was combusted to yield water, whose tritium concentration was measured by liquid scintillation counting. Rigorous statistical treatment proved the significance of the increased tritium concentration caused by the tritium anomaly, which occurred during the growing season. The long-term trends of local atmospheric tritium, including the 1974 peak, were also well reflected by analysis of a 24-year ring sequence from a single tree in the contaminated area. The tritium data gained by the given method can be used at present qualitatively and a better understanding of the possible sources of contamination is required in order that the quantitative criteria be satisfied. (Author)

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees

OpenAIRE

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-01-01

Background Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA T...
Estimation of Tree Cover in an Agricultural Parkland of Senegal Using Rule-Based Regression Tree Modeling

Directory of Open Access Journals (Sweden)

Stefanie M. Herrmann

2013-10-01

Full Text Available Field trees are an integral part of the farmed parkland landscape in West Africa and provide multiple benefits to the local environment and livelihoods. While field trees have received increasing interest in the context of strengthening resilience to climate variability and change, the actual extent of farmed parkland and spatial patterns of tree cover are largely unknown. We used the rule-based predictive modeling tool Cubist® to estimate field tree cover in the west-central agricultural region of Senegal. A collection of rules and associated multiple linear regression models was constructed from (1 a reference dataset of percent tree cover derived from very high spatial resolution data (2 m Orbview as the dependent variable, and (2 ten years of 10-day 250 m Moderate Resolution Imaging Spectrometer (MODIS Normalized Difference Vegetation Index (NDVI composites and derived phenological metrics as independent variables. Correlation coefficients between modeled and reference percent tree cover of 0.88 and 0.77 were achieved for training and validation data respectively, with absolute mean errors of 1.07 and 1.03 percent tree cover. The resulting map shows a west-east gradient from high tree cover in the peri-urban areas of horticulture and arboriculture to low tree cover in the more sparsely populated eastern part of the study area. A comparison of current (2000s tree cover along this gradient with historic cover as seen on Corona images reveals dynamics of change but also areas of remarkable stability of field tree cover since 1968. The proposed modeling approach can help to identify locations of high and low tree cover in dryland environments and guide ground studies and management interventions aimed at promoting the integration of field trees in agricultural systems.
Spatial Distribution and Site-Specific Spraying of Main Sucking Pests of Elm Trees.

Science.gov (United States)

Karimzadeh, R; Iranipour, S

2017-06-01

Elm trees are important landscape trees and sucking insects weaken the elm trees and produce large amounts of honeydew. The main objectives of this study were to identify main honeydew-producing pests of elm trees and do site-specific spraying against these pests. To map the spatial distribution of the sucking pests in the large scale, the study area was divided into 40 × 40 m grids and one tree was chosen randomly from each grid (a total of 55 trees). These trees were sampled twice a year in 2011 and 2012. Each sample was a 30-cm branch terminal. Eight samples were taken from each tree in four cardinal directions and two canopy levels. The number of sucking insects and leaves of each sample were counted and recorded. Spatial analysis of the data was carried out using geostatistics. Kriging was used for producing prediction maps. Insecticide application was restricted to the regions with populations higher than threshold. To identify within-tree distribution of the honeydew-producing pests, six and four elm trees were chosen in 2011 and 2012 respectively, and sampled weekly. These trees were sampled as described previously. European elm scale (EES), Gossyparia spuria (Modeer) and two species of aphids were the dominant honeydew-producing pests. The results revealed that the effects of direction, canopy level and their interactions on insect populations were not statistically significant (P < 0.05). Site-specific spraying decreased the amount of insecticides used by ca. 20%, while satisfactory control of the sucking pests and honeydew excretion was obtained. Considering the environmental and economic benefits of site-specific spraying, it is worth doing more complementary works in this area.
Environmental tritium in trees

International Nuclear Information System (INIS)

Brown, R.M.

1979-01-01

The distribution of environmental tritium in the free water and organically bound hydrogen of trees growing in the vicinity of the Chalk River Nuclear Laboratories (CRNL) has been studied. The regional dispersal of HTO in the atmosphere has been observed by surveying the tritium content of leaf moisture. Measurement of the distribution of organically bound tritium in the wood of tree ring sequences has given information on past concentrations of HTO taken up by trees growing in the CRNL Liquid Waste Disposal Area. For samples at background environmental levels, cellulose separation and analysis was done. The pattern of bomb tritium in precipitation of 1955-68 was observed to be preserved in the organically bound tritium of a tree ring sequence. Reactor tritium was discernible in a tree growing at a distance of 10 km from CRNL. These techniques provide convenient means of monitoring dispersal of HTO from nuclear facilities. (author)
On the structure of path-like trees

OpenAIRE

Muntaner Batle, Francesc Antoni; Rius Font, Miquel

2007-01-01

We study the structure of path-like trees. In order to do this, we introduce a set of trees that we call expandable trees. In this paper we also generalize the concept of path-like trees and we call such generalization generalized path-like trees. As in the case of path-like trees, generalized path-like trees, have very nice labeling properties.
Effect of pH on lead removal from water using tree fern as the sorbent.

Science.gov (United States)

Ho, Yuh-Shan

2005-07-01

The sorption of lead from water onto an agricultural by-product, tree fern, was examined as a function of pH. The sorption processes were carried out using an agitated and baffled system. Pseudo-second-order kinetic analyses were performed to determine the rate constant of sorption, the equilibrium sorption capacity, and the initial sorption rate. Application of the pseudo-second-order kinetics model produced very high coefficients of determination. Results showed the efficiency of tree fern as a sorbent for lead. The optimum pH for lead removal was between 4 and 7, with pH 4.9 resulting in better lead removal. Ion exchange occurred in the initial reaction period. In addition, a relation between the change in the solution hydrogen ion concentration and equilibrium capacity was developed and is presented.
Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

Science.gov (United States)

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

Directory of Open Access Journals (Sweden)

Debissa Lemessa

Full Text Available 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.
Shade Trees Spatial Distribution and Its Effect on Grains and Beverage Quality of Shaded Coffee Trees

Directory of Open Access Journals (Sweden)

Francisco José da Silva Neto

2018-01-01

Full Text Available Shading coffee trees has gained importance, especially among smallholders, as an option to improve the products’ quality, therefore acquiring place at the specialty coffee market, where consumers are willing to give bonus for quality. This work aims to evaluate the influence of shade trees’ spatial distribution among coffee trees’ agronomic characteristics, yield, and beans and cup quality of shaded coffee trees. The experimental design consisted of completely randomized blocks with six repetitions and four treatments: coffee trees on shade trees planting rows, distant one meter from the trunk; coffee trees on shade trees planting row, distant six meters from the trunk; and coffee plants between the rows of shade trees, parallel to the previous treatments. The parameters analyzed were plant height, canopy diameter, plagiotropic branches’ length, yield, coffee fruits’ phenological stage, ripe cherries’ Brix degree, percentage of black, unripe, and insect damaged beans, bean size, and beverage quality. Shade trees quickened coffee fruits’ phenological stage of coffee trees nearest to them. This point also showed the best beverage quality, except for overripe fruits. The remaining parameters evaluated were not affected by shade trees’ spatial distribution.
Decision trees in epidemiological research

Directory of Open Access Journals (Sweden)

Ashwini Venkatasubramaniam

2017-09-01

Full Text Available Abstract Background In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. Main text We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART technique and the newer Conditional Inference tree (CTree technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Conclusions Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.
Human action analysis with randomized trees

CERN Document Server

Yu, Gang; Liu, Zicheng

2014-01-01

This book will provide a comprehensive overview on human action analysis with randomized trees. It will cover both the supervised random trees and the unsupervised random trees. When there are sufficient amount of labeled data available, supervised random trees provides a fast method for space-time interest point matching. When labeled data is minimal as in the case of example-based action search, unsupervised random trees is used to leverage the unlabelled data. We describe how the randomized trees can be used for action classification, action detection, action search, and action prediction.
Edge-Disjoint Fibonacci Trees in Hypercube

Directory of Open Access Journals (Sweden)

Indhumathi Raman

2014-01-01

Full Text Available The Fibonacci tree is a rooted binary tree whose number of vertices admit a recursive definition similar to the Fibonacci numbers. In this paper, we prove that a hypercube of dimension h admits two edge-disjoint Fibonacci trees of height h, two edge-disjoint Fibonacci trees of height h-2, two edge-disjoint Fibonacci trees of height h-4 and so on, as subgraphs. The result shows that an algorithm with Fibonacci trees as underlying data structure can be implemented concurrently on a hypercube network with no communication latency.
TreeCluster: Massively scalable transmission clustering using phylogenetic trees

OpenAIRE

Moshiri, Alexander

2018-01-01

Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...
Value tree analysis

International Nuclear Information System (INIS)

Keeney, R.; Renn, O.; Winterfeldt, D. von; Kotte, U.

1985-01-01

What are the targets and criteria on which national energy policy should be based. What priorities should be set, and how can different social interests be matched. To answer these questions, a new instrument of decision theory is presented which has been applied with good results to controversial political issues in the USA. The new technique is known under the name of value tree analysis. Members of important West German organisations (BDI, VDI, RWE, the Catholic and Protestant Church, Deutscher Naturschutzring, and ecological research institutions) were asked about the goals of their organisations. These goals were then ordered systematically and arranged in a hierarchical tree structure. The value trees of different groups can be combined into a catalogue of social criteria of acceptability and policy assessment. The authors describe the philosophy and methodology of value tree analysis and give an outline of its application in the development of a socially acceptable energy policy. (orig.) [de
Adjustable chain trees for proteins

DEFF Research Database (Denmark)

Winter, Pawel; Fonseca, Rasmus

2012-01-01

A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....
Introduction to fault tree analysis

International Nuclear Information System (INIS)

Barlow, R.E.; Lambert, H.E.

1975-01-01

An elementary, engineering oriented introduction to fault tree analysis is presented. The basic concepts, techniques and applications of fault tree analysis, FTA, are described. The two major steps of FTA are identified as (1) the construction of the fault tree and (2) its evaluation. The evaluation of the fault tree can be qualitative or quantitative depending upon the scope, extensiveness and use of the analysis. The advantages, limitations and usefulness of FTA are discussed
Steiner trees in industry

CERN Document Server

Du, Ding-Zhu

2001-01-01

This book is a collection of articles studying various Steiner tree prob lems with applications in industries, such as the design of electronic cir cuits, computer networking, telecommunication, and perfect phylogeny. The Steiner tree problem was initiated in the Euclidean plane. Given a set of points in the Euclidean plane, the shortest network interconnect ing the points in the set is called the Steiner minimum tree. The Steiner minimum tree may contain some vertices which are not the given points. Those vertices are called Steiner points while the given points are called terminals. The shortest network for three terminals was first studied by Fermat (1601-1665). Fermat proposed the problem of finding a point to minimize the total distance from it to three terminals in the Euclidean plane. The direct generalization is to find a point to minimize the total distance from it to n terminals, which is still called the Fermat problem today. The Steiner minimum tree problem is an indirect generalization. Sch...
Water, gravity and trees: Relationship of tree-ring widths and total water storage dynamics

Science.gov (United States)

Creutzfeldt, B.; Heinrich, I.; Merz, B.; Blume, T.; Güntner, 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
The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series

Directory of Open Access Journals (Sweden)

Alfredo eDi Filippo

2015-05-01

Full Text Available Understanding the factors controlling the expression of longevity in trees is still an outstanding challenge for tree biologists and forest ecologists. We gathered tree-ring data and literature for broadleaf deciduous (BD temperate trees growing in closed-canopy old-growth forests in the Northern Hemisphere to explore the role of geographic patterns, climate variability, and growth rates on longevity. Our pan-continental analysis, covering 32 species from 12 genera, showed that 300-400 years can be considered a baseline threshold for maximum tree lifespan in many temperate deciduous forests. Maximum age varies greatly in relation to environmental features, even within the same species. Tree longevity is generally promoted by reduced growth rates across large genetic differences and environmental gradients. We argue that slower growth rates, and the associated smaller size, provide trees with an advantage against biotic and abiotic disturbance agents, supporting the idea that size, not age, is the main constraint to tree longevity. The oldest trees were living most of their life in subordinate canopy conditions and/or within primary forests in cool temperate environments and outside major storm tracks. Very old trees are thus characterized by slow growth and often live in forests with harsh site conditions and infrequent disturbance events that kill much of the trees. Temperature inversely controls the expression of longevity in mesophilous species (Fagus spp., but its role in Quercus spp. is more complex and warrants further research in disturbance ecology. Biological, ecological and historical drivers must be considered to understand the constraints imposed to longevity within different forest landscapes.
Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Science.gov (United States)

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.

Root activity patterns of some tree crops

International Nuclear Information System (INIS)

1975-01-01

A coordinated research programme was followed using a soil injection method which employed 32 P-labelled superphosphate solution. The technique was applied for determining the root activity distribution of various crops. Field experiments were carried out in Uganda on bananas, Spain and Taiwan on citrus, Ghana on cocoa, Columbia and Kenya on coffee, and Ivory Coast and Malaysia on oil palms, to study the patterns of root activity as a function of depth and distance from the tree base, soil type, tree age and season. A few weeks after injection, leaf samples of similar age were taken from well-defined morphological positions on the tree and analyzed for 32 P. The activity of the label in the sample reflects the root activity at the various positions in the soil. Some preliminary experiments were also carried out using 32 P-superphosphate to evaluate the efficiency of different methods of fertilizer placement in relation to phosphate uptake by the plantation as a whole
Modelling tree biomasses in Finland

Energy Technology Data Exchange (ETDEWEB)

Repola, J.

2013-06-01

Biomass equations for above- and below-ground tree components of Scots pine (Pinus sylvestris L), Norway spruce (Picea abies [L.] Karst) and birch (Betula pendula Roth and Betula pubescens Ehrh.) were compiled using empirical material from a total of 102 stands. These stands (44 Scots pine, 34 Norway spruce and 24 birch stands) were located mainly on mineral soil sites representing a large part of Finland. The biomass models were based on data measured from 1648 sample trees, comprising 908 pine, 613 spruce and 127 birch trees. Biomass equations were derived for the total above-ground biomass and for the individual tree components: stem wood, stem bark, living and dead branches, needles, stump, and roots, as dependent variables. Three multivariate models with different numbers of independent variables for above-ground biomass and one for below-ground biomass were constructed. Variables that are normally measured in forest inventories were used as independent variables. The simplest model formulations, multivariate models (1) were mainly based on tree diameter and height as independent variables. In more elaborated multivariate models, (2) and (3), additional commonly measured tree variables such as age, crown length, bark thickness and radial growth rate were added. Tree biomass modelling includes consecutive phases, which cause unreliability in the prediction of biomass. First, biomasses of sample trees should be determined reliably to decrease the statistical errors caused by sub-sampling. In this study, methods to improve the accuracy of stem biomass estimates of the sample trees were developed. In addition, the reliability of the method applied to estimate sample-tree crown biomass was tested, and no systematic error was detected. Second, the whole information content of data should be utilized in order to achieve reliable parameter estimates and applicable and flexible model structure. In the modelling approach, the basic assumption was that the biomasses of
Geodesic atlas-based labeling of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Petersen, Jens; Owen, Megan

2015-01-01

We present a fast and robust atlas-based algorithm for labeling airway trees, using geodesic distances in a geometric tree-space. Possible branch label configurations for an unlabeled airway tree are evaluated using distances to a training set of labeled airway trees. In tree-space, airway tree t...... equally complete airway trees, and comparable in performance to that of experts in pulmonary medicine, emphasizing the suitability of the labeling algorithm for clinical use....
Current and potential tree locations in tree line ecotone of Changbai Mountains, Northeast China: the controlling effects of topography.

Science.gov (United States)

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.
Morphological and physiological characteristics of columnar apple trees

OpenAIRE

Gelvonauskis, Bronislovas; Brazaitytė, Aušra; Sasnauskas, Audrius; Duchovskis, Pavelas; Gelvonauskienė, Dalia

2006-01-01

There were investigated two columnar apple cultivars ‘Arbat’ and No. 24217 and apple cultivar ‘Aldas’ in an orchard at the Lithuanian Institute of Horticulture. The two latter cultivars were released at the Lithuanian Institute of Horticulture, ‘Arbat’ – in Russia. Cultivars and selections were budded on rootstocks P 60, M.26 and MM.106. In orchard apple trees were spaced at 1.0 x 3.5 m. Tree height, stem diameter, total length of one-year-old shoot, leaf area on a tree was measured and numbe...
Temple tree; Frangipani-common name; Gopur- champa - Sanskrit

Indian Academy of Sciences (India)

Plumeria rubraL. Syn. P. acutifoliaPoir. (Temple tree; Frangipani-common name; Gopur- champa - Sanskrit, Hindi) of Apocynaceae is an ornamental tree that is often cultivated in gardens and near temples. Both leaves and flowers are showy and contain milky latex. Flowers are in bunches, large and white with yellow ...
Moose?tree interactions: rebrowsing is common across tree species

OpenAIRE

Mathisen, Karen Marie; Milner, Jos M.; Skarpe, Christina

2017-01-01

Background Plant strategies to resist herbivory include tolerance and avoidance. Tolerance strategies, such as rapid regrowth which increases the palatability of new shoots, can lead to positive feedback loops between plants and herbivores. An example of such a positive feedback occurs when moose (Alces alces) browse trees in boreal forests. We described the degree of change in tree morphology that accumulated over time in response to repeated browsing by moose, using an index of accumulated ...
Rootstock Effects on Pistachio Trees Grown in Verticillium dahliae-Infested Soil.

Science.gov (United States)

Epstein, L; Beede, R; Kaur, S; Ferguson, L

2004-04-01

ABSTRACT In a field trial in soil infested with Verticillium dahliae, we compared the yield, growth, incidence of symptoms of Verticillium wilt, and mortality of two interspecific hybrid pistachio tree rootstocks (UCBI and PGII) with the standard rootstocks: the V. dahliae-resistant and susceptible Pistacia integerrima and P. atlantica, respectively. After 10 years, the trees were destructively sampled for V. dahliae in the xylem at the graft union. The results indicate that trees on the (P. atlantica 'KAC' x P. integerrima) hybrid UCBI rootstock grew and yielded as well as those on P. integerrima. Trees on the hybrid PGII yielded the least. Analysis of variance and log-linear models indicate that in soil infested with V. dahliae, three associations significantly affect pistachio nut yield. Rootstock affects scion vigor and extent of infection. Third, the extent of infection and scion vigor are inversely associated. Although trees on the P. integerrima rootstock had the highest ratings in a visual assessment of vigor, 65% were infected with V. dahliae in the trunk in the graft region compared with 73% in P. atlantica and 25% in UCBI. Thus, P. integerrima and UCBI have at least one different mechanism for resistance to V. dahliae.
Mitered fractal trees: constructions and properties

NARCIS (Netherlands)

Verhoeff, T.; Verhoeff, K.; Bosch, R.; McKenna, D.; Sarhangi, R.

2012-01-01

Tree-like structures, that is, branching structures without cycles, are attractive for artful expression. Especially interesting are fractal trees, where each subtree is a scaled and possibly otherwise transformed version of the entire tree. Such trees can be rendered in 3D by using beams with a
Genetic transformation of forest trees

African Journals Online (AJOL)

Admin

In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...
How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

Science.gov (United States)

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. © The Author 2014. Published by Oxford University Press. All rights reserved
Influence of Acacia trees on soil nutrient levels in arid lands

Science.gov (United States)

De Boever, Maarten; Gabriels, Donald; Ouessar, Mohamed; Cornelis, Wim

2014-05-01

The potential of scattered trees as keystone structures in restoring degraded environments is gaining importance. Scattered trees have strong influence on their abiotic environment, mainly causing changes in microclimate, water budget and soil properties. They often function as 'nursing trees', facilitating the recruitment of other plants. Acacia raddiana is such a keystone species which persists on the edge of the Sahara desert. The study was conducted in a forest-steppe ecosystem in central Tunisia where several reforestation campaigns with Acacia took place. To indentify the impact of those trees on soil nutrients, changes in nutrient levels under scattered trees of three age stages were examined for the upper soil layer (0-10 cm) at five microsites with increasing distance from the trunk. In addition, changes in soil nutrient levels with depth underneath and outside the canopy were determined for the 0-30 cm soil layer. Higher concentrations of organic matter (OM) were found along the gradient from underneath to outside the canopy for large trees compared to medium and small trees, especially at microsites close to the trunk. Levels of soluble K, electrical conductivity (EC), available P, OM, total C and N decreased whereas pH and levels of soluble Mg increased with increasing distance from tree. Levels of soluble Ca and Na remained unchanged along the gradient. At the microsite closest to the trunk a significant decrease in levels of soluble K, EC, OM, available P, total C and N, while a significant increase in pH was found with increasing depth. The concentration of other nutrients remained unchanged or declined not differently underneath compared to outside the canopy with increasing depth. Differences in nutrient levels were largely driven by greater inputs of organic matter under trees. Hence, Acacia trees can affect the productivity and reproduction of understory species with the latter in term an important source of organic matter. This positive feedback
Temporal changes in tree-ring nitrogen of Pinus thunbergii trees exposed to Black-tailed Gull (Larus crassirostris) breeding colonies

Energy Technology Data Exchange (ETDEWEB)

Larry, Lopez C.M., E-mail: larry@iwate-u.ac.jp [United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550 (Japan); Chitoshi, Mizota [Faculty of Agriculture, Iwate University, Morioka 020-8550 (Japan); Toshiro, Yamanaka [Division of Earth Science, Graduate School of Natural Science and Technology, Okayama University, 1-1, Naka 3-Chome, Tsushima, Okayama 700-8530 (Japan); Yoshihiro, Nobori [Faculty of Agriculture, Yamagata University, 1-23 Wakabamachi, Tsuruoka, Yamagata 997-8555 (Japan)

2010-11-15

Research highlights: {yields} N concentration and isotope ratio on tree-rings can be an important tool to infer past N soil conditions where trees grow. {yields} Changes in avian population on established or new breeding grounds caused by natural or anthropogenic mechanism could be inferred from the analysis shown in this paper. {yields} The property of trees to retain N concentration and N isotope characteristics is found in Pinus thunbergii. The use of other trees for similar analysis have to be determined because other species (Pinus densiflora, for example) do not have this property. - Abstract: Natural abundances of {sup 15}N/{sup 14}N ratios (commonly designated by {delta}{sup 15}N notation) of annual rings from Pinus thunbergii trees were determined after transplantation from a nursery to breeding colonies of Black-tailed Gull (Larus crassirostris) in Miyagi and Aomori and a control site in Yamagata, in northeastern Japan. Tree-rings were collected in July/August/September, 2009. Transplanting was conducted in the year 2000 in the Miyagi site, whereas there is no information about transplanting data in the Aomori and Yamagata sites. Soils associated with piscivorous (fish eating) avian colonies receive large seasonal input of organic N in the form of feces. The organic N is microbiologically transformed into inorganic N in soils, from which P. thunbergii derives its N. The resulting NH{sub 4}{sup -} and NO{sub 3}{sup -}N are characterized by distinctly heavy {delta}{sup 15}N ratios, due to coupled processes of mineralization, volatilization, nitrification and denitrification of feces. In general, total N concentration along with {delta}{sup 15}N values stored in the annual rings of P. thunbergii increased steadily after transplanting from the nursery to locations under continued avian N input. Tree-ring N content and isotopic ratios provided a reliable record of past annual available soil N caused by changes in the Black-tailed Gull population, and thus can
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.

Science.gov (United States)

Soria-Carrasco, Víctor; Talavera, Gerard; Igea, Javier; Castresana, Jose

2007-11-01

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree. http://molevol.ibmb.csic.es/Ktreedist.html
Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Directory of Open Access Journals (Sweden)

Steffen Boch

Full Text Available 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.
Tree Notation: an antifragile program notation

OpenAIRE

Yunits, Breck

2017-01-01

This paper presents Tree Notation, a new simple, universal syntax. Language designers can invent new programming languages, called Tree Languages, on top of Tree Notation. Tree Languages have a number of advantages over traditional programming languages. We include a Visual Abstract to succinctly display the problem and discovery. Then we describe the problem--the BNF to abstract syntax tree (AST) parse step--and introduce the novel solution we discovered: a new family of 2D programming langu...
Tree growth visualization

Science.gov (United States)

L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

2005-01-01

In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...
Individual tree control

Science.gov (United States)

Harvey A. Holt

1989-01-01

Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...
Using tree diversity to compare phylogenetic heuristics.

Science.gov (United States)

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

2009-04-29

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

International Nuclear Information System (INIS)

Nai Fovino, Igor; Masera, Marcelo; De Cian, Alessio

2009-01-01

In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.

Integrating cyber attacks within fault trees

Energy Technology Data Exchange (ETDEWEB)

Nai Fovino, Igor [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy)], E-mail: igor.nai@jrc.it; Masera, Marcelo [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy); De Cian, Alessio [Department of Electrical Engineering, University di Genova, Genoa (Italy)

2009-09-15

In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.
Tree and shrub expansion over the past 34 years at the tree-line near Abisko, Sweden.

Science.gov (United States)

Rundqvist, Sara; Hedenås, Henrik; Sandström, Anneli; Emanuelsson, Urban; Eriksson, Håkan; Jonasson, Christer; Callaghan, Terry V

2011-09-01

Shrubs and trees are expected to expand in the sub-Arctic due to global warming. Our study was conducted in Abisko, sub-arctic Sweden. We recorded the change in coverage of shrub and tree species over a 32- to 34-year period, in three 50 x 50 m plots; in the alpine-tree-line ecotone. The cover of shrubs and trees (tree stems (> or =3.5 cm) were noted and positions determined. There has been a substantial increase of cover of shrubs and trees, particularly dwarf birch (Betula nana), and mountain birch (Betula pubescens ssp. czerepanovii), and an establishment of aspen (Populus tremula). The other species willows (Salix spp.), juniper (Juniperus communis), and rowan (Sorbus aucuparia) revealed inconsistent changes among the plots. Although this study was unable to identify the causes for the change in shrubs and small trees, they are consistent with anticipated changes due to climate change and reduced herbivory.
Tree Species Richness Promotes Invertebrate Herbivory on Congeneric Native and Exotic Tree Saplings in a Young Diversity Experiment.

Directory of Open Access Journals (Sweden)

Annika Wein

Full Text Available Tree diversity in forests is an important driver of ecological processes including herbivory. Empirical evidence suggests both negative and positive effects of tree diversity on herbivory, which can be, respectively, attributed to associational resistance or associational susceptibility. Tree diversity experiments allow testing for associational effects, but evidence regarding which pattern predominates is mixed. Furthermore, it is unknown if herbivory on tree species of native vs. exotic origin is influenced by changing tree diversity in a similar way, or if exotic tree species escape natural enemies, resulting in lower damage that is unrelated to tree diversity. To address these questions, we established a young tree diversity experiment in temperate southwestern Germany that uses high planting density (49 trees per plot; plot size 13 m2. The species pool consists of six congeneric species pairs of European and North American origin (12 species in total planted in monocultures and mixtures (1, 2, 4, 6 species. We assessed leaf damage by leaf-chewing insects on more than 5,000 saplings of six broadleaved tree species. Plot-level tree species richness increased leaf damage, which more than doubled from monocultures to six-species mixtures, strongly supporting associational susceptibility. However, leaf damage among congeneric native and exotic species pairs was similar. There were marked differences in patterns of leaf damage across tree genera, and only the genera likely having a predominately generalist herbivore community showed associational susceptibility, irrespective of the geographical origin of a tree species. In conclusion, an increase in tree species richness in young temperate forests may result in associational susceptibility to feeding by generalist herbivores.
Effects of tree-to-tree variations on sap flux-based transpiration estimates in a forested watershed

Science.gov (United States)

Kume, Tomonori; Tsuruta, Kenji; Komatsu, Hikaru; Kumagai, Tomo'omi; Higashi, Naoko; Shinohara, Yoshinori; Otsuki, Kyoichi

2010-05-01

To estimate forest stand-scale water use, we assessed how sample sizes affect confidence of stand-scale transpiration (E) estimates calculated from sap flux (Fd) and sapwood area (AS_tree) measurements of individual trees. In a Japanese cypress plantation, we measured Fd and AS_tree in all trees (n = 58) within a 20 × 20 m study plot, which was divided into four 10 × 10 subplots. We calculated E from stand AS_tree (AS_stand) and mean stand Fd (JS) values. Using Monte Carlo analyses, we examined potential errors associated with sample sizes in E, AS_stand, and JS by using the original AS_tree and Fd data sets. Consequently, we defined optimal sample sizes of 10 and 15 for AS_stand and JS estimates, respectively, in the 20 × 20 m plot. Sample sizes greater than the optimal sample sizes did not decrease potential errors. The optimal sample sizes for JS changed according to plot size (e.g., 10 × 10 m and 10 × 20 m), while the optimal sample sizes for AS_stand did not. As well, the optimal sample sizes for JS did not change in different vapor pressure deficit conditions. In terms of E estimates, these results suggest that the tree-to-tree variations in Fd vary among different plots, and that plot size to capture tree-to-tree variations in Fd is an important factor. This study also discusses planning balanced sampling designs to extrapolate stand-scale estimates to catchment-scale estimates.
Neutron activation studies of trace elements in tree rings

International Nuclear Information System (INIS)

Tout, R.E.; Gilboy, W.B.; Spyrou, N.M.

1977-01-01

The levels of twelve elements most of which are either considered essential to plant growth or have been detected in air filter samples in an air pollution survey have been monitored in three transverse sections of trees, two elms (ring-porous trees) and one cedar (a conifer). An irradiation time of 10 minutes and a waiting time of 1 minute were selected followed by a 10-minute count. The activated samples were placed on a specially shaped perspex disc situated on a 45-cm 3 Ge(Li) detector. The gamma-ray spectra were subsequently analysed on a 6600 computer, using the library program 'SAMPO' to which subroutines have been added for peak identification and for calculating the mass of elements present. All irradiations were carried out using a thermal neutron flux of 1.5x10 12 ncm -2 sec -1 . Two dimensional distributions of the elements around the tree rings of the section and radially from ring to ring, have been obtained to see if tree rings can be analysed for use as a record of historical pollution. Definite movement of most of these elements between the two main parts of the xylem has occured in all three trees. This makes it seem unlikely that any pollution products taken up from the atmosphere would be retained in the same ring in which they were originally accumulated. Exceptions may occur in the sapwood rings, where a few elements, especially Cl, show directional peaks which do not persist in the heartwood. (T.G.)
Wading bird guano enrichment of soil nutrients in tree islands of the Florida Everglades

Energy Technology Data Exchange (ETDEWEB)

Irick, Daniel L. [University of Florida, Soil and Water Science Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL 33031 (United States); Gu, Binhe [University of Florida, Soil and Water Science Department, 2181 McCarty Hall, Gainesville, FL 32611 (United States); Li, Yuncong C., E-mail: yunli@ufl.edu [University of Florida, Soil and Water Science Department, Tropical Research and Education Center, 18905 SW 280th St., Homestead, FL 33031 (United States); Inglett, Patrick W. [University of Florida, Soil and Water Science Department, 2181 McCarty Hall, Gainesville, FL 32611 (United States); Frederick, Peter C. [University of Florida, Department of Wildlife Ecology and Conservation, 110 Newins-Ziegler Hall, PO Box 110430, Gainesville, FL 32611 (United States); Ross, Michael S. [Florida International University, Department of Earth and Environment, Southeast Environmental Research Center, 11200 SW 8th St, Miami, FL 33199 (United States); Wright, Alan L. [University of Florida, Soil and Water Science Department, Everglades Research and Education Center, 3200 E. Palm Beach Rd., Belle Glade, FL 33430 (United States); Ewe, Sharon M.L. [Ecology and Environment, Inc., 12300 South Shore Blvd, Wellington, FL 33414 (United States)

2015-11-01

Differential distribution of nutrients within an ecosystem can offer insight of ecological and physical processes that are otherwise unclear. This study was conducted to determine if enrichment of phosphorus (P) in tree island soils of the Florida Everglades can be explained by bird guano deposition. Concentrations of total carbon, nitrogen (N), and P, and N stable isotope ratio (δ{sup 15}N) were determined on soil samples from 46 tree islands. Total elemental concentrations and δ{sup 15}N were determined on wading bird guano. Sequential chemical extraction of P pools was also performed on guano. Guano contained between 53.1 and 123.7 g-N kg{sup −1} and 20.7 and 56.7 g-P kg{sup −1}. Most of the P present in guano was extractable by HCl, which ranged from 82 to 97% of the total P. Total P of tree islands classified as having low or high P soils averaged 0.71 and 40.6 g kg{sup −1}, respectively. Tree island soil with high total P concentration was found to have a similar δ{sup 15}N signature and total P concentration as bird guano. Phosphorus concentrations and δ{sup 15}N were positively correlated in tree island soils (r = 0.83, p < 0.0001). Potential input of guano with elevated concentrations of N and P, and {sup 15}N enriched N, relative to other sources suggests that guano deposition in tree island soils is a mechanism contributing to this pattern. - Highlights: • Tree island soil P concentration and δ{sup 15}N values exceed other Everglades soils. • Characteristics of Everglades tree island soil may indicate guano deposition. • Deposition of stable guano P can exceed other P sources to tree island soil.
The Hopi Fruit Tree Book.

Science.gov (United States)

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…
Rectilinear Full Steiner Tree Generation

DEFF Research Database (Denmark)

Zachariasen, Martin

1999-01-01

The fastest exact algorithm (in practice) for the rectilinear Steiner tree problem in the plane uses a two-phase scheme: First, a small but sufficient set of full Steiner trees (FSTs) is generated and then a Steiner minimum tree is constructed from this set by using simple backtrack search, dynamic...
Reconciliation with non-binary species trees.

Science.gov (United States)

Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton; Durand, Dannie

2008-10-01

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

Directory of Open Access Journals (Sweden)

Giovambattista Sorrenti

2017-06-01

Full Text Available Given that nursery is a peculiar environment, the amount of nutrients removed by nursery trees represents a fundamental acquisition to optimise fertilisation strategies, with economic and environmental implications. In this context, we determined nutrient removal by apple, pear and cherry nursery trees at the end of the nursery growing cycle. We randomly removed 5 leafless apple (Golden Delicious/EMLA M9; density of 30,000 trees ha–1, pear (Santa Maria/Adams; density of 30,000 trees ha–1 and cherry (AlexTM/Gisela 6®; density of 40,000 trees ha–1 trees from a commercial nursery. Trees were divided into roots (below the root collar, rootstock (above-ground wood between root collar and grafting point and variety (1-year-old wood above the grafting point. For each organ we determined biomass, macro- (N, P, K, Ca, Mg, S, and micro- (Fe, Mn, Zn, Cu, and B nutrient concentration. Pear trees were the most developed (650 g (dw tree–1, equal to 1.75 and 2.78 folds than apple and cherry trees, respectively whereas, independently of the species, variety mostly contributed (>50% to the total tree biomass, followed by roots and then above-ground rootstock. However, the dry biomass and nutrient amount measured in rootstocks (including roots represent the cumulative amount of 2 and 3 seasons, for Gisela® 6 (tissue culture and pome fruit species (generated by mound layering, respectively. Macro and micronutrients were mostly concentrated in roots, followed by variety and rootstock, irrespective of the species. Independently of the tissue, macronutrients concentration hierarchy was N>Ca>K> P>Mg>S. Removed N by whole tree accounted for 6.58, 3.53 and 2.49 g tree–1 for pear, apple and cherry, respectively, corresponding to almost 200, 107 and 100 kg N ha–1, respectively. High amounts of K and Ca were used by pear (130-140 kg ha–1 and apple trees (~50 and 130 kg ha–1 of K and Ca, respectively, while ~25 kg K ha–1 and 55 kg Ca ha–1 were
Annually resolved atmospheric radiocarbon records reconstructed from tree-rings

Science.gov (United States)

Wacker, Lukas; Bleicher, Niels; Büntgen, Ulf; Friedrich, Michael; Friedrich, Ronny; Diego Galván, Juan; Hajdas, Irka; Jull, Anthony John; Kromer, Bernd; Miyake, Fusa; Nievergelt, Daniel; Reinig, Frederick; Sookdeo, Adam; Synal, Hans-Arno; Tegel, Willy; Wesphal, Torsten

2017-04-01

The IntCal13 calibration curve is mainly based on data measured by decay counting with a resolution of 10 years. Thus high frequency changes like the 11-year solar cycles or cosmic ray events [1] are not visible, or at least not to their full extent. New accelerator mass spectrometry (AMS) systems today are capable of measuring at least as precisely as decay counters [2], with the advantage of using 1000 times less material. The low amount of material required enables more efficient sample preparation. Thus, an annually resolved re-measurement of the tree-ring based calibration curve can now be envisioned. We will demonstrate with several examples the multitude of benefits resulting from annually resolved radiocarbon records from tree-rings. They will not only allow for more precise radiocarbon dating but also contain valuable new astrophysical information. The examples shown will additionally indicate that it can be critical to compare AMS measurements with a calibration curve that is mainly based on decay counting. We often see small offsets between the two measurement techniques, while the reason is yet unknown. [1] Miyake F, Nagaya K, Masuda K, Nakamura T. 2012. A signature of cosmic-ray increase in AD 774-775 from tree rings in Japan. Nature 486(7402):240-2. [2] Wacker L, Bonani G, Friedrich M, Hajdas I, Kromer B, Nemec M, Ruff M, Suter M, Synal H-A, Vockenhuber C. 2010. MICADAS: Routine and high-precision radiocarbon dating. Radiocarbon 52(2):252-62.
Heterogeneous Compression of Large Collections of Evolutionary Trees.

Science.gov (United States)

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.
Multiloop calculations in p-adic string theory and Bruhat-Tits trees.2

International Nuclear Information System (INIS)

Zabrodin, A.V.; Mironov, A.D.; Chekhov, L.O.

1989-01-01

The open p-adic string world sheet as a coset space F=T/Γ, where T is the Bruhat-Tits tree for the p-adic linear group GL(2.Q p ) is some Schottky group is treated. The boundary of this world sheet corresponds to p-adic Mumford curve of finite genus. The string dynamics is governed by the local Gaussian action on the coset space F. The tachyon amplitudes expressed in terms of p-adic Θ-functions are proposed for the Mumford curve of arbitrary genus and compared with the corresponding usual archimedian amplitudes. 41 refs.; 14 figs
‘FUJI’ APPLE TREE RESPONSE TO PHOSPHORUS FERTILIZATION

Directory of Open Access Journals (Sweden)

GILBERTO NAVA

Full Text Available ABSTRACT The aim of this work was to evaluate the effects of orchard fertilization with increasing rates of phosphorus (P on yield and critical levels of P in the soil and in the leaf of ‘Fuji’ apple trees. The experiment was conducted in São Joaquim, state of Santa Catarina, southern Brazil, from 2010 to 2015, in an Inceptisol soil. The three apple orchards were planted in 2004 with the Fuji cultivar grafted on Marubakaido/ M9 rootstock and grown under a high-plant-density system (1984 trees ha-1. Annual fertilizer levels of 0, 40, 80, 120 and 160 kg ha-1 of P2O5 (as triple superphosphate were applied to the soil surface, without incorporation, in a randomized block design with five replicates. In the first and last years (2011 and 2015, soil samples were collected from 0-10, 10-20 and 0-20 cm layers and the available P content was analyzed. Annually, whole leaves were collected and analyzed for P content. The number and weight of fruits per tree and hfruit yield were also evaluated. Application of P increased the content of available P in the soil, but this increase was not accompanied by increased leaf P content nor by increased fruit yield. This suggests that, in soils with medium to high content of organic matter and well fertilized with P before planting, there is no response of apple trees for P reapplication in the 10 subsequent years.
Fault tree graphics

International Nuclear Information System (INIS)

Bass, L.; Wynholds, H.W.; Porterfield, W.R.

1975-01-01

Described is an operational system that enables the user, through an intelligent graphics terminal, to construct, modify, analyze, and store fault trees. With this system, complex engineering designs can be analyzed. This paper discusses the system and its capabilities. Included is a brief discussion of fault tree analysis, which represents an aspect of reliability and safety modeling
Environmental Fate of Emamectin Benzoate After Tree Micro Injection of Horse Chestnut Trees

OpenAIRE

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

2014-01-01

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 an...
Factors that influence Christmas tree sales

Science.gov (United States)

Thomas H. Pendleton; Lawrence D. Garrett

1970-01-01

An analysis of the metropolitan Christmas tree market in Winston-Salem, N. C., shows that to sell more trees, Christmas tree retailers should locate their lots on heavily traveled streets in business areas, have adequate parking facilities, advertise, and have attractive displays of trees. Retailers who follow these practices can expect to receive higher prices for...
The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees.

Science.gov (United States)

Freas, Cody A; Wystrach, Antione; Narendra, Ajay; Cheng, Ken

2018-01-01

Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas , whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees.
The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees

Directory of Open Access Journals (Sweden)

Cody A. Freas

2018-01-01

Full Text Available Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas, whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees.
Encoding phylogenetic trees in terms of weighted quartets.

Science.gov (United States)

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

2008-04-01

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

Microwave sensing of tree trunks

Science.gov (United States)

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
TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.

Science.gov (United States)

Sauvage, Thomas; Plouviez, Sophie; Schmidt, William E; Fredericq, Suzanne

2018-03-05

The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.
Modelling modulus of elasticity of Pinus pinaster Ait. in northwestern Spain with standing tree acoustic measurements, tree, stand and site variables

Directory of Open Access Journals (Sweden)

Esther Merlo

2014-04-01

Full Text Available Aim of study: Modelling the structural quality of Pinus pinaster Ait. wood on the basis of measurements made on standing trees is essential because of the importance of the species in the Galician forestry and timber industries and the good mechanical properties of its wood. In this study, we investigated how timber stiffness is affected by tree and stand properties, climatic and edaphic characteristics and competition. Area of study: The study was performed in Galicia, north-western Spain.Material and methods: Ten pure and even-aged P. pinaster stands were selected and tree and stand variables and the stress wave velocity of 410 standing trees were measured. A sub-sample of 73 trees, representing the variability in acoustic velocity, were felled and sawed into structural timber pieces (224 which were subjected to a bending test to determine the modulus of elasticity (MOE. Main results: Linear models including wood properties explained more than 97%, 73% and 60% of the observed MOE variability at site, tree and board level, respectively, with acoustic velocity and wood density as the main regressors. Other linear models, which did not include wood density, explained more than 88%, 69% and 55% of the observed MOE variability at site, tree and board level, respectively, with acoustic velocity as the main regressor. Moreover, a classification tree for estimating the visual grade according to standard UNE 56544:2011 was developed. Research highlights: The results have demonstrated the usefulness of acoustic velocity for predicting MOE in standing trees. The use of the fitted equations together with existing dynamic growth models will enable preliminary assessment of timber stiffness in relation to different silvicultural alternatives used with this species.Keywords: stress wave velocity, modulus of elasticity, site index, competition index, stepwise regression, CART.
Public Reactions to New Street Tree Planting

Directory of Open Access Journals (Sweden)

Ruth A. Rae

2010-01-01

Full Text Available MillionTreesNYC, which has the goal of planting one million trees in New York City by 2017, is intended to make New York City a greener, more sustainable city and is part of the Mayor’s comprehensive long term strategic plan, PlaNYC. Through planting a tree at every suitable sidewalk location in the city, the City of New York is transforming blocks and communities, and providing a variety of environmental, social and aesthetic benefits. This article examines the large scale municipal planting of new street trees and the reaction by some of the pubic to this planting.Trees offer benefits to the city overall, but the public may not understand these benefits or the street tree planting process. Between 2007 and 2009, the Department of Parks & Recreation planted 53,235 new street trees, and received 4,108 items of correspondence from the public. The majority of this correspondence consisted of public comments about the City’s new street tree planting policies and processes including placement objections, maintenance concerns, reports of resultant damage from tree planting operations, requests for new street trees and reports of tree conditions.This study describes the operational policies that guide New York City's municipal street tree planting, and results of content and spatial analysis of the correspondence. Qualitative analysis of the correspondence revealed the public perceptions and concerns related to the MillionTreesNYC program. Spatial analysis explored the relationship between the planting locations of new street trees and the locations of the citizen correspondence.Public reactions to this large scale municipal planting are related to the dual public and private nature of the sidewalk, issues of territoriality, responsibility, aesthetics and place attachment. Correspondence volume was associated with the scale of the new street tree block planting program, and the effectiveness of NYC’s 311 Customer Service Center. The discussion
Rootstock effects on pistachio trees grown in Verticillium dahliae-infested soil

OpenAIRE

Epstein, Lynn; Beede, R; Kaur, S; Ferguson, L

2004-01-01

In a field trial in soil infested with Verticillium dahliae, we compared the yield, growth, incidence of symptoms of Verticillium wilt, and mortality of two interspecific hybrid pistachio tree rootstocks (UCBI and PGII) with the standard rootstocks: the V dahliae-resistant and susceptible Pistacia integerrima and P. atlantica, respectively. After 10 years, the trees were destructively sampled for V dahliae in the xylem at the graft union. The results indicate that trees on the (P. atlantica '...
Generic physical protection logic trees

International Nuclear Information System (INIS)

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
Generic physical protection logic trees

Energy Technology Data Exchange (ETDEWEB)

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.
Tree-Based Unrooted Phylogenetic Networks.

Science.gov (United States)

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

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.
A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees

DEFF Research Database (Denmark)

Sand, Andreas; Pedersen, Christian Nørgaard Storm; Mailund, Thomas

2013-01-01

rooted binary trees in time O (n log2 n). The algorithm is related to an algorithm for computing the quartet distance between two unrooted binary trees in time O (n log n). While the quartet distance algorithm has a very severe overhead in the asymptotic time complexity that makes it impractical compared......The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equal or different. We present an algorithm that computes the triplet distance between two...
Improved prediction of hardwood tree biomass derived from wood density estimates and form factors for whole trees

Science.gov (United States)

David W. MacFarlane; Neil R. Ver Planck

2012-01-01

Data from hardwood trees in Michigan were analyzed to investigate how differences in whole-tree form and wood density between trees of different stem diameter relate to residual error in standard-type biomass equations. The results suggested that whole-tree wood density, measured at breast height, explained a significant proportion of residual error in standard-type...
Wood density variation and tree ring distinctness in Gmelina arborea trees by x-ray densitometry

Directory of Open Access Journals (Sweden)

Roger Moya

2009-03-01

Full Text Available Due to its relationship with other properties, wood density is the main wood quality parameter. Modern, accuratemethods such as X-ray densitometry - are applied to determine the spatial distribution of density in wood sections and to evaluatewood quality. The objectives of this study were to determinate the influence of growing conditions on wood density variation andtree ring demarcation of gmelina trees from fast growing plantations in Costa Rica. The wood density was determined by X-raydensitometry method. Wood samples were cut from gmelina trees and were exposed to low X-rays. The radiographic films weredeveloped and scanned using a 256 gray scale with 1000 dpi resolution and the wood density was determined by CRAD and CERDsoftware. The results showed tree-ring boundaries were distinctly delimited in trees growing in site with rainfall lower than 2510 mm/year. It was demonstrated that tree age, climatic conditions and management of plantation affects wood density and its variability. Thespecific effect of variables on wood density was quantified by for multiple regression method. It was determined that tree yearexplained 25.8% of the total variation of density and 19.9% were caused by climatic condition where the tree growing. Wood densitywas less affected by the intensity of forest management with 5.9% of total variation.
Autumn frost hardiness in Norway spruce plus tree progeny and trees of the local and transferred provenances in central Sweden.

Science.gov (United States)

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.
Inferences from growing trees backwards

Science.gov (United States)

David W. Green; Kent A. McDonald

1997-01-01

The objective of this paper is to illustrate how longitudinal stress wave techniques can be useful in tracking the future quality of a growing tree. Monitoring the quality of selected trees in a plantation forest could provide early input to decisions on the effectiveness of management practices, or future utilization options, for trees in a plantation. There will...
The stopping rules for winsorized tree

Science.gov (United States)

Ch'ng, Chee Keong; Mahat, Nor Idayu

2017-11-01

Winsorized tree is a modified tree-based classifier that is able to investigate and to handle all outliers in all nodes along the process of constructing the tree. It overcomes the tedious process of constructing a classical tree where the splitting of branches and pruning go concurrently so that the constructed tree would not grow bushy. This mechanism is controlled by the proposed algorithm. In winsorized tree, data are screened for identifying outlier. If outlier is detected, the value is neutralized using winsorize approach. Both outlier identification and value neutralization are executed recursively in every node until predetermined stopping criterion is met. The aim of this paper is to search for significant stopping criterion to stop the tree from further splitting before overfitting. The result obtained from the conducted experiment on pima indian dataset proved that the node could produce the final successor nodes (leaves) when it has achieved the range of 70% in information gain.
Meta-learning in decision tree induction

CERN Document Server

Grąbczewski, Krzysztof

2014-01-01

The book focuses on different variants of decision tree induction but also describes the meta-learning approach in general which is applicable to other types of machine learning algorithms. The book discusses different variants of decision tree induction and represents a useful source of information to readers wishing to review some of the techniques used in decision tree learning, as well as different ensemble methods that involve decision trees. It is shown that the knowledge of different components used within decision tree learning needs to be systematized to enable the system to generate and evaluate different variants of machine learning algorithms with the aim of identifying the top-most performers or potentially the best one. A unified view of decision tree learning enables to emulate different decision tree algorithms simply by setting certain parameters. As meta-learning requires running many different processes with the aim of obtaining performance results, a detailed description of the experimen...
Nutrient content of biomass components of Hamlin sweet orange trees

Directory of Open Access Journals (Sweden)

Mattos Jr. Dirceu

2003-01-01

Full Text Available The knowledge of the nutrient distribution in trees is important to establish sound nutrient management programs for citrus production. Six-year-old Hamlin orange trees [Citrus sinensis (L. Osb.] on Swingle citrumelo [Poncirus trifoliata (L. Raf. x Citrus paradisi Macfad.] rootstock, grown on a sandy Entisol in Florida were harvested to investigate the macro and micronutrient distributions of biomass components. The biomass of aboveground components of the tree represented the largest proportion of the total. The distribution of the total tree dry weight was: fruit = 30.3%, leaf = 9.7%, twig = 26.1%, trunk = 6.3%, and root = 27.8%. Nutrient concentrations of recent mature leaves were in the adequate to optimal range as suggested by interpretation of leaf analysis in Florida. Concentrations of Ca in older leaves and woody tissues were much greater than those in the other parts of the tree. Concentrations of micronutrients were markedly greater in fibrous root as compared to woody roots. Calcium made up the greatest amount of nutrient in the citrus tree (273.8 g per tree, followed by N and K (234.7 and 181.5 g per tree, respectively. Other macronutrients comprised about 11% of the total nutrient content of trees. The contents of various nutrients in fruits were: N = 1.20, K = 1.54, P = 0.18, Ca = 0.57, Mg = 0.12, S = 0.09, B = 1.63 x 10-3, Cu = 0.39 x 10-3, Fe = 2.1 x 10-3, Mn = 0.38 10-3, and Zn = 0.40 10-3 (kg ton-1. Total contents of N, K, and P in the orchard corresponded to 66.5, 52.0, and 8.3 kg ha-1, respectively, which were equivalent to the amounts applied annually by fertilization.
Generic Ising trees

DEFF Research Database (Denmark)

Durhuus, Bergfinnur Jøgvan; Napolitano, George Maria

2012-01-01

The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove that they......The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove...... that they exhibit no spontaneous magnetization. Furthermore, the values of the Hausdorff and spectral dimensions of the underlying trees are calculated and found to be, respectively,¯dh =2 and¯ds = 4/3....
Tree growth-climate relationships in a forest-plot network on Mediterranean mountains.

Science.gov (United States)

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

2017-11-15

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

Science.gov (United States)

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.
Tritium concentrations in tree ring cellulose

International Nuclear Information System (INIS)

Kaji, Toshio; Momoshima, Noriyuki; Takashima, Yoshimasa.

1989-01-01

Measurements of tritium (tissue bound tritium; TBT) concentration in tree rings are presented and discussed. Such measurement is expected to provide a useful means of estimating the tritium level in the environment in the past. The concentration of tritium bound in the tissue (TBT) in a tree ring considered to reflect the environmental tritium level in the area at the time of the formation of the ring, while the concentration of tritium in the free water in the tissue represents the current environmental tritium level. First, tritium concentration in tree ring cellulose sampled from a cedar tree grown in a typical environment in Fukuoka Prefecture is compared with the tritium concentration in precipitation in Tokyo. Results show that the year-to-year variations in the tritium concentration in the tree rings agree well with those in precipitation. The maximum concentration, which occurred in 1963, is attibuted to atmospheric nuclear testing which was performed frequently during the 1961 - 1963 period. Measurement is also made of the tritium concentration in tree ring cellulose sampled from a pine tree grown near the Isotope Center of Kyushu University (Fukuoka). Results indicate that the background level is higher probably due to the release of tritium from the facilities around the pine tree. Thus, measurement of tritium in tree ring cellulose clearly shows the year-to-year variation in the tritium concentration in the atmosphere. (N.K.)

Trees for future forests

DEFF Research Database (Denmark)

Lobo, Albin

Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... organisms. The aim of the present thesis is therefore to explore genetic resilience and phenotypic plasticity mechanisms that allows trees to adapt and evolve with changing climates. The thesis focus on the abiotic factors associated with climate change, especially raised temperatures and lack...... age of these tree species and the uncertainty around the pace and effect of climate, it remains an open question if the native populations can respond fast enough. Phenotypic plasticity through epigenetic regulation of spring phenology is found to be present in a tree species which might act...
A Durable Flash Memory Search Tree

OpenAIRE

Clay III, James; Wortman, Kevin

2012-01-01

We consider the task of optimizing the B-tree data structure, used extensively in operating systems and databases, for sustainable usage on multi-level flash memory. Empirical evidence shows that this new flash memory tree, or FM Tree, extends the operational lifespan of each block of flash memory by a factor of roughly 27 to 70 times, while still supporting logarithmic-time search tree operations.
The Problem of Predecessors on Spanning Trees

Directory of Open Access Journals (Sweden)

V. S. Poghosyan

2011-01-01

Full Text Available We consider the equiprobable distribution of spanning trees on the square lattice. All bonds of each tree can be oriented uniquely with respect to an arbitrary chosen site called the root. The problem of predecessors is to find the probability that a path along the oriented bonds passes sequentially fixed sites i and j. The conformal field theory for the Potts model predicts the fractal dimension of the path to be 5/4. Using this result, we show that the probability in the predecessors problem for two sites separated by large distance r decreases as P(r ∼ r −3/4. If sites i and j are nearest neighbors on the square lattice, the probability P(1 = 5/16 can be found from the analytical theory developed for the sandpile model. The known equivalence between the loop erased random walk (LERW and the directed path on the spanning tree states that P(1 is the probability for the LERW started at i to reach the neighboring site j. By analogy with the self-avoiding walk, P(1 can be called the return probability. Extensive Monte-Carlo simulations confirm the theoretical predictions.
Are There Infinite Irrigation Trees?

Science.gov (United States)

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

2006-08-01

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

Science.gov (United States)

2011-03-01

To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...
Estimation of Tree Lists from Airborne Laser Scanning Using Tree Model Clustering and k-MSN Imputation

Directory of Open Access Journals (Sweden)

Jörgen Wallerman

2013-04-01

Full Text Available Individual tree crowns may be delineated from airborne laser scanning (ALS data by segmentation of surface models or by 3D analysis. Segmentation of surface models benefits from using a priori knowledge about the proportions of tree crowns, which has not yet been utilized for 3D analysis to any great extent. In this study, an existing surface segmentation method was used as a basis for a new tree model 3D clustering method applied to ALS returns in 104 circular field plots with 12 m radius in pine-dominated boreal forest (64°14'N, 19°50'E. For each cluster below the tallest canopy layer, a parabolic surface was fitted to model a tree crown. The tree model clustering identified more trees than segmentation of the surface model, especially smaller trees below the tallest canopy layer. Stem attributes were estimated with k-Most Similar Neighbours (k-MSN imputation of the clusters based on field-measured trees. The accuracy at plot level from the k-MSN imputation (stem density root mean square error or RMSE 32.7%; stem volume RMSE 28.3% was similar to the corresponding results from the surface model (stem density RMSE 33.6%; stem volume RMSE 26.1% with leave-one-out cross-validation for one field plot at a time. Three-dimensional analysis of ALS data should also be evaluated in multi-layered forests since it identified a larger number of small trees below the tallest canopy layer.
Tree-Substrate Water Relations and Root Development in Tree Plantations Used for Mine Tailings Reclamation.

Science.gov (United States)

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

2016-05-01

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

Science.gov (United States)

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
VC-dimension of univariate decision trees.

Science.gov (United States)

Yildiz, Olcay Taner

2015-02-01

In this paper, we give and prove the lower bounds of the Vapnik-Chervonenkis (VC)-dimension of the univariate decision tree hypothesis class. The VC-dimension of the univariate decision tree depends on the VC-dimension values of its subtrees and the number of inputs. Via a search algorithm that calculates the VC-dimension of univariate decision trees exhaustively, we show that our VC-dimension bounds are tight for simple trees. To verify that the VC-dimension bounds are useful, we also use them to get VC-generalization bounds for complexity control using structural risk minimization in decision trees, i.e., pruning. Our simulation results show that structural risk minimization pruning using the VC-dimension bounds finds trees that are more accurate as those pruned using cross validation.
Tree growth and competition in an old-growth Picea abies forest of boreal Sweden: influence of tree spatial patterning

Science.gov (United States)

Fraver, Shawn; D'Amato, Anthony W.; Bradford, John B.; Jonsson, Bengt Gunnar; Jönsson, Mari; Esseen, Per-Anders

2013-01-01

Question: What factors best characterize tree competitive environments in this structurally diverse old-growth forest, and do these factors vary spatially within and among stands? Location: Old-growth Picea abies forest of boreal Sweden. Methods: Using long-term, mapped permanent plot data augmented with dendrochronological analyses, we evaluated the effect of neighbourhood competition on focal tree growth by means of standard competition indices, each modified to include various metrics of trees size, neighbour mortality weighting (for neighbours that died during the inventory period), and within-neighbourhood tree clustering. Candidate models were evaluated using mixed-model linear regression analyses, with mean basal area increment as the response variable. We then analysed stand-level spatial patterns of competition indices and growth rates (via kriging) to determine if the relationship between these patterns could further elucidate factors influencing tree growth. Results: Inter-tree competition clearly affected growth rates, with crown volume being the size metric most strongly influencing the neighbourhood competitive environment. Including neighbour tree mortality weightings in models only slightly improved descriptions of competitive interactions. Although the within-neighbourhood clustering index did not improve model predictions, competition intensity was influenced by the underlying stand-level tree spatial arrangement: stand-level clustering locally intensified competition and reduced tree growth, whereas in the absence of such clustering, inter-tree competition played a lesser role in constraining tree growth. Conclusions: Our findings demonstrate that competition continues to influence forest processes and structures in an old-growth system that has not experienced major disturbances for at least two centuries. The finding that the underlying tree spatial pattern influenced the competitive environment suggests caution in interpreting traditional tree
Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

Science.gov (United States)

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

2010-05-01

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.
Which trees should be removed in thinning?

Directory of Open Access Journals (Sweden)

Timo Pukkala

2015-12-01

Full Text Available Background: In economically optimal management, trees that are removed in a thinning treatment should be selected on the basis of their value, relative value increment and the effect of removal on the growth of remaining trees. Large valuable trees with decreased value increment should be removed, especially when they overtop smaller trees. Methods: This study optimized the tree selection rule in the thinning treatments of continuous cover management when the aim is to maximize the profitability of forest management. The weights of three criteria (stem value, relative value increment and effect of removal on the competition of remaining trees were optimized together with thinning intervals. Results and conclusions: The results confirmed the hypothesis that optimal thinning involves removing predominantly large trees. Increasing stumpage value, decreasing relative value increment, and increasing competitive influence increased the likelihood that removal is optimal decision. However, if the spatial distribution of trees is irregular, it is optimal to leave large trees in sparse places and remove somewhat smaller trees from dense places. However, the benefit of optimal thinning, as compared to diameter limit cutting is not usually large in pure one-species stands. On the contrary, removing the smallest trees from the stand may lead to significant (30–40 % reductions in the net present value of harvest incomes. Keywords: Continuous cover forestry, Tree selection, High thinning, Optimal management, Spatial distribution, Spatial growth model
CAN Tree Routing for Content-Addressable Network

Directory of Open Access Journals (Sweden)

Zhongtao LI

2014-01-01

Full Text Available We propose a novel topology to improve the routing performance of Content- Addressable Network overlays while minimizing the maintenance overhead during nodes churn. The key idea of our approach is to establish a P2P tree structure (CAN tree by means of equipping each node with a few long links towards some distant nodes. The long links enhance routing flexibility and robustness against failures. Nodes automatically adapt routing table to cope with network change. The routing complexity is O(log n, which is much better than a uniform greedy routing, while each node maintains two long links in average.
Folding and unfolding phylogenetic trees and networks.

Science.gov (United States)

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

2016-12-01

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

Science.gov (United States)

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.
Fuzzy tree automata and syntactic pattern recognition.

Science.gov (United States)

Lee, E T

1982-04-01

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

Science.gov (United States)

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

Science.gov (United States)

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. Published 2014 SETAC.
The transposition distance for phylogenetic trees

OpenAIRE

Rossello, Francesc; Valiente, Gabriel

2006-01-01

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this paper, we generalize the transposition distance from fully resolved to arbi...
Uniqueness of Steiner minimal trees on boundaries in general position

International Nuclear Information System (INIS)

Ivanov, A O; Tuzhilin, A A

2006-01-01

The following result is proved: there exists an open dense subset U of R 2n such that each P element of U (regarded as an enumerated subset of the standard Euclidean plane R 2 ) is spanned by a unique Steiner minimal tree, that is, a shortest non-degenerate network. Several interesting consequences are also obtained: in particular, it is proved that each planar Steiner tree is planar equivalent to a Steiner minimal tree.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

Directory of Open Access Journals (Sweden)

Auberval Nicolas

2009-05-01

Full Text Available Abstract Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/ and the source code can be downloaded from: http://code.google.com/p/taxomanie/.
ETE: a python Environment for Tree Exploration.

Science.gov (United States)

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

2010-01-13

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

Directory of Open Access Journals (Sweden)

Gabaldón Toni

2010-01-01

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

Energy Technology Data Exchange (ETDEWEB)

Bearup, Lindsay A., E-mail: lbearup@mines.edu [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Hydrological Science and Engineering Program, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Mikkelson, Kristin M. [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Hydrological Science and Engineering Program, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Wiley, Joseph F. [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Navarre-Sitchler, Alexis K.; Maxwell, Reed M. [Hydrological Science and Engineering Program, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Department of Geology and Geological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Sharp, Jonathan O.; McCray, John E. [Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States); Hydrological Science and Engineering Program, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (United States)

2014-10-15

Recent mountain pine beetle infestation in the Rocky Mountains of North America has killed an unprecedented acreage of pine forest, creating an opportunity to observe an active re-equilibration in response to widespread land cover perturbation. This work investigates metal mobility in beetle-impacted forests using parallel rainwater and acid leaches to estimate solid–liquid partitioning coefficients and a complete sequential extraction procedure to determine how metals are fractionated in soils under trees experiencing different phases of mortality. Geochemical model simulations analyzed in consideration with experimental data provide additional insight into the mechanisms controlling metal complexation. Metal and base-cation mobility consistently increased in soils under beetle-attacked trees relative to soil under healthy trees. Mobility increases were more pronounced on south facing slopes and more strongly correlated to pH under attacked trees than under healthy trees. Similarly, soil moisture was significantly higher under dead trees, related to the loss of transpiration and interception. Zinc and cadmium content increased in soils under dead trees relative to living trees. Cadmium increases occurred predominantly in the exchangeable fraction, indicating increased mobilization potential. Relative increases of zinc were greatest in the organic fraction, the only fraction where increases in copper were observed. Model results reveal that increased organic complexation, not changes in pH or base cation concentrations, can explain the observed differences in metal partitioning for zinc, nickel, cadmium, and copper. Predicted concentrations would be unlikely to impair human health or plant growth at these sites; however, higher exchangeable metals under beetle-killed trees relative to healthy trees suggest a possible decline in riverine ecosystem health and water quality in areas already approaching criteria limits and drinking water standards. Impairment of
Effects of liana load, tree diameter and distances between conspecifics on seed production in tropical timber trees

DEFF Research Database (Denmark)

Nabe-Nielsen, Jacob; Kollmann, Johannes Christian; Peña-Claros, Marielos

2009-01-01

Seed production in tropical timber trees is limited by abiotic resources, pollination and pre-dispersal seed predation. Resource availability is influenced by the number of competing trees and by lianas that often reach high densities in disturbed parts of tropical forests. The distance between...... conspecific trees affects pollination efficiency and seed predation intensity, and may therefore indirectly affect the long-term sustainability of selective logging. Here we investigate how reproductive status and the number of seeds dispersed per tree are affected by liana load, distance to the nearest...... and positively with tree diameter. In C. ianeirensis the most liana-infested trees dispersed fewer seeds. In T. oblonga the intensity of pre-dispersal seed predation decreased with distance to the nearest conspecifics. There was no evidence that seed viability or seed production decreased with distance...
The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

Science.gov (United States)

O'Reilly, Joseph E; Donoghue, Philip C J

2018-03-01

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.
Distance labeling schemes for trees

DEFF Research Database (Denmark)

Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

2016-01-01

We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille...... variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta...
Long-term monitoring of Sacramento Shade program trees: tree survival, growth and energy-saving performance

Science.gov (United States)

Yekang Ko; Jun-Hak Lee; E. Gregory McPherson; Lara A. Roman

2015-01-01

Long-term survival and growth of urban forests are critical to achieve the targeted benefits of urban tree planting programs, such as building energy savings from tree shade. However, little is known about how trees perform in the long-term, especially in residential areas. Given this gap in the literature, we monitored 22-years of post-planting survival, growth, and...
Atmospheric carbon reduction by urban trees

International Nuclear Information System (INIS)

Nowak, D.J.

1993-01-01

Trees, because they sequester atmospheric carbon through their growth process and conserve energy in urban areas, have been suggested as one means to combat increasing levels of atmospheric carbon. Analysis of the urban forest in Oakland, California (21% tree cover), reveals a tree carbon storage level of 11·0 metric tons/hectare. Trees in the area of the 1991 fire in Oakland stored approximately 14,500 metric tons of carbon, 10% of the total amount stored by Oakland's urban forest. National urban forest carbon storage in the United States (28% tree cover) is estimated at between 350 and 750 million metric tons. Establishment of 10 million urban trees annually over the next 10 years is estimated to sequester and offset the production of 363 million metric tons of carbon over the next 50 years-less than 1% of the estimated carbon emissions in the United States over the same time period. Advantages and limitations of managing urban trees to reduce atmospheric carbon are discussed. 36 refs., 2 figs., 3 tabs
Dimensional Reduction for the General Markov Model on Phylogenetic Trees.

Science.gov (United States)

Sumner, Jeremy G

2017-03-01

We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.
Systems analysis programs for hands-on integrated reliability evaluations (SAPHIRE) Version 5.0. Fault tree, event tree, and piping ampersand instrumentation diagram (FEP) editors reference manual: Volume 7

International Nuclear Information System (INIS)

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

1994-07-01

The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) refers to a set of several microcomputer programs that were developed to create and analyze probabilistic risk assessments (PRAs), primarily for nuclear power plants. The Fault Tree, Event Tree, and Piping and Instrumentation Diagram (FEP) editors allow the user to graphically build and edit fault trees, and event trees, and piping and instrumentation diagrams (P and IDs). The software is designed to enable the independent use of the graphical-based editors found in the Integrated Reliability and Risk Assessment System (IRRAS). FEP is comprised of three separate editors (Fault Tree, Event Tree, and Piping and Instrumentation Diagram) and a utility module. This reference manual provides a screen-by-screen guide of the entire FEP System
Navigation and Tree Mapping in Orchards

DEFF Research Database (Denmark)

Jæger-Hansen, Claes Lund; Griepentrog, Hans W.; Andersen, Jens Christian

In this paper an algorithm for estimating tree positions is presented. The sensors used for the algorithm is GNSS and LIDAR, and data is collected in an orchard with grapefruit trees while driving along the rows. The positions of the trees are estimated using ellipse fitting on point clouds....... The average accuracy for the center point estimation is 0.2 m in the along track direction and 0.35 m in the across track direction. The goal of the tree mapping algorithm is create a database of individual trees, and be the basis for creation of a graph map that can be used for mission planning...
Computer aided construction of fault tree

International Nuclear Information System (INIS)

Kovacs, Z.

1982-01-01

Computer code CAT for the automatic construction of the fault tree is briefly described. Code CAT makes possible simple modelling of components using decision tables, it accelerates the fault tree construction process, constructs fault trees of different complexity, and is capable of harmonized co-operation with programs PREPandKITT 1,2 for fault tree analysis. The efficiency of program CAT and thus the accuracy and completeness of fault trees constructed significantly depends on the compilation and sophistication of decision tables. Currently, program CAT is used in co-operation with programs PREPandKITT 1,2 in reliability analyses of nuclear power plant systems. (B.S.)
Computing Refined Buneman Trees in Cubic Time

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Östlin, A.

2003-01-01

Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence...... in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each...... proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our...
Tree Species Identity Shapes Earthworm Communities

Directory of Open Access Journals (Sweden)

Stephanie Schelfhout

2017-03-01

Full Text Available Earthworms are key organisms in forest ecosystems because they incorporate organic material into the soil and affect the activity of other soil organisms. Here, we investigated how tree species affect earthworm communities via litter and soil characteristics. In a 36-year old common garden experiment, replicated six times over Denmark, six tree species were planted in blocks: sycamore maple (Acer pseudoplatanus, beech (Fagus sylvatica, ash (Fraxinus excelsior, Norway spruce (Picea abies, pedunculate oak (Quercus robur and lime (Tilia cordata. We studied the chemical characteristics of soil and foliar litter, and determined the forest floor turnover rate and the density and biomass of the earthworm species occurring in the stands. Tree species significantly affected earthworm communities via leaf litter and/or soil characteristics. Anecic earthworms were abundant under Fraxinus, Acer and Tilia, which is related to calcium-rich litter and low soil acidification. Epigeic earthworms were indifferent to calcium content in leaf litter and were shown to be mainly related to soil moisture content and litter C:P ratios. Almost no earthworms were found in Picea stands, likely because of the combined effects of recalcitrant litter, low pH and low soil moisture content.
Efficient Algorithms for Computing the Triplet and Quartet Distance Between Trees of Arbitrary Degree

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas

2013-01-01

), respectively, and counting how often the induced topologies in the two input trees are different. In this paper we present efficient algorithms for computing these distances. We show how to compute the triplet distance in time O(n log n) and the quartet distance in time O(d n log n), where d is the maximal......The triplet and quartet distances are distance measures to compare two rooted and two unrooted trees, respectively. The leaves of the two trees should have the same set of n labels. The distances are defined by enumerating all subsets of three labels (triplets) and four labels (quartets...... degree of any node in the two trees. Within the same time bounds, our framework also allows us to compute the parameterized triplet and quartet distances, where a parameter is introduced to weight resolved (binary) topologies against unresolved (non-binary) topologies. The previous best algorithm...
Tree-centered spot firing - a technique for prescribed burning beneath standing trees.

Science.gov (United States)

C. Phillip Weatherspoon; George A. Almond; Carl N. Skinner

1989-01-01

Prescribed burning beneath standing trees normally requires efforts to protect residual trees from excessive fire damage. Damage to both crowns and boles is strongly influenced by flame length, a fire characteristic functionally related to fireline intensity (Albini 1976). In a good prescribed burn, therefore, the prescription specifies desired or maximum flame lengths...
Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment betw...
Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...
Characterizing root activity of guava trees by radiotracer technique

International Nuclear Information System (INIS)

Purohit, A.G.; Mukherjee, S.K.

1974-01-01

The distribution pattern of root activity of 12-year-old trees of guava (Psidium guajava L.) was determined by radiotracer technique. 32 P soloution was injected into the soil at lateral distances of 120, 240 and 360 cm from the tree trunk at depths of 15,30,60 and 90 cm. The 32 P uptake by the tree was determined by leaf analysis. In the rainy season the root activity or 32 P uptake was greater near the soil surface and midway between the trunk and the drip-line. The root activity decreased with an increase in the depth and distance from trunk. These results compared well with the actual distribution of feeder roots as determined by the soil-auger method. In summer the roots near the surface become less active in 32 P absorption with a drcrease in surface soil moisture. A decrease in the root activity in the surface soil was accompanied by an increase in 32 P uptake from lower depths. (author)

Application of Goal Tree-Success Tree model as the knowledge-base of operator advisory systems

International Nuclear Information System (INIS)

Kim, I.S.; Modarres, M.

1987-01-01

The most important portion of an expert system development is the articulation of knowledge by the expert and its satisfactory formulation in a suitable knowledge representation scheme for mechanization by a computer. A 'deep knowledge' approach called Goal Tree-Success Tree model is devised to represent complex dynamic domain knowledge. This approach can hierarchically model the underlying principles of a given process domain (for example nuclear power plant operations domain). The Goal Tree-Success Tree can then be used to represent the knowledge-base and provide means of selecting an efficient search routine in the inference engine of an expert system. A prototype expert system has been developed to demonstrate the method. This expert system models the operation of a typical system used in the pressurized water reactors. The expert system is modeled for real-time operations if an interface between plant parameters and the expert system is established. The real-time operation provides an ability to quickly remedy minor disturbances that can quickly lead to a system malfunction or trip. A description of both the Goal Tree-Success Tree model and the prototype expert system is presented. (orig.)
Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

Science.gov (United States)

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.
The dynamics of strangling among forest trees.

Science.gov (United States)

Okamoto, Kenichi W

2015-11-07

Strangler trees germinate and grow on other trees, eventually enveloping and potentially even girdling their hosts. This allows them to mitigate fitness costs otherwise incurred by germinating and competing with other trees on the forest floor, as well as minimize risks associated with host tree-fall. If stranglers can themselves host other strangler trees, they may not even seem to need non-stranglers to persist. Yet despite their high fitness potential, strangler trees neither dominate the communities in which they occur nor is the strategy particularly common outside of figs (genus Ficus). Here we analyze how dynamic interactions between strangling and non-strangling trees can shape the adaptive landscape for strangling mutants and mutant trees that have lost the ability to strangle. We find a threshold which strangler germination rates must exceed for selection to favor the evolution of strangling, regardless of how effectively hemiepiphytic stranglers may subsequently replace their hosts. This condition describes the magnitude of the phenotypic displacement in the ability to germinate on other trees necessary for invasion by a mutant tree that could potentially strangle its host following establishment as an epiphyte. We show how the relative abilities of strangling and non-strangling trees to occupy empty sites can govern whether strangling is an evolutionarily stable strategy, and obtain the conditions for strangler coexistence with non-stranglers. We then elucidate when the evolution of strangling can disrupt stable coexistence between commensal epiphytic ancestors and their non-strangling host trees. This allows us to highlight parallels between the invasion fitness of strangler trees arising from commensalist ancestors, and cases where strangling can arise in concert with the evolution of hemiepiphytism among free-standing ancestors. Finally, we discuss how our results can inform the evolutionary ecology of antagonistic interactions more generally
The relationship between tree height and leaf area: sapwood area ratio.

Science.gov (United States)

McDowell, N; Barnard, H; Bond, B; Hinckley, T; Hubbard, R; Ishii, H; Köstner, B; Magnani, F; Marshall, J; Meinzer, F; Phillips, N; Ryan, M; Whitehead, D

2002-06-01

The leaf area to sapwood area ratio (A l :A s ) of trees has been hypothesized to decrease as trees become older and taller. Theory suggests that A l :A s must decrease to maintain leaf-specific hydraulic sufficiency as path length, gravity, and tortuosity constrain whole-plant hydraulic conductance. We tested the hypothesis that A l :A s declines with tree height. Whole-tree A l :A s was measured on 15 individuals of Douglas-fir (Pseudotsuga menziesii var. menziesii) ranging in height from 13 to 62 m (aged 20-450 years). A l :A s declined substantially as height increased (P=0.02). Our test of the hypothesis that A l :A s declines with tree height was extended using a combination of original and published data on nine species across a range of maximum heights and climates. Meta-analysis of 13 whole-tree studies revealed a consistent and significant reduction in A l :A s with increasing height (P<0.05). However, two species (Picea abies and Abies balsamea) exhibited an increase in A l :A s with height, although the reason for this is not clear. The slope of the relationship between A l :A s and tree height (ΔA l :A s /Δh) was unrelated to mean annual precipitation. Maximum potential height was positively correlated with ΔA l :A s /Δh. The decrease in A l :A s with increasing tree size that we observed in the majority of species may be a homeostatic mechanism that partially compensates for decreased hydraulic conductance as trees grow in height.
Metal fate and partitioning in soils under bark beetle-killed trees.

Science.gov (United States)

Bearup, Lindsay A; Mikkelson, Kristin M; Wiley, Joseph F; Navarre-Sitchler, Alexis K; Maxwell, Reed M; Sharp, Jonathan O; McCray, John E

2014-10-15

Recent mountain pine beetle infestation in the Rocky Mountains of North America has killed an unprecedented acreage of pine forest, creating an opportunity to observe an active re-equilibration in response to widespread land cover perturbation. This work investigates metal mobility in beetle-impacted forests using parallel rainwater and acid leaches to estimate solid-liquid partitioning coefficients and a complete sequential extraction procedure to determine how metals are fractionated in soils under trees experiencing different phases of mortality. Geochemical model simulations analyzed in consideration with experimental data provide additional insight into the mechanisms controlling metal complexation. Metal and base-cation mobility consistently increased in soils under beetle-attacked trees relative to soil under healthy trees. Mobility increases were more pronounced on south facing slopes and more strongly correlated to pH under attacked trees than under healthy trees. Similarly, soil moisture was significantly higher under dead trees, related to the loss of transpiration and interception. Zinc and cadmium content increased in soils under dead trees relative to living trees. Cadmium increases occurred predominantly in the exchangeable fraction, indicating increased mobilization potential. Relative increases of zinc were greatest in the organic fraction, the only fraction where increases in copper were observed. Model results reveal that increased organic complexation, not changes in pH or base cation concentrations, can explain the observed differences in metal partitioning for zinc, nickel, cadmium, and copper. Predicted concentrations would be unlikely to impair human health or plant growth at these sites; however, higher exchangeable metals under beetle-killed trees relative to healthy trees suggest a possible decline in riverine ecosystem health and water quality in areas already approaching criteria limits and drinking water standards. Impairment of water
Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

Science.gov (United States)

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

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

Science.gov (United States)

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

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

Science.gov (United States)

Pawlik, Łukasz; Kasprzak, Marek

2018-01-01

Following previous findings regarding the influence of vascular plants (mainly trees) on weathering, soil production and hillslope stability, in this study, we attempted to test a hypothesis regarding significant impacts of tree root systems on soil and regolith properties. Different types of impacts from tree root system (direct and indirect) are commonly gathered under the key term of "biomechanical effects". To add to the discussion of the biomechanical effects of trees, we used a non-invasive geophysical method, electrical resistivity tomography (ERT), to investigate the profiles of four different configurations at three study sites within the Polish section of the Outer Western Carpathians. At each site, one long profile (up to 189 m) of a large section of a hillslope and three short profiles (up to 19.5 m), that is, microsites occupied by trees or their remnants, were made. Short profiles included the tree root zone of a healthy large tree, the tree stump of a decaying tree and the pit-and-mound topography formed after a tree uprooting. The resistivity of regolith and bedrock presented on the long profiles and in comparison with the short profiles through the microsites it can be seen how tree roots impact soil and regolith properties and add to the complexity of the whole soil/regolith profile. Trees change soil and regolith properties directly through root channels and moisture migration and indirectly through the uprooting of trees and the formation of pit-and-mound topography. Within tree stump microsites, the impact of tree root systems, evaluated by a resistivity model, was smaller compared to microsites with living trees or those with pit-and-mound topography but was still visible even several decades after the trees were windbroken or cut down. The ERT method is highly useful for quick evaluation of the impact of tree root systems on soils and regolith. This method, in contrast to traditional soil analyses, offers a continuous dataset for the entire
Mean-field lattice trees

NARCIS (Netherlands)

Borgs, C.; Chayes, J.T.; Hofstad, van der R.W.; Slade, G.

1999-01-01

We introduce a mean-field model of lattice trees based on embeddings into d of abstract trees having a critical Poisson offspring distribution. This model provides a combinatorial interpretation for the self-consistent mean-field model introduced previously by Derbez and Slade [9], and provides an
The space of ultrametric phylogenetic trees.

Science.gov (United States)

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
Differences in xylogenesis between dominant and suppressed trees.

Science.gov (United States)

Liu, Shushan; Li, Xiaoxia; Rossi, Sergio; Wang, Lily; Li, Wei; Liang, Eryuan; Leavitt, Steven W

2018-05-01

Most dendroecological studies focus on dominant trees, but little is known about the growing season of trees belonging to different size classes and their sensitivity to biotic factors. The objective of this study was to compare the dynamics of xylem formation between dominant and suppressed trees of Abies fabri of similar age growing in the Gongga Mountains, southeastern Tibetan Plateau, and to identify the association between xylem growth and climate. The timing and duration of xylogenesis in histological sections were investigated weekly during the 2013-2015 growing seasons. Our investigation found that timing and duration of xylogenesis varied with canopy position and its associated tree size. Xylogenesis started 6-14 days earlier, and ended 5-11 days later in dominant trees than in suppressed trees, resulting in a significantly longer growing season. Dominant trees also exhibited higher temperature sensitivity of tracheid production rate than suppressed trees. The observed differences in xylogenesis among trees suggested that competition affects tree growth by reducing the growing period in suppressed trees. Representative climate-growth relationships should involve trees of all size classes when evaluating the effects of the environment on forest dynamics. © 2018 Botanical Society of America.
Track treeing mechanism and its application

International Nuclear Information System (INIS)

Li Boyang

1993-01-01

Based on electrostriction and fracture mechanics, experiment observation and data-processing, two models (restriction among tree tracks and induction of tree track onto stress concentrated spots) and factors (restriction and induction) are proposed; The existence of four types of plastic zone (spot-block pz, single crack isolate pz, transition from isolate to block pz and crack-block pz) and two types of annex (plastic zone and crack zone) are pointed out. The development regularities of Gp (diameter of plastic zone), G(diameter of tree track), S(tree track density) and total areal of tree track (SG 2 ) in two basic experiments (H=H+dH, H=Hc H-field strength) are described by using four basic formulae. (author)
Influence of fuelwood trees on sodic soils

International Nuclear Information System (INIS)

Garg, V.K.; Jain, R.K.

1992-01-01

The persistent acute fuelwood shortage problem in India has necessitated having tree plantations on waste lands to obtain renewable energy. Fuelwood production screening trials initiated in 1981 at the Biomass Research Centre in Banthra, India identified babul, Acacia nilotica (L.) Wild. ex Delile, and mesquite, Prosopis juliflora (Swartz) DC., to be the most promising and suitable leguminous trees in terms of biomass production on sodic sites. A study was carried out to assess soil enrichment due to the growth of these fuelwood trees planted a decade past on sordic soil that had had no other amendments. Results showed preferential nutrient accumulation and greater reduction in soil pH (from 9.5 to 7.9) and exchangeable sodium (from 30 to 8%) at the P. juliflora plantation compared with at the A. nilotica plantation. There was also a reduction in surface soil (0-15 cm) bulk density, but an enhancement in porosity and water holding capacity, making soil more friable. The P. juliflora plantation produced markedly more leaf litter than the A. nilotica plantation. Both the species had fibrous lateral root systems on the surface in the sodic soil. However, the penetration and spread of roots were almost 2-fold greater in P. juliflora than in A. nilotica. Thus, the potential magnitude of changes in soil properties was related to the distribution of roots and amount of litter falling on the soil surface. Prosopis juliflora appeared to be better than A. nilotica under adverse sodic soil conditions in establishing an enlarged plant-litter nutrient cycle relationship. This study also provides an assessment of soil amelioration by leguminous trees under short-rotation forestry practices. 16 refs., 7 figs., 4 tabs
Influence of fuelwood trees on sodic soils

Energy Technology Data Exchange (ETDEWEB)

Garg, V.K.; Jain, R.K. (National Botanical Research Inst., Lucknow (India))

1992-01-01

The persistent acute fuelwood shortage problem in India has necessitated having tree plantations on waste lands to obtain renewable energy. Fuelwood production screening trials initiated in 1981 at the Biomass Research Centre in Banthra, India identified babul, Acacia nilotica (L.) Wild. ex Delile, and mesquite, Prosopis juliflora (Swartz) DC., to be the most promising and suitable leguminous trees in terms of biomass production on sodic sites. A study was carried out to assess soil enrichment due to the growth of these fuelwood trees planted a decade past on sordic soil that had had no other amendments. Results showed preferential nutrient accumulation and greater reduction in soil pH (from 9.5 to 7.9) and exchangeable sodium (from 30 to 8%) at the P. juliflora plantation compared with at the A. nilotica plantation. There was also a reduction in surface soil (0-15 cm) bulk density, but an enhancement in porosity and water holding capacity, making soil more friable. The P. juliflora plantation produced markedly more leaf litter than the A. nilotica plantation. Both the species had fibrous lateral root systems on the surface in the sodic soil. However, the penetration and spread of roots were almost 2-fold greater in P. juliflora than in A. nilotica. Thus, the potential magnitude of changes in soil properties was related to the distribution of roots and amount of litter falling on the soil surface. Prosopis juliflora appeared to be better than A. nilotica under adverse sodic soil conditions in establishing an enlarged plant-litter nutrient cycle relationship. This study also provides an assessment of soil amelioration by leguminous trees under short-rotation forestry practices. 16 refs., 7 figs., 4 tabs.
Values for rooted-tree and sink-tree digraphs games and sharing a river

NARCIS (Netherlands)

Khmelnitskaya, Anna Borisovna

We introduce values for rooted-tree and sink-tree digraph games axiomatically and provide their explicit formula representation. These values may be considered as natural extensions of the lower equivalent and upper equivalent solutions for line-graph games studied in Brink, Laan, and Vasil'ev
Wood for the trees

Directory of Open Access Journals (Sweden)

Rob Garbutt

2013-10-01

Full Text Available Our paper focuses on the materiality, cultural history and cultural relations of selected artworks in the exhibition Wood for the trees (Lismore Regional Gallery, New South Wales, Australia, 10 June – 17 July 2011. The title of the exhibition, intentionally misreading the aphorism “Can’t see the wood for the trees”, by reading the wood for the resource rather than the collective wood[s], implies conservation, preservation, and the need for sustaining the originating resource. These ideas have particular resonance on the NSW far north coast, a region once rich in rainforest. While the Indigenous population had sustainable practices of forest and land management, the colonists deployed felling and harvesting in order to convert the value of the local, abundant rainforest trees into high-value timber. By the late twentieth century, however, a new wave of settlers launched a protest movements against the proposed logging of remnant rainforest at Terania Creek and elsewhere in the region. Wood for the trees, curated by Gallery Director Brett Adlington, plays on this dynamic relationship between wood, trees and people. We discuss the way selected artworks give expression to the themes or concepts of productive labour, nature and culture, conservation and sustainability, and memory. The artworks include Watjinbuy Marrawilil’s (1980 Carved ancestral figure ceremonial pole, Elizabeth Stops’ (2009/10 Explorations into colonisation, Hossein Valamanesh’s (2008 Memory stick, and AñA Wojak’s (2008 Unread book (in a forgotten language. Our art writing on the works, a practice informed by Bal (2002, Muecke (2008 and Papastergiadis (2004, becomes a conversation between the works and the themes or concepts. As a form of material excess of the most productive kind (Grosz, 2008, p. 7, art seeds a response to that which is in the air waiting to be said of the past, present and future.
TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

Energy Technology Data Exchange (ETDEWEB)

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.
Maintenance of carbohydrate transport in tall trees

DEFF Research Database (Denmark)

Savage, Jessica A.; Beecher, Sierra D.; Clerx, Laura

2017-01-01

Trees present a critical challenge to long-distance transport because as a tree grows in height and the transport pathway increases in length, the hydraulic resistance of the vascular tissue should increase. This has led many to question whether trees can rely on a passive transport mechanism to ...... that reduce transport resistance. As a result, the key to the long-standing mystery of how trees maintain phloem transport as they increase in size lies in the structure of the phloem and its ability to change hydraulic properties with plant height.......Trees present a critical challenge to long-distance transport because as a tree grows in height and the transport pathway increases in length, the hydraulic resistance of the vascular tissue should increase. This has led many to question whether trees can rely on a passive transport mechanism...... in the leaves of a tall tree in situ. Across nine deciduous species, we find that hydraulic resistance in the phloem scales inversely with plant height because of a shift in sieve element structure along the length of individual trees. This scaling relationship seems robust across multiple species despite large...
Objective consensus from decision trees.

Science.gov (United States)

Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Dal Pra, Alan; Hundsberger, Thomas; Plasswilm, Ludwig

2014-12-05

Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties.
Longest common extensions in trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2016-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

Longest Common Extensions in Trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2015-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...
Objective consensus from decision trees

International Nuclear Information System (INIS)

Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Pra, Alan Dal; Hundsberger, Thomas; Plasswilm, Ludwig

2014-01-01

Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties
Sub-pixel estimation of tree cover and bare surface densities using regression tree analysis

Directory of Open Access Journals (Sweden)

Carlos Augusto Zangrando Toneli

2011-09-01

Full Text Available Sub-pixel analysis is capable of generating continuous fields, which represent the spatial variability of certain thematic classes. The aim of this work was to develop numerical models to represent the variability of tree cover and bare surfaces within the study area. This research was conducted in the riparian buffer within a watershed of the São Francisco River in the North of Minas Gerais, Brazil. IKONOS and Landsat TM imagery were used with the GUIDE algorithm to construct the models. The results were two index images derived with regression trees for the entire study area, one representing tree cover and the other representing bare surface. The use of non-parametric and non-linear regression tree models presented satisfactory results to characterize wetland, deciduous and savanna patterns of forest formation.
Reconciliation of Gene and Species Trees

Directory of Open Access Journals (Sweden)

L. Y. Rusin

2014-01-01

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

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

Science.gov (United States)

Lin, Yi; Jiang, Miao; Pellikka, Petri; Heiskanen, Janne

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology-light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.
Twentieth-century decline of large-diameter trees in Yosemite National Park, California, USA

Science.gov (United States)

Lutz, J.A.; van Wagtendonk, J.W.; Franklin, J.F.

2009-01-01

Studies of forest change in western North America often focus on increased densities of small-diameter trees rather than on changes in the large tree component. Large trees generally have lower rates of mortality than small trees and are more resilient to climate change, but these assumptions have rarely been examined in long-term studies. We combined data from 655 historical (1932-1936) and 210 modern (1988-1999) vegetation plots to examine changes in density of large-diameter trees in Yosemite National Park (3027 km2). We tested the assumption of stability for large-diameter trees, as both individual species and communities of large-diameter trees. Between the 1930s and 1990s, large-diameter tree density in Yosemite declined 24%. Although the decrease was apparent in all forest types, declines were greatest in subalpine and upper montane forests (57.0% of park area), and least in lower montane forests (15.3% of park area). Large-diameter tree densities of 11 species declined while only 3 species increased. Four general patterns emerged: (1) Pinus albicaulis, Quercus chrysolepis, and Quercus kelloggii had increases in density of large-diameter trees occur throughout their ranges; (2) Pinus jeffreyi, Pinus lambertiana, and Pinus ponderosa, had disproportionately larger decreases in large-diameter tree densities in lower-elevation portions of their ranges; (3) Abies concolor and Pinus contorta, had approximately uniform decreases in large-diameter trees throughout their elevational ranges; and (4) Abies magnifica, Calocedrus decurrens, Juniperus occidentalis, Pinus monticola, Pseudotsuga menziesii, and Tsuga mertensiana displayed little or no change in large-diameter tree densities. In Pinus ponderosa-Calocedrus decurrens forests, modern large-diameter tree densities were equivalent whether or not plots had burned since 1936. However, in unburned plots, the large-diameter trees were predominantly A. concolor, C. decurrens, and Q. chrysolepis, whereas P. ponderosa
Sampling the quality of hardwood trees

Science.gov (United States)

Adrian M. Gilbert

1959-01-01

Anyone acquainted with the conversion of hardwood trees into wood products knows that timber has a wide range in quality. Some trees will yield better products than others. So, in addition to rate of growth and size, tree values are affected by the quality of products yielded.
Nonbinary tree-based phylogenetic networks

OpenAIRE

Jetten, Laura; van Iersel, Leo

2016-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and st...
Speeding Up Neighbour-Joining Tree Construction

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas

A widely used method for constructing phylogenetic trees is the neighbour-joining method of Saitou and Nei. We develope heuristics for speeding up the neighbour-joining method which generate the same phylogenetic trees as the original method. All heuristics are based on using a quad-tree to guide...... the search for the next pair of nodes to join, but di#er in the information stored in quad-tree nodes, the way the search is performed, and in the way the quad-tree is updated after a join. We empirically evaluate the performance of the heuristics on distance matrices obtained from the Pfam collection...... of alignments, and compare the running time with that of the QuickTree tool, a well-known and widely used implementation of the standard neighbour-joining method. The results show that the presented heuristics can give a significant speed-up over the standard neighbour-joining method, already for medium sized...
An efficient and extensible approach for compressing phylogenetic trees

KAUST Repository

Matthews, Suzanne J

2011-01-01

Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.
Can live tree size-density relationships provide a mechanism for predicting down and dead tree resources?

Science.gov (United States)

Christopher Woodall; James Westfall

2009-01-01

Live tree size-density relationships in forests have long provided a framework for understanding stand dynamics. There has been little examination of the relationship between the size-density attributes of live and standing/down dead trees (e.g., number and mean tree size per unit area, such information could help in large-scale efforts to estimate dead wood resources...
Object-based methods for individual tree identification and tree species classification from high-spatial resolution imagery

Science.gov (United States)

Wang, Le

2003-10-01

Modern forest management poses an increasing need for detailed knowledge of forest information at different spatial scales. At the forest level, the information for tree species assemblage is desired whereas at or below the stand level, individual tree related information is preferred. Remote Sensing provides an effective tool to extract the above information at multiple spatial scales in the continuous time domain. To date, the increasing volume and readily availability of high-spatial-resolution data have lead to a much wider application of remotely sensed products. Nevertheless, to make effective use of the improving spatial resolution, conventional pixel-based classification methods are far from satisfactory. Correspondingly, developing object-based methods becomes a central challenge for researchers in the field of Remote Sensing. This thesis focuses on the development of methods for accurate individual tree identification and tree species classification. We develop a method in which individual tree crown boundaries and treetop locations are derived under a unified framework. We apply a two-stage approach with edge detection followed by marker-controlled watershed segmentation. Treetops are modeled from radiometry and geometry aspects. Specifically, treetops are assumed to be represented by local radiation maxima and to be located near the center of the tree-crown. As a result, a marker image was created from the derived treetop to guide a watershed segmentation to further differentiate overlapping trees and to produce a segmented image comprised of individual tree crowns. The image segmentation method developed achieves a promising result for a 256 x 256 CASI image. Then further effort is made to extend our methods to the multiscales which are constructed from a wavelet decomposition. A scale consistency and geometric consistency are designed to examine the gradients along the scale-space for the purpose of separating true crown boundary from unwanted
A bicriterion Steiner tree problem on graph

Directory of Open Access Journals (Sweden)

Vujošević Mirko B.

2003-01-01

Full Text Available This paper presents a formulation of bicriterion Steiner tree problem which is stated as a task of finding a Steiner tree with maximal capacity and minimal length. It is considered as a lexicographic multicriteria problem. This means that the bottleneck Steiner tree problem is solved first. After that, the next optimization problem is stated as a classical minimums Steiner tree problem under the constraint on capacity of the tree. The paper also presents some computational experiments with the multicriteria problem.
STANDING HERBAGE BIOMASS UNDER DIFFERENT TREE SPECIES DISPERSED IN PASTURES OF CATTLE FARMS

Directory of Open Access Journals (Sweden)

Humberto Esquivel-Mimenza

2013-08-01

Full Text Available The study conducted in a tropical dry ecosystem at CaÃ±as, Guanacaste, Costa Rica (10o 11Â´ N and 84o15Â´W measure the standing herbage biomass (SHB availability and quality under six isolated tree species of different canopy architecture dispersed in active Brachiaria brizantha pastures and compare it to that growing at full sun light. Standing herbage biomass (HB harvesting and Photosynthetic active radiation (PAR readings were taken at three different periods in a paired sample scheme. Of the six tree species studied, Enterolobium cyclocarpum had the largest mean crown cover while Acrocomia aculeata had the smallest. Significant differences were observed between species (P = 0.0002 and seasons (P<0.008 for the percentage of PAR transmitted under the canopy but PAR levels obtained under all species were consistent throughout seasons since the interaction between species and season was not significantly different (P=0.98. Lower PAR readings (<50% were taken under the canopies E. cyclocarpum and Guazuma ulmifolia (21.7 and 33.7 % respectively. Standing herbage biomass (SHB harvested under the crown of isolated mature individual tree species was significantly lower (P<0.001 than in open pasture areas for all tree species except that of A. aculeate but SHB crude protein content, was higher underneath all tree canopies. It can conclude that light reduction caused by tree canopies reduces SHB availability and increases the quality underneath tree canopies compared to areas of full sun but these varies accordingly to tree species and seasons.
The impact of tree age on biomass growth and carbon accumulation capacity: A retrospective analysis using tree ring data of three tropical tree species grown in natural forests of Suriname.

Science.gov (United States)

Köhl, Michael; Neupane, Prem R; Lotfiomran, Neda

2017-01-01

The world's forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime. We developed time series of diameter growth and related annual carbon accumulation for 61 trees of the species Cedrela odorata L. (Meliacea), Hymenaea courbaril L. (Fabacea) and Goupia glabra Aubl. (Goupiacea). The trees grew in unmanaged tropical wet-forests of Suriname and reached ages from 84 to 255 years. Most of the trees show positive trends of diameter growth and carbon accumulation over time. For some trees we observed fluctuating growth-periods of lower growth alternate with periods of increased growth. In the last quarter of their lifetime trees accumulate on average between 39 percent (C. odorata) and 50 percent (G. glabra) of their final carbon stock. This suggests that old-growth trees in tropical forests do not only contribute to carbon stocks by long carbon resistance times, but maintain high rates of carbon accumulation at later stages of their life time.
The gravity apple tree

International Nuclear Information System (INIS)

Aldama, Mariana Espinosa

2015-01-01

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. (paper)
An Investigation of the Relationship Between Tritium in Groundwater and the Dendrochronology of Tritium in Trees at the Savannah River Site. Final report

International Nuclear Information System (INIS)

Murphy, C.E. Jr.; Kalin, R.M.

1995-01-01

This project was supported through ERDA to demonstrate that the temporal distribution of tritium can be documented by the analysis of bound hydrogen in annual tree-ring samples. The project focuses on two sample locations at the Savannah River Site (SRS), a nuclear material production facility located in Aiken, SC. The SRS provided samples of cross-sections from a single tree that were to be pooled together for analysis. Annual tree-rings were identified in each cross-section sample and separated for the period 1954 to 1993. These annual samples were ground and chemically treated to separate the hollocellulose fraction of the wood, then subsequently combusted and the resulting water counting using low-level liquid scintillation counting equipment. Additionally, the ground annual tree-rings were gamma-counted to determine any temporal variation in radionuclide activity and analyzed with x-ray fluorescence to find any temporal variation in trace-element concentrations. This report presents the results and is intended to be a compilation of the work
Trees as templates for tropical litter arthropod diversity.

Science.gov (United States)

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

2010-09-01

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

Science.gov (United States)

Kevin T. Smith; Walter C. Shortle

1996-01-01

Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

Tree biomass in the Swiss landscape: nationwide modelling for improved accounting for forest and non-forest trees.

Science.gov (United States)

Price, B; Gomez, A; Mathys, L; Gardi, O; Schellenberger, A; Ginzler, C; Thürig, E

2017-03-01

Trees outside forest (TOF) can perform a variety of social, economic and ecological functions including carbon sequestration. However, detailed quantification of tree biomass is usually limited to forest areas. Taking advantage of structural information available from stereo aerial imagery and airborne laser scanning (ALS), this research models tree biomass using national forest inventory data and linear least-square regression and applies the model both inside and outside of forest to create a nationwide model for tree biomass (above ground and below ground). Validation of the tree biomass model against TOF data within settlement areas shows relatively low model performance (R 2 of 0.44) but still a considerable improvement on current biomass estimates used for greenhouse gas inventory and carbon accounting. We demonstrate an efficient and easily implementable approach to modelling tree biomass across a large heterogeneous nationwide area. The model offers significant opportunity for improved estimates on land use combination categories (CC) where tree biomass has either not been included or only roughly estimated until now. The ALS biomass model also offers the advantage of providing greater spatial resolution and greater within CC spatial variability compared to the current nationwide estimates.
A whole-tree chamber system for examining tree-level physiological responses of field-grown trees to environmental variation and climate change.

Science.gov (United States)

Medhurst, Jane; Parsby, Jan; Linder, Sune; Wallin, Göran; Ceschia, Eric; Slaney, Michelle

2006-09-01

A whole-tree chamber (WTC) system was installed at Flakaliden in northern Sweden to examine the long-term physiological responses of field-grown 40-year-old Norway spruce trees [Picea abies (L.) Karst.] to climate change. The WTCs were designed as large cuvettes to allow the net tree-level CO(2) and water fluxes to be measured on a continuous basis. A total of 12 WTCs were used to impose combinations of atmospheric carbon dioxide concentration, [CO(2)], and air temperature treatments. The air inside the ambient and elevated [CO(2)] WTCs was maintained at 365 and 700 micromol mol(-1), respectively. The air temperature inside the ambient temperature WTCs tracked air temperature outside the WTCs. Elevated temperatures were altered on a monthly time-step and ranged between +2.8 and +5.6 degrees C above ambient temperature. The system allowed continuous, long-term measurement of whole-tree photosynthesis, night-time respiration and transpiration. The performance of the WTCs was assessed using winter and spring data sets. The ability of the WTC system to measure tree-level physiological responses is demonstrated. All WTCs displayed a high level of control over tracking of air temperatures. The set target of 365 micromol mol(-1) in the ambient [CO(2)] chambers was too low to be maintained during winter because of tree dormancy and the high natural increase in [CO(2)] over winter at high latitudes such as the Flakaliden site. Accurate control over [CO(2)] in the ambient [CO(2)] chambers was restored during the spring and the system maintained the elevated [CO(2)] target of 700 micromol mol(-1) for both measurement periods. Air water vapour deficit (VPD) was accurately tracked in ambient temperature WTCs. However, as water vapour pressure in all 12 WTCs was maintained at the level of non-chambered (reference) air, VPD of elevated temperature WTCs was increased.
Molecular basis of angiosperm tree architecture.

Science.gov (United States)

Hollender, Courtney A; Dardick, Chris

2015-04-01

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.
snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

DEFF Research Database (Denmark)

Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund

2012-01-01

identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed...... to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic...... skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can...
Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

Directory of Open Access Journals (Sweden)

Yi Lin

2018-02-01

Full Text Available Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR. Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.
Tree species effect on the redistribution of soil metals

International Nuclear Information System (INIS)

Mertens, Jan; Van Nevel, Lotte; De Schrijver, An; Piesschaert, Frederic; Oosterbaan, Anne; Tack, Filip M.G.; Verheyen, Kris

2007-01-01

Phytostabilization of metals using trees is often promoted although the influence of different tree species on the mobilization of metals is not yet clear. Soil and biomass were sampled 33 years after planting four tree species (Quercus robur, Fraxinus excelsior, Acer pseudoplatanus, Populus 'Robusta') in a plot experiment on dredged sediment. Poplar took up high amounts of Cd and Zn and this was associated with increased Cd and Zn concentrations in the upper soil layer. The other species contained normal concentrations of Cd, Cu, Cr, Pb and Zn in their tissues. Oak acidified the soil more than the other species and caused a decrease in the concentration of metals in the upper soil layer. The pH under poplar was lower than expected and associated with high carbon concentrations in the top soil. This might be assigned to retardation of the litter decomposition due to elevated Cd and Zn concentrations in the litter. - Trees (33-year-old) growing on polluted dredged sediment have influenced the metal concentration in the upper soil layer and there was a significant tree species effect
The Tree of Industrial Life

DEFF Research Database (Denmark)

Andersen, Esben Sloth

2002-01-01

The purpose of this paper is to bring forth an interaction between evolutionary economics and industrial systematics. The suggested solution is to reconstruct the "family tree" of the industries. Such a tree is based on similarities, but it may also reflect the evolutionary history in industries....... For this purpose the paper shows how matrices of input-output coefficients can be transformed into binary characteristics matrices and to distance matrices, and it also discusses the possible evolutionary meaning of this translation. Then these derived matrices are used as inputs to algorithms for the heuristic...... finding of optimal industrial trees. The results are presented as taxonomic trees that can easily be compared with the hierarchical structure of existing systems of industrial classification....
Decision tree modeling using R.

Science.gov (United States)

Zhang, Zhongheng

2016-08-01

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

Science.gov (United States)

F.C. Meinzer; S.A. James; G. Goldstein; D. Woodruff

2003-01-01

The present study examines the manner in which several whole-tree water transport properties scale with species specific variation in sapwood water storage capacity. The hypothesis that constraints on relationships between sapwood capacitance and other water relations characteristics lead to predictable scaling relationships between intrinsic capacitance and whole-tree...
Ecological Importance of Large-Diameter Trees in a Temperate Mixed-Conifer Forest

Science.gov (United States)

Lutz, James A.; Larson, Andrew J.; Swanson, Mark E.; Freund, James A.

2012-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. Although both scaling theory and competition theory make predictions about the relative composition and spatial patterns of large-diameter trees compared to smaller diameter trees, these predictions are rarely tested. We established a 25.6 ha permanent plot within which we tagged and mapped all trees ≥1 cm dbh, all snags ≥10 cm dbh, and all shrub patches ≥2 m2. We sampled downed woody debris, litter, and duff with line intercept transects. Aboveground live biomass of the 23 woody species was 507.9 Mg/ha, of which 503.8 Mg/ha was trees (SD = 114.3 Mg/ha) and 4.1 Mg/ha was shrubs. Aboveground live and dead biomass was 652.0 Mg/ha. Large-diameter trees comprised 1.4% of individuals but 49.4% of biomass, with biomass dominated by Abies concolor and Pinus lambertiana (93.0% of tree biomass). The large-diameter component dominated the biomass of snags (59.5%) and contributed significantly to that of woody debris (36.6%). Traditional scaling theory was not a good model for either the relationship between tree radii and tree abundance or tree biomass. Spatial patterning of large-diameter trees of the three most abundant species differed from that of small-diameter conspecifics. For A. concolor and P. lambertiana, as well as all trees pooled, large-diameter and small-diameter trees were spatially segregated through inter-tree distances trees and spatial relationships between large-diameter and small-diameter trees. Long-term observations may reveal regulation of forest biomass and spatial structure by fire, wind, pathogens, and insects in Sierra Nevada mixed-conifer forests. Sustaining ecosystem functions such as carbon storage or provision of specialist species habitat will likely require different management strategies when the functions are performed primarily by a few large trees as opposed to many smaller trees. PMID:22567132
Relationship of Climatic and Forest Factors to Drought- and Heat-Induced Tree Mortality.

Directory of Open Access Journals (Sweden)

Qingyin Zhang

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

OpenAIRE

Brousseau, Louise; Baraloto, Christopher

2016-01-01

The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original mult...
Effects of nurse trees, spacing, and tree species on biomass production in mixed forest plantations

DEFF Research Database (Denmark)

Nord-Larsen, Thomas; Meilby, Henrik

2016-01-01

Growing concern about increasing concentrations of greenhouse gases in the atmosphere, and resulting global climate change, has spurred a growing demand for renewable energy. In this study, we hypothesized that a nurse tree crop may provide additional early yields of biomass for fuel, while...... was in most cases reduced due to competition. However, provided timely thinning of nurse trees, the qualitative development of the trees will allow for long-term timber production....
The Tree Inclusion Problem: In Linear Space and Faster

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li

2011-01-01

Given two rooted, ordered, and labeled trees P and T the tree inclusion problem is to determine if P can be obtained from T by deleting nodes in T. This problem has recently been recognized as an important query primitive in XML databases. Kilpel äinen and Mannila [1995] presented the first....... This is particularly important in practical applications, such as XML databases, where the space is likely to be a bottleneck. © 2011 ACM....
Modeling Caribbean tree stem diameters from tree height and crown width measurements

Science.gov (United States)

Thomas Brandeis; KaDonna Randolph; Mike Strub

2009-01-01

Regression models to predict diameter at breast height (DBH) as a function of tree height and maximum crown radius were developed for Caribbean forests based on data collected by the U.S. Forest Service in the Commonwealth of Puerto Rico and Territory of the U.S. Virgin Islands. The model predicting DBH from tree height fit reasonably well (R2 = 0.7110), with...
Field guide to red tree vole nests

Science.gov (United States)

Damon B. Lesmeister; James K. Swingle

2017-01-01

Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (â¥80 years old) that are structurally complex, but are often...
Growing Greener Cities: A Tree-Planting Handbook.

Science.gov (United States)

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…
The tree BVOC index

Science.gov (United States)

J.R. Simpson; E.G. McPherson

2011-01-01

Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...
Structural Equation Model Trees

Science.gov (United States)

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…
Automated Generation of Attack Trees

DEFF Research Database (Denmark)

Vigo, Roberto; Nielson, Flemming; Nielson, Hanne Riis

2014-01-01

Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error-prone and impractica......Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error......-prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...... are automatically inferred from a process algebraic specification in a syntax-directed fashion, encompassing a great many application domains and avoiding incurring systematically an exponential explosion. Moreover, we show how the standard propositional denotation of an attack tree can be used to phrase...

Computer-aided Fault Tree Analysis

International Nuclear Information System (INIS)

Willie, R.R.

1978-08-01

A computer-oriented methodology for deriving minimal cut and path set families associated with arbitrary fault trees is discussed first. Then the use of the Fault Tree Analysis Program (FTAP), an extensive FORTRAN computer package that implements the methodology is described. An input fault tree to FTAP may specify the system state as any logical function of subsystem or component state variables or complements of these variables. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. FTAP can also identify certain subsystems associated with the tree as system modules and provide a collection of minimal cut set families that essentially expresses the state of the system as a function of these module state variables. Another FTAP feature allows a subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily consists only of sets that are interesting to the analyst in a special sense
Assessing the Effects of Periodic Flooding on the Population Structure and Recruitment Rates of Riparian Tree Forests

Directory of Open Access Journals (Sweden)

Jean-Sébastien Berthelot

2014-08-01

Full Text Available Riparian forest stands are subjected to a variety of hydrological stresses as a result of annual fluctuations in water levels during the growing season. Spring floods create additional water-related stress as a result of a major inflow of water that floods riverside land. This exploratory study assesses the impacts of successive floods on tree dynamics and regeneration in an active sedimentation area, while determining the age of the stands using the recruitment rates, tree structure and tree rings based on dendrochronological analysis. Environmental data were also recorded for each vegetation quadrat. In total, 2633 tree stems were tallied throughout the quadrats (200 m2, and tree specimens were analyzed based on the various flood zones. A total of 720 specimens were counted (100 m2 strip to measure natural regeneration. Higher recruitment rates are noted for the no-flood zones and lower rates in active floodplains. During the period of the establishment of tree species, the survival rates are comparable between the flood zones and the no-flood zones. Tree diameter distribution reveals a strong predominance of young trees in flooded areas. Different factors appear to come into play in the dynamics of riparian forest stands, including the disruptions associated with successive flooding.
Analyzing and synthesizing phylogenies using tree alignment graphs.

Directory of Open Access Journals (Sweden)

Stephen A Smith

Full Text Available 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
Analyzing and synthesizing phylogenies using tree alignment graphs.

Science.gov (United States)

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.
Variability of the tree-rings structure of Gmelin’s larch at northern tree line (peninsula of Taymyr

Directory of Open Access Journals (Sweden)

V. V. Fakhrutdinova

2017-04-01

Full Text Available The study of tree-ring cell structure changes as the result of tree adaptation to varying environmental conditions becomes increasingly important to predict future vegetation shifts under projected climate changes. The estimate of intrapopulation annual variability of wood anatomy characteristics is particularly informative. It helps to divide the contribution of different ecological factors to total features dispersion. In this work, a comparative analysis of individual and climatic variability of tree ring structure characteristics of Gmelin’s larch Larix gmelinii (Rupr. growth within northernmost forest was carried out. The trees from forest-tundra boundary has greater radial growth intensity, forms the bigger conductive zone in rings with wider mean lumen area in comparison with trees from closed forest. This result can be explained by adaptive features and height ecological xylem plasticity of larch. The tree rings structure of larch from boundary with tundra is determined by largely current weather conditions. Is because these ones evince high adaptive plasticity on the level of xylem structure. The xylem reflects joint changes of climate factors and local ecological conditions. The trees from closed forest are characterized by larger individual variability. The local conditions in oldest forest (for example, bad hydrothermal soil conditions inhibit the radial growth and sensitivity to environmental factors. In this case, the trees on individual level are tended to save the normal functioning of water-transport system. The significant differences in ratio individual to climate variability of tree ring structure characteristics can be caused by the different in the level of ecological habitat heterogeneity or the different in the level genetic within-population heterogeneity.
Cafts: computer aided fault tree analysis

International Nuclear Information System (INIS)

Poucet, A.

1985-01-01

The fault tree technique has become a standard tool for the analysis of safety and reliability of complex system. In spite of the costs, which may be high for a complete and detailed analysis of a complex plant, the fault tree technique is popular and its benefits are fully recognized. Due to this applications of these codes have mostly been restricted to simple academic examples and rarely concern complex, real world systems. In this paper an interactive approach to fault tree construction is presented. The aim is not to replace the analyst, but to offer him an intelligent tool which can assist him in modeling complex systems. Using the CAFTS-method, the analyst interactively constructs a fault tree in two phases: (1) In a first phase he generates an overall failure logic structure of the system; the macrofault tree. In this phase, CAFTS features an expert system approach to assist the analyst. It makes use of a knowledge base containing generic rules on the behavior of subsystems and components; (2) In a second phase the macrofault tree is further refined and transformed in a fully detailed and quantified fault tree. In this phase a library of plant-specific component failure models is used
Human reliability analysis using event trees

International Nuclear Information System (INIS)

Heslinga, G.

1983-01-01

The shut-down procedure of a technologically complex installation as a nuclear power plant consists of a lot of human actions, some of which have to be performed several times. The procedure is regarded as a chain of modules of specific actions, some of which are analyzed separately. The analysis is carried out by making a Human Reliability Analysis event tree (HRA event tree) of each action, breaking down each action into small elementary steps. The application of event trees in human reliability analysis implies more difficulties than in the case of technical systems where event trees were mainly used until now. The most important reason is that the operator is able to recover a wrong performance; memory influences play a significant role. In this study these difficulties are dealt with theoretically. The following conclusions can be drawn: (1) in principle event trees may be used in human reliability analysis; (2) although in practice the operator will recover his fault partly, theoretically this can be described as starting the whole event tree again; (3) compact formulas have been derived, by which the probability of reaching a specific failure consequence on passing through the HRA event tree after several times of recovery is to be calculated. (orig.)
On the book thickness of $k$-trees

OpenAIRE

Dujmović, Vida; Wood, David R.

2009-01-01

Graphs and Algorithms; International audience; Every k-tree has book thickness at most k + 1, and this bound is best possible for all k \\textgreater= 3. Vandenbussche et al. [SIAM J. Discrete Math., 2009] proved that every k-tree that has a smooth degree-3 tree decomposition with width k has book thickness at most k. We prove this result is best possible for k \\textgreater= 4, by constructing a k-tree with book thickness k + 1 that has a smooth degree-4 tree decomposition with width k. This s...
Border trees of complex networks

International Nuclear Information System (INIS)

Villas Boas, Paulino R; Rodrigues, Francisco A; Travieso, Gonzalo; Fontoura Costa, Luciano da

2008-01-01

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small-world properties of real networks were fundamental to stimulate more realistic models and to understand important dynamical processes related to network growth. However, the properties of the network borders (nodes with degree equal to 1), one of its most fragile parts, remained little investigated and understood. The border nodes may be involved in the evolution of structures such as geographical networks. Here we analyze the border trees of complex networks, which are defined as the subgraphs without cycles connected to the remainder of the network (containing cycles) and terminating into border nodes. In addition to describing an algorithm for identification of such tree subgraphs, we also consider how their topological properties can be quantified in terms of their depth and number of leaves. We investigate the properties of border trees for several theoretical models as well as real-world networks. Among the obtained results, we found that more than half of the nodes of some real-world networks belong to the border trees. A power-law with cut-off was observed for the distribution of the depth and number of leaves of the border trees. An analysis of the local role of the nodes in the border trees was also performed
Acidity of tree bark as a bioindicator of forest pollution in southern Poland

Energy Technology Data Exchange (ETDEWEB)

Grodzinska, K

1977-05-01

pH values and buffering capacity were determined for bark samples of five deciduous trees (oak, alder, hornbeam, ash, linden), one shrub (hazel) and one coniferous tree (scots pine) in the Cracow Industrial Region (southern Poland) and, for comparison, in the Bialowieza Forest (northeastern Poland). The correlation was found between acidification of tree bark and air pollution by SO/sub 2/ in these areas. All trees showed the least acidic reaction in the control area (Bialowieza Forest), more acidic in Niepolomice Forest and the most acidic in the center of Cracow. The buffering capacity of the bark against alkali increased with increasing air pollution. The seasonal fluctuations of pH values and buffering capacity were found. Tree bark is recommended as a sensitive and simple indicator of air pollution.
A Method to Quantify Plant Availability and Initiating Event Frequency Using a Large Event Tree, Small Fault Tree Model

International Nuclear Information System (INIS)

Kee, Ernest J.; Sun, Alice; Rodgers, Shawn; Popova, ElmiraV; Nelson, Paul; Moiseytseva, Vera; Wang, Eric

2006-01-01

South Texas Project uses a large fault tree to produce scenarios (minimal cut sets) used in quantification of plant availability and event frequency predictions. On the other hand, the South Texas Project probabilistic risk assessment model uses a large event tree, small fault tree for quantifying core damage and radioactive release frequency predictions. The South Texas Project is converting its availability and event frequency model to use a large event tree, small fault in an effort to streamline application support and to provide additional detail in results. The availability and event frequency model as well as the applications it supports (maintenance and operational risk management, system engineering health assessment, preventive maintenance optimization, and RIAM) are briefly described. A methodology to perform availability modeling in a large event tree, small fault tree framework is described in detail. How the methodology can be used to support South Texas Project maintenance and operations risk management is described in detail. Differences with other fault tree methods and other recently proposed methods are discussed in detail. While the methods described are novel to the South Texas Project Risk Management program and to large event tree, small fault tree models, concepts in the area of application support and availability modeling have wider applicability to the industry. (authors)
Success tree method of resources evaluation

International Nuclear Information System (INIS)

Chen Qinglan; Sun Wenpeng

1994-01-01

By applying the reliability theory in system engineering, the success tree method is used to transfer the expert's recognition on metallogenetic regularities into the form of the success tree. The aim of resources evaluation is achieved by means of calculating the metallogenetic probability or favorability of the top event of the success tree. This article introduces in detail, the source, principle of the success tree method and three kinds of calculation methods, expounds concretely how to establish the success tree of comprehensive uranium metallogenesis as well as the procedure from which the resources evaluation is performed. Because this method has not restrictions on the number of known deposits and calculated area, it is applicable to resources evaluation for different mineral species, types and scales and possesses good prospects of development
Critical wind speed at which trees break

Science.gov (United States)

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.
Critical wind speed at which trees break.

Science.gov (United States)

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 (≃42m/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.
Neutron activation analysis of absolutely-dated tree rings

International Nuclear Information System (INIS)

Uenlue, K.; Hauck, D.K.; Kuniholm, P.I.; Chiment, J.J.

2005-01-01

Gold concentration was determined for dendrochronologically-dated wood samples using neutron activation analysis (NAA) and correlation sought with known environmental changes, e.g., volcanic activities, during historic periods. Uptake of gold is sensitive to soil pH for many plants. Data presented are from a single, cross-dated tree that grew in Greece. Using NAA, gold was measured with parts-per-billion sensitivity in individual tree rings from 1411 to 1988 AD. (author)
Belowground uptake strategies: how fine-root traits determine tree growth

NARCIS (Netherlands)

Weemstra, Monique

2017-01-01

<p>The growth of trees depends on photosynthetic carbon gain by the leaves, which in turn relies on water and nutrient acquisition by the fine roots. Because the availability of carbon, water and nutrients fluctuates, trees can adjust their leaf and fine-root functional traits to maintain their
Markers inside wood : tree rings as archives of insect outbreaks, drift-sand dynamics, and spring flooding

NARCIS (Netherlands)

Copini, P.

2015-01-01

<p>MARKERS INSIDE WOOD – TREE RINGS AS ARCHIVES OF INSECT OUTBREAKS, DRIFT-SAND DYNAMICS AND SPRING FLOODINGp> <p>Trees are long-living organisms that record ecologically relevant information in their xylem that can be accessed by dendrochronology, the study of tree rings. Specific environmental
Comprehensive decision tree models in bioinformatics.

Directory of Open Access Journals (Sweden)

Gregor Stiglic

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

Science.gov (United States)

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

2012-01-01

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

NARCIS (Netherlands)

S. Canzar (Stefan); K. Elbassioni; G.W. Klau (Gunnar); J. Mestre

2011-01-01

htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that

Aspects of insertion in random trees

NARCIS (Netherlands)

Bagchi, Arunabha; Reingold, E.M.

1982-01-01

A method formulated by Yao and used by Brown has yielded bounds on the fraction of nodes with specified properties in trees bult by a sequence of random internal nodes in a random tree built by binary search and insertion, and show that in such a tree about bounds better than those now known. We
Visual exploration of parameter influence on phylogenetic trees.

Science.gov (United States)

Hess, Martin; Bremm, Sebastian; Weissgraeber, Stephanie; Hamacher, Kay; Goesele, Michael; Wiemeyer, Josef; von Landesberger, Tatiana

2014-01-01

Evolutionary relationships between organisms are frequently derived as phylogenetic trees inferred from multiple sequence alignments (MSAs). The MSA parameter space is exponentially large, so tens of thousands of potential trees can emerge for each dataset. A proposed visual-analytics approach can reveal the parameters' impact on the trees. Given input trees created with different parameter settings, it hierarchically clusters the trees according to their structural similarity. The most important clusters of similar trees are shown together with their parameters. This view offers interactive parameter exploration and automatic identification of relevant parameters. Biologists applied this approach to real data of 16S ribosomal RNA and protein sequences of ion channels. It revealed which parameters affected the tree structures. This led to a more reliable selection of the best trees.
GuiaTreeKey, a multi-access electronic key to identify tree genera in French Guiana.

Science.gov (United States)

Engel, Julien; Brousseau, Louise; Baraloto, Christopher

2016-01-01

The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines. The electronic key is accessible with the free access software Xper ², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550).
Rooted triple consensus and anomalous gene trees

Directory of Open Access Journals (Sweden)

Schmidt Heiko A

2008-04-01

Full Text Available Abstract Background Anomalous gene trees (AGTs are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. Results Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny. Conclusion Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.
Benefits of tree mixes in carbon plantings

Science.gov (United States)

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.
Visualizing Contour Trees within Histograms

DEFF Research Database (Denmark)

Kraus, Martin

2010-01-01

Many of the topological features of the isosurfaces of a scalar volume field can be compactly represented by its contour tree. Unfortunately, the contour trees of most real-world volume data sets are too complex to be visualized by dot-and-line diagrams. Therefore, we propose a new visualization...... that is suitable for large contour trees and efficiently conveys the topological structure of the most important isosurface components. This visualization is integrated into a histogram of the volume data; thus, it offers strictly more information than a traditional histogram. We present algorithms...... to automatically compute the graph layout and to calculate appropriate approximations of the contour tree and the surface area of the relevant isosurface components. The benefits of this new visualization are demonstrated with the help of several publicly available volume data sets....
Algorithms for Decision Tree Construction

KAUST Repository

Chikalov, Igor

2011-01-01

The study of algorithms for decision tree construction was initiated in 1960s. The first algorithms are based on the separation heuristic [13, 31] that at each step tries dividing the set of objects as evenly as possible. Later Garey and Graham [28] showed that such algorithm may construct decision trees whose average depth is arbitrarily far from the minimum. Hyafil and Rivest in [35] proved NP-hardness of DT problem that is constructing a tree with the minimum average depth for a diagnostic problem over 2-valued information system and uniform probability distribution. Cox et al. in [22] showed that for a two-class problem over information system, even finding the root node attribute for an optimal tree is an NP-hard problem. © Springer-Verlag Berlin Heidelberg 2011.
Multiscale singularity trees

DEFF Research Database (Denmark)

Somchaipeng, Kerawit; Sporring, Jon; Johansen, Peter

2007-01-01

We propose MultiScale Singularity Trees (MSSTs) as a structure to represent images, and we propose an algorithm for image comparison based on comparing MSSTs. The algorithm is tested on 3 public image databases and compared to 2 state-of-theart methods. We conclude that the computational complexity...... of our algorithm only allows for the comparison of small trees, and that the results of our method are comparable with state-of-the-art using much fewer parameters for image representation....
Wind-Induced Reconfigurations in Flexible Branched Trees

Science.gov (United States)

Ojo, Oluwafemi; Shoele, Kourosh

2017-11-01

Wind induced stresses are the major mechanical cause of failure in trees. We know that the branching mechanism has an important effect on the stress distribution and stability of a tree in the wind. Eloy in PRL 2011, showed that Leonardo da Vinci's original observation which states the total cross section of branches is conserved across branching nodes is the best configuration for resisting wind-induced fracture in rigid trees. However, prediction of the fracture risk and pattern of a tree is also a function of their reconfiguration capabilities and how they mitigate large wind-induced stresses. In this studies through developing an efficient numerical simulation of flexible branched trees, we explore the role of the tree flexibility on the optimal branching. Our results show that the probability of a tree breaking at any point depends on both the cross-section changes in the branching nodes and the level of tree flexibility. It is found that the branching mechanism based on Leonardo da Vinci's original observation leads to a uniform stress distribution over a wide range of flexibilities but the pattern changes for more flexible systems.
Measuring and analyzing urban tree cover

Science.gov (United States)

David J. Nowak; Rowan A. Rowntree; E. Gregory McPherson; Susan M. Sisinni; Esther R. Kirkmann; Jack C. Stevens

1996-01-01

Measurement of city tree cover can aid in urban vegetation planning, management, and research by revealing characteristics of vegetation across a city. Urban tree cover in the United States ranges from 0.4% in Lancaster, California, to 55% in Baton Rouge, Louisiana. Two important factors that affect the amount of urban tree cover are the natural environment and land...
Do you believe in palm trees?

Science.gov (United States)

Kevin T. Smith

2013-01-01

Palms are real, but are they really trees? The answer depends on definitions. As usually tall, peremrial plants with roots, stems, and leaves, palms seem to qualify. Palms should also qualify because arborists care for them, and arborists care for trees, right? My introduction to botany class defined trees as plants that produce wood. Unraveling the question of whether...
Taxonomic identity determines N2 fixation by canopy trees across lowland tropical forests.

Science.gov (United States)

Wurzburger, Nina; Hedin, Lars O

2016-01-01

Legumes capable of fixing atmospheric N2 are abundant and diverse in many tropical forests, but the factors determining ecological patterns in fixation are unresolved. A long-standing idea is that fixation depends on soil nutrients (N, P or Mo), but recent evidence shows that fixation may also differ among N2-fixing species. We sampled canopy-height trees across five species and one species group of N2-fixers along a landscape P gradient, and manipulated P and Mo to seedlings in a shadehouse. Our results identify taxonomy as the major determinant of fixation, with P (and possibly Mo) only influencing fixation following tree-fall disturbances. While 44% of trees did not fix N2, other trees fixed at high rates, with two species functioning as superfixers across the landscape. Our results raise the possibility that fixation is determined by biodiversity, evolutionary history and species-specific traits (tree growth rate, canopy stature and response to disturbance) in the tropical biome. © 2015 John Wiley & Sons Ltd/CNRS.
Modeling Ecosystem Services for Park Trees: Sensitivity of i-Tree Eco Simulations to Light Exposure and Tree Species Classification

Directory of Open Access Journals (Sweden)

Rocco Pace

2018-02-01

Full Text Available Ecosystem modeling can help decision making regarding planting of urban trees for climate change mitigation and air pollution reduction. Algorithms and models that link the properties of plant functional types, species groups, or single species to their impact on specific ecosystem services have been developed. However, these models require a considerable effort for initialization that is inherently related to uncertainties originating from the high diversity of plant species in urban areas. We therefore suggest a new automated method to be used with the i-Tree Eco model to derive light competition for individual trees and investigate the importance of this property. Since competition depends also on the species, which is difficult to determine from increasingly used remote sensing methodologies, we also investigate the impact of uncertain tree species classification on the ecosystem services by comparing a species-specific inventory determined by field observation with a genus-specific categorization and a model initialization for the dominant deciduous and evergreen species only. Our results show how the simulation of competition affects the determination of carbon sequestration, leaf area, and related ecosystem services and that the proposed method provides a tool for improving estimations. Misclassifications of tree species can lead to large deviations in estimates of ecosystem impacts, particularly concerning biogenic volatile compound emissions. In our test case, monoterpene emissions almost doubled and isoprene emissions decreased to less than 10% when species were estimated to belong only to either two groups instead of being determined by species or genus. It is discussed that this uncertainty of emission estimates propagates further uncertainty in the estimation of potential ozone formation. Overall, we show the importance of using an individual light competition approach and explicitly parameterizing all ecosystem functions at the
Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement.

Science.gov (United States)

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. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
A Characterization of 2-Tree Probe Interval Graphs

Directory of Open Access Journals (Sweden)

Brown David E.

2014-08-01

Full Text Available A graph is a probe interval graph if its vertices correspond to some set of intervals of the real line and can be partitioned into sets P and N so that vertices are adjacent if and only if their corresponding intervals intersect and at least one belongs to P. We characterize the 2-trees which are probe interval graphs and extend a list of forbidden induced subgraphs for such graphs created by Pržulj and Corneil in [2-tree probe interval graphs have a large obstruction set, Discrete Appl. Math. 150 (2005 216-231
Are the birch trees in Southern England a source of Betula pollen for North London?

Science.gov (United States)

Skjøth, C. A.; Smith, M.; Brandt, J.; Emberlin, J.

2009-01-01

Birch pollen is highly allergenic. Knowledge of daily variations, atmospheric transport and source areas of birch pollen is important for exposure studies and for warnings to the public, especially for large cities such as London. Our results show that broad-leaved forests with high birch tree densities are located to the south and west of London. Bi-hourly Betula pollen concentrations for all the days included in the study, and for all available days with high birch pollen counts (daily average birch pollen counts >80 grains/m3), show that, on average, there is a peak between 1400 hours and 1600 hours. Back-trajectory analysis showed that, on days with high birch pollen counts ( n = 60), 80% of air masses arriving at the time of peak diurnal birch pollen count approached North London from the south in a 180 degree arc from due east to due west. Detailed investigations of three Betula pollen episodes, with distinctly different diurnal patterns compared to the mean daily cycle, were used to illustrate how night-time maxima (2200-0400 hours) in Betula pollen counts could be the result of transport from distant sources or long transport times caused by slow moving air masses. We conclude that the Betula pollen recorded in North London could originate from sources found to the west and south of the city and not just trees within London itself. Possible sources outside the city include Continental Europe and the Betula trees within the broad-leaved forests of Southern England.
Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological?

Science.gov (United States)

Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C

2018-02-19

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.
Investigation of Growth and Survival of Transplanted Plane and Pine Trees According to IBA Application, Tree Age, Transplanting Time and Method

Directory of Open Access Journals (Sweden)

N. Etemadi

2015-03-01

Full Text Available The major problems in transplanting the landscape trees are high level of mortality and low establishment rate of transplanted trees, especially in the first year. In order to achieve the best condition for successful transplanting of pine and plane trees in Isfahan landscape, the present study was carried out based on a completely randomized block design with four replicates and three treatments including transplanting method (balled and burlapped and bare root, tree age (immature and mature and IBA application (0 and 150 mg/L. Trees were transplanted during 2009 and 2010 in three times (dormant season, early and late growing season. Survival rate and Relative Growth Rate index based on tree height (RGRH and trunk diameter (RGRD were measured during the first and second years. Trees transplanted early in the growing season showed the most survival percentage during the two years, as compared to other transplanting dates. Survival of Balled and burlapped and immature transplanted trees was significantly greater than bare root or mature trees. The significant effect of age treatment was continued in the second year. IBA treatment had no effect on survival rate of the studied species. Balled and burlapped and immature transplanted pine trees also had higher RGRH and RGRD compared to bare root or mature trees. According to the results of this study, early growing season is the best time for transplanting pine and plane trees. Also, transplanting of immature trees using balled and burlapped method is recommended to increase the survival and establishment rate.
IND - THE IND DECISION TREE PACKAGE

Science.gov (United States)

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
Timing-Driven-Testable Convergent Tree Adders

Directory of Open Access Journals (Sweden)

Johnnie A. Huang

2002-01-01

Full Text Available Carry lookahead adders have been, over the years, implemented in complex arithmetic units due to their regular structure which leads to efficient VLSI implementation for fast adders. In this paper, timing-driven testability synthesis is first performed on a tree adder. It is shown that the structure of the tree adder provides for a high fanout with an imbalanced tree structure, which likely contributes to a racing effect and increases the delay of the circuit. The timing optimization is then realized by reducing the maximum fanout of the adder and by balancing the tree circuit. For a 56-b testable tree adder, the optimization produces a 6.37%increase in speed of the critical path while only contributing a 2.16% area overhead. The full testability of the circuit is achieved in the optimized adder design.

Phylogenetic search through partial tree mixing

Science.gov (United States)

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449
Seeing the forest for the trees

DEFF Research Database (Denmark)

Ribbons, Relena Rose

Tree species influence soils above and belowground communities through leaf litter and root inputs. Soil microbial communities can directly influence tree growth and development through processes such as decomposition of leaves, and indirectly through chemical transformation of nutrients in soils...... as an influence of altered C:N ratios due to leaf litter inputs. This thesis aims to document some of the mechanisms by which trees influence soil microbial communities and nitrogen cycling processes like gross and net ammonification and nitrification. This thesis also aims to determine the role of site nitrogen...... status on modulating those tree species effects. The effects of tree species on ammonification and nitrification rates in forest floors and mineral soils were explored, and related to functional genetic markers for ammonia-oxidation by archaea and bacteria (amoA AOA and AOB), bacterial denitrification...
Tree agency and urban forest governance

DEFF Research Database (Denmark)

Konijnendijk, Cecil Cornelis

2016-01-01

governance also involving businesses and civic society. However, governance theory usually does not consider the role of non-human agency, which can be considered problematic due to, for example, the important role of urban trees in place making. The purpose of this paper is to provide further insight...... into the importance of considering tree agency in governance. Design/methodology/approach – Taking an environmental governance and actor network theory perspective, the paper presents a critical view of current urban forest governance, extending the perspective to include not only a wide range of human actors......, but also trees as important non-human actors. Findings – Urban forest governance has become more complex and involves a greater range of actors and actor networks. However, the agency of trees in urban forest governance is seldom well developed. Trees, in close association with local residents, create...
Selecting Landscape Plants: Shade Trees

OpenAIRE

Relf, Diane; Appleton, Bonnie Lee, 1948-2012; Close, David

2015-01-01

Because of the permanency of trees and their importance in the landscape, care must be taken to select the best species for each situation. This publication goes over how to choose landscape trees that are shade tolerant.
Tree health and physiology in a changing environment

Science.gov (United States)

Walter C. Shortle; Kevin T. Smith; Rakesh Minocha; Subhash Minocha; Philip M. Wargo; Kristina A. Vogt

2000-01-01

A tree is a large, long-lived, perennial, compartmented, woody, shedding, walling plant. This definition is based on new tree biology concepts (Shigo, 1986a,b, 1991) and explains much about how mature trees function through their unique structure. When the tree begins its life, it is mostly leaf in mass (Fig. 7.la). As a tree grows in stature, it becomes mostly stem in...
Urban trees and forests of the Chicago region

Science.gov (United States)

David J. Nowak; Robert E. III Hoehn; Allison R. Bodine; Daniel E. Crane; John F. Dwyer; Veta Bonnewell; Gary Watson

2013-01-01

An analysis of trees in the Chicago region of Illinois reveals that this area has about 157,142,000 trees with tree and shrub canopy that covers 21.0 percent of the region. The most common tree species are European buckthorn, green ash, boxelder, black cherry, and American elm. Trees in the Chicago region currently store about 16.9 million tons of carbon (61.9 million...
Benefits and costs of street trees in Lisbon

Science.gov (United States)

A.L. Soares; F.C. Rego; E.G. McPherson; J.R. Simpson; P.J. Peper; Q. Xiao

2011-01-01

It is well known that urban trees produce various types of benefits and costs. The computer tool i-Tree STRATUM helps quantify tree structure and function, as well as the value of some of these tree services in different municipalities. This study describes one of the first applications of STRATUM outside the U.S. Lisbonâs street trees are dominated by Celtis australis...
Field theory of relativistic strings: I. Trees

International Nuclear Information System (INIS)

Kaku, M.; Kikkawa, K.

1985-01-01

The authors present an entirely new kind of field theory, a field theory quantized not at space-time points, but quantized along an extended set of multilocal points on a string. This represents a significant departure from the usual quantum field theory, whose free theory represents a definite set of elementary particles, because the field theory on relativistic strings can accommodate an infinite set of linearly rising Regge trajectories. In this paper, the authors (1) present canonical quantization and the Green's function of the free string, (2) introduce three-string interactions, (3) resolve the question of multiple counting, (4) complete the counting arguments for all N-point trees, and (5) introduce four-string interactions which yield a Yang-Mills structure when the zero-slope limit is taken
Directional phytoscreening: contaminant gradients in trees for plume delineation.

Science.gov (United States)

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.
Probabilistic risk assessment course documentation. Volume 4. System reliability and analysis techniques sessions B/C - event trees/fault trees

International Nuclear Information System (INIS)

Haasl, D.; Young, J.

1985-08-01

This course will employ a combination of lecture material and practical problem solving in order to develop competence and understanding of th principles and techniques of event tree and fault tree analysis. The role of these techniques in the overall context of PRA will be described. The emphasis of this course will be on the basic, traditional methods of event tree and fault tree analysis
Urban tree species show the same hydraulic response to vapor pressure deficit across varying tree size and environmental conditions.

Directory of Open Access Journals (Sweden)

Lixin Chen

Full Text Available The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations.We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP. The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1 the influence of tree species and size on transpiration, and 2 the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH and tree canopy transpiration amount (E(c was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between G(c at VPD = 1 kPa (G(cref and the G(c sensitivity to VPD (-dG(c/dlnVPD across studied species as well as under contrasting soil water and R(s conditions in the urban area.We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of G(cref.
Urban tree species show the same hydraulic response to vapor pressure deficit across varying tree size and environmental conditions.

Science.gov (United States)

Chen, Lixin; Zhang, Zhiqiang; Ewers, Brent E

2012-01-01

The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations. We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP). The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1) the influence of tree species and size on transpiration, and 2) the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH) and tree canopy transpiration amount (E(c)) was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between G(c) at VPD = 1 kPa (G(cref)) and the G(c) sensitivity to VPD (-dG(c)/dlnVPD) across studied species as well as under contrasting soil water and R(s) conditions in the urban area. We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of G(cref).
A transportable magnetic resonance imaging system for in situ measurements of living trees: the Tree Hugger.

Science.gov (United States)

Jones, M; Aptaker, P S; Cox, J; Gardiner, B A; McDonald, P J

2012-05-01

This paper presents the design of the 'Tree Hugger', an open access, transportable, 1.1 MHz (1)H nuclear magnetic resonance imaging system for the in situ analysis of living trees in the forest. A unique construction employing NdFeB blocks embedded in a reinforced carbon fibre frame is used to achieve access up to 210 mm and to allow the magnet to be transported. The magnet weighs 55 kg. The feasibility of imaging living trees in situ using the 'Tree Hugger' is demonstrated. Correlations are drawn between NMR/MRI measurements and other indicators such as relative humidity, soil moisture and net solar radiation. Copyright © 2012 Elsevier Inc. All rights reserved.
Utilization of nitrogen fixing trees

Energy Technology Data Exchange (ETDEWEB)

Brewbaker, J.L.; Beldt, R. van den; MacDicken, K.; Budowski, G.; Kass, D.C.L.; Russo, R.O.; Escalante, G.; Herrera, R.; Aranguren, J.; Arkcoll, D.B.; Doebereinger, J. (cord.)

1983-01-01

Six papers from the symposium are noted. Brewbaker, J.L., Beldt, R. van den, MacDicken, K. Fuelwood uses and properties of nitrogen-fixing trees, pp 193-204, (Refs. 15). Includes a list of 35 nitrogen-fixing trees of high fuelwood value. Budowski, G.; Kass, D.C.L.; Russo, R.O. Leguminous trees for shade, pp 205-222, (Refs. 68). Escalante, G., Herrera, R., Aranguren, J.; Nitrogen fixation in shade trees (Erythrina poeppigiana) in cocoa plantations in northern Venezuela, pp 223-230, (Refs. 13). Arkcoll, D.B.; Some leguminous trees providing useful fruits in the North of Brazil, pp 235-239, (Refs. 13). This paper deals with Parkia platycephala, Pentaclethra macroloba, Swartzia sp., Cassia leiandra, Hymenaea courbaril, dipteryz odorata, Inga edulis, I. macrophylla, and I. cinnamonea. Baggio, A.J.; Possibilities of the use of Gliricidia sepium in agroforestry systems in Brazil, pp 241-243; (Refs. 15). Seiffert, N.F.; Biological nitrogen and protein production of Leucaena cultivars grown to supplement the nutrition of ruminants, pp 245-249, (Refs. 14). Leucaena leucocephala cv. Peru, L. campina grande (L. leucocephala), and L. cunningham (L. leucocephalae) were promising for use as browse by beef cattle in central Brazil.
Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

Science.gov (United States)

Deepak, Akshay; Fernández-Baca, David

2014-01-01

A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.
A voxel-based technique to estimate the volume of trees from terrestrial laser scanner data

Science.gov (United States)

Bienert, A.; Hess, C.; Maas, H.-G.; von Oheimb, G.

2014-06-01

The precise determination of the volume of standing trees is very important for ecological and economical considerations in forestry. If terrestrial laser scanner data are available, a simple approach for volume determination is given by allocating points into a voxel structure and subsequently counting the filled voxels. Generally, this method will overestimate the volume. The paper presents an improved algorithm to estimate the wood volume of trees using a voxel-based method which will correct for the overestimation. After voxel space transformation, each voxel which contains points is reduced to the volume of its surrounding bounding box. In a next step, occluded (inner stem) voxels are identified by a neighbourhood analysis sweeping in the X and Y direction of each filled voxel. Finally, the wood volume of the tree is composed by the sum of the bounding box volumes of the outer voxels and the volume of all occluded inner voxels. Scan data sets from several young Norway maple trees (Acer platanoides) were used to analyse the algorithm. Therefore, the scanned trees as well as their representing point clouds were separated in different components (stem, branches) to make a meaningful comparison. Two reference measurements were performed for validation: A direct wood volume measurement by placing the tree components into a water tank, and a frustum calculation of small trunk segments by measuring the radii along the trunk. Overall, the results show slightly underestimated volumes (-0.3% for a probe of 13 trees) with a RMSE of 11.6% for the individual tree volume calculated with the new approach.
Biocontrol of Fusarium circinatum Infection of Young Pinus radiata Trees

Directory of Open Access Journals (Sweden)

Eugenia Iturritxa

2017-01-01

Full Text Available Pitch canker, caused by the fungus Fusarium circinatum, is a major disease of Pinus radiata currently controlled to some extent in nurseries by good hygiene and application of synthetic fungicides. The aim of this study was to evaluate alternative strategies to control fungal infections in nurseries and young pine plantations. The antagonistic effects of biocontrol bacteria and essential oils against F. circinatum in vitro and in young P. radiata trees were assessed. Pseudomonas fluorescens, Erwinia billingiae, and Bacillus simplex reduced the growth of the fungus in vitro by 17%–29%, and decreased the density of the mycelial mat. In young P. radiata trees, the length of F. circinatum lesions was reduced by 22%–25% by the same bacterial strains. Direct application of cinnamon and/or clove essential oils to wounds in stems of two-year-old P. radiata trees also limited the damage caused by F. circinatum. Lesion length was reduced by 51% following treatment with cinnamon oil (10% v/v, and by 45% following treatment with clove oil (15% v/v or a combination of both oils. However, the oils were toxic to younger trees. The biocontrol bacteria and essential oils show promise as prophylactic treatments to reduce the devastating effects of F. circinatum on P. radiata.
Diversity of shrub tree layer, leaf litter decomposition and N release in a Brazilian Cerrado under N, P and N plus P additions

International Nuclear Information System (INIS)

Khan Baiocchi Jacobson, Tamiel; Cunha Bustamante, Mercedes Maria da; Rodrigues Kozovits, Alessandra

2011-01-01

This study investigated changes in diversity of shrub-tree layer, leaf decomposition rates, nutrient release and soil NO fluxes of a Brazilian savanna (cerrado sensu stricto) under N, P and N plus P additions. Simultaneous addition of N and P affected density, dominance, richness and diversity patterns more significantly than addition of N or P separately. Leaf litter decomposition rates increased in P and NP plots but did not differ in N plots in comparison to control plots. N addition increased N mass loss, while the combined addition of N and P resulted in an immobilization of N in leaf litter. Soil NO emissions were also higher when N was applied without P. The results indicate that if the availability of P is not increased proportionally to the availability of N, the losses of N are intensified. - Highlights: → Simultaneous addition of N and P affected richness and diversity of the shrub-tree layer of a Brazilian savanna more significantly than addition of N or P separately. → Leaf litter decomposition rates increased in P and NP plots but did not differ in N plots in comparison to control plots. N addition increased N mass loss, while the combined addition of N and P resulted in an immobilization of N in leaf litter. Soil NO emissions were also higher when N was applied without P. → The results indicated that if increases in N deposition in Cerrado ecosystems are not accompanied by P additions, higher N losses through leaching and gas emissions can occur with other ecosystem impacts. - Shrub-tree diversity and functioning of Brazilian savanna are affected by increasing nutrient availability.
Diversity of shrub tree layer, leaf litter decomposition and N release in a Brazilian Cerrado under N, P and N plus P additions

Energy Technology Data Exchange (ETDEWEB)

Khan Baiocchi Jacobson, Tamiel, E-mail: tamiel@unb.br [Departamento de Ecologia, Universidade de Brasilia, Brasilia-DF 70919-970 (Brazil); Cunha Bustamante, Mercedes Maria da, E-mail: mercedes@unb.br [Departamento de Ecologia, Universidade de Brasilia, Brasilia-DF 70919-970 (Brazil); Rodrigues Kozovits, Alessandra, E-mail: kozovits@icep.ufop.br [Departamento de Ecologia, Universidade de Brasilia, Brasilia-DF 70919-970 (Brazil)

2011-10-15

This study investigated changes in diversity of shrub-tree layer, leaf decomposition rates, nutrient release and soil NO fluxes of a Brazilian savanna (cerrado sensu stricto) under N, P and N plus P additions. Simultaneous addition of N and P affected density, dominance, richness and diversity patterns more significantly than addition of N or P separately. Leaf litter decomposition rates increased in P and NP plots but did not differ in N plots in comparison to control plots. N addition increased N mass loss, while the combined addition of N and P resulted in an immobilization of N in leaf litter. Soil NO emissions were also higher when N was applied without P. The results indicate that if the availability of P is not increased proportionally to the availability of N, the losses of N are intensified. - Highlights: > Simultaneous addition of N and P affected richness and diversity of the shrub-tree layer of a Brazilian savanna more significantly than addition of N or P separately. > Leaf litter decomposition rates increased in P and NP plots but did not differ in N plots in comparison to control plots. N addition increased N mass loss, while the combined addition of N and P resulted in an immobilization of N in leaf litter. Soil NO emissions were also higher when N was applied without P. > The results indicated that if increases in N deposition in Cerrado ecosystems are not accompanied by P additions, higher N losses through leaching and gas emissions can occur with other ecosystem impacts. - Shrub-tree diversity and functioning of Brazilian savanna are affected by increasing nutrient availability.
Flowering T Flowering Trees

Indian Academy of Sciences (India)

Adansonia digitata L. ( The Baobab Tree) of Bombacaceae is a tree with swollen trunk that attains a dia. of 10m. Leaves are digitately compound with leaflets up to 18cm. long. Flowers are large, solitary, waxy white, and open at dusk. They open in 30 seconds and are bat pollinated. Stamens are many. Fruit is about 30 cm ...

Trees and Climate Change

OpenAIRE

Dettenmaier, Megan; Kuhns, Michael; Unger, Bethany; McAvoy, Darren

2017-01-01

This fact sheet describes the complex relationship between forests and climate change based on current research. It explains ways that trees can mitigate some of the risks associated with climate change. It details the impacts that forests are having on the changing climate and discuss specific ways that trees can be used to reduce or counter carbon emissions directly and indirectly.
Tree Ordination as Invented Tradition

Directory of Open Access Journals (Sweden)

Avery Morrow

2012-01-01

Full Text Available The symbolic ordination of trees as monks in Thailand is widely perceived in Western scholarship to be proof of the power of Buddhism to spur ecological thought. However, a closer analysis of tree ordination demonstrates that it is not primarily about Buddhist teaching, but rather is an invented tradition based on the sanctity of Thai Buddhist symbols as well as those of spirit worship and the monarchy. Tree ordinations performed by non-Buddhist minorities in Thailand do not demonstrate a religious commitment but rather a political one.
Generalising tree traversals to DAGs

DEFF Research Database (Denmark)

Bahr, Patrick; Axelsson, Emil

2015-01-01

We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal and then apply it to compact graph representations of trees instead. The resulting graph traversals avoid...... is not sound. Therefore, we complement our implementation of the recursion scheme with a number of correspondence theorems that ensure soundness for various classes of traversals. We illustrate the practical applicability of the implementation as well as the complementing theory with a number of examples....
Occurrence of leguminous trees

Energy Technology Data Exchange (ETDEWEB)

Kirkbride, J.H.; Arkcoll, D.B.A.; Turnbull, J.W.; Magalhaes, L.M.S.; Fernandes, N.P.

1984-01-01

Five papers from the symposium are presented. Kirkbride, J.H. Jr.; Legumes of the cerrado. pp 23-46 (Refs. 55) A review is given. Some 548 legume species in 59 genera are listed that have been reported from cerrado vegetation. Felker, P.; Legume trees in semi-arid and arid areas. pp 47-59 (Refs. 41) A review is given of worldwide research activities. Arkcoll, D.B.; A comparison of some fast growing species suitable for woodlots in the wet tropics. pp 61-68 (Refs. 9) Studies are described near Manaus on intensive silviculture (for fuelwood production) of Eucalyptus deglupta, Cedrelinga catanaeformis (catenaeformis), Jacaranda copaia, and Inga edulis. Turnbull, J.W.; Six phyllodinous Acacia species for planting in the humid tropical lowlands. pp 69-73 (Refs. 14) Distribution, ecology, growth, and utilization are described for A. auriculiformis, A. mangium, A. aulacocarpa, A. crassicarpa, A. cincinnata, and A. polystachya. Magalhaes, L.M.S., Fernandes, N.P.; Experimental stands of leguminous trees in the Manaus region. pp 75-79 (Refs. 8) Performance up to age 20 yr of Cedrelinga catenaeformis, Dalbergia nigra, Dinizia excelsa, Dipteryx odorata, Dipteryx sp., Diplotropis sp., Eperua bijuga, Pithecellobium racemosum, Vouacapoua pallidior, and Hymenaea sp. is described.
Fruit load governs transpiration of olive trees

Science.gov (United States)

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

2016-01-01

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
Modular representation and analysis of fault trees

Energy Technology Data Exchange (ETDEWEB)

Olmos, J; Wolf, L [Massachusetts Inst. of Tech., Cambridge (USA). Dept. of Nuclear Engineering

1978-08-01

An analytical method to describe fault tree diagrams in terms of their modular compositions is developed. Fault tree structures are characterized by recursively relating the top tree event to all its basic component inputs through a set of equations defining each of the modulus for the fault tree. It is shown that such a modular description is an extremely valuable tool for making a quantitative analysis of fault trees. The modularization methodology has been implemented into the PL-MOD computer code, written in PL/1 language, which is capable of modularizing fault trees containing replicated components and replicated modular gates. PL-MOD in addition can handle mutually exclusive inputs and explicit higher order symmetric (k-out-of-n) gates. The step-by-step modularization of fault trees performed by PL-MOD is demonstrated and it is shown how this procedure is only made possible through an extensive use of the list processing tools available in PL/1. A number of nuclear reactor safety system fault trees were analyzed. PL-MOD performed the modularization and evaluation of the modular occurrence probabilities and Vesely-Fussell importance measures for these systems very efficiently. In particular its execution time for the modularization of a PWR High Pressure Injection System reduced fault tree was 25 times faster than that necessary to generate its equivalent minimal cut-set description using MOCUS, a code considered to be fast by present standards.
TRAINING TREE ADJOINING GRAMMARS WITH HUGE TEXT CORPUS USING SPARK MAP REDUCE

Directory of Open Access Journals (Sweden)

Vijay Krishna Menon

2015-07-01

Full Text Available Tree adjoining grammars (TAGs are mildly context sensitive formalisms used mainly in modelling natural languages. Usage and research on these psycho linguistic formalisms have been erratic in the past decade, due to its demanding construction and difficulty to parse. However, they represent promising future for formalism based NLP in multilingual scenarios. In this paper we demonstrate basic synchronous Tree adjoining grammar for English-Tamil language pair that can be used readily for machine translation. We have also developed a multithreaded chart parser that gives ambiguous deep structures and a par dependency structure known as TAG derivation. Furthermore we then focus on a model for training this TAG for each language using a large corpus of text through a map reduce frequency count model in spark and estimation of various probabilistic parameters for the grammar trees thereafter; these parameters can be used to perform statistical parsing on the trained grammar.
Totally optimal decision trees for Boolean functions

KAUST Repository

Chikalov, Igor; Hussain, Shahid; Moshkov, Mikhail

2016-01-01

We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters
Are temperate canopy spiders tree-species specific?

Science.gov (United States)

Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

2014-01-01

Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.
Efficient fault tree handling - the Asea-Atom approach

International Nuclear Information System (INIS)

Ericsson, G.; Knochenhauer, M.; Mills, R.

1985-01-01

In recent years there has been a trend in Swedish Probabilistic Safety Analysis (PSA) work towards coordination of the tools and methods used, in order to facilitate exchange of information and review. Thus, standardized methods for fault tree drawing and basic event coding have been developed as well as a number of computer codes for fault tree handling. The computer code used by Asea-Atom is called SUPER-TREE. As indicated by the name, the key feature is the concept of one super tree containing all the information necessary in the fault tree analysis, i.e. system fault trees, sequence fault trees and component data base. The code has proved to allow great flexibility in the choice of level of detail in the analysis
Topological and categorical properties of binary trees

Directory of Open Access Journals (Sweden)

H. Pajoohesh

2008-04-01

Full Text Available Binary trees are very useful tools in computer science for estimating the running time of so-called comparison based algorithms, algorithms in which every action is ultimately based on a prior comparison between two elements. For two given algorithms A and B where the decision tree of A is more balanced than that of B, it is known that the average and worst case times of A will be better than those of B, i.e., ₸A(n ≤₸B(n and TWA (n≤TWB (n. Thus the most balanced and the most imbalanced binary trees play a main role. Here we consider them as semilattices and characterize the most balanced and the most imbalanced binary trees by topological and categorical properties. Also we define the composition of binary trees as a commutative binary operation, *, such that for binary trees A and B, A * B is the binary tree obtained by attaching a copy of B to any leaf of A. We show that (T,* is a commutative po-monoid and investigate its properties.
Recent tree cover increases in eastern China linked to low, declining human pressure, steep topography, and climatic conditions favoring tree growth.

Directory of Open Access Journals (Sweden)

Jonas Nüchel

Full Text Available Globally, the extent of forest continues to decline, however, some countries have increased their forest extent in recent years. China is one of these countries and has managed to increase their tree cover through huge reforestation and afforestation programs during recent decades as well as land abandonment dynamics. This study investigates tree cover change in the eastern half of China between 2000 and 2010 on three different scales, using random forest modeling of remote sensing data for tree cover in relation to environmental and anthropogenic predictor variables. Our results show that between the years 2000 and 2010 2,667,875 km2 experienced an increase in tree cover while 1,854,900 km2 experienced a decline in tree cover. The area experiencing ≥10% increase in tree cover is almost twice as large as the area with ≥10% drop in tree cover. There is a clear relation between topography and tree cover change with steeper and mid-elevation areas having a larger response on tree cover increase than other areas. Furthermore, human influence, change in population density, and actual evapotranspiration are also important factors in explaining where tree cover has changed. This study adds to the understanding of tree cover change in China, as it has focus on the entire eastern half of China on three different scales and how tree cover change is linked to topography and anthropogenic pressure. Though, our results show an increase in tree cover in China, this study emphasizes the importance of incorporating anthropogenic factors together with biodiversity protection into the reforestation and afforestation programs in the future.
Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest.

Science.gov (United States)

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate.
Recent tree cover increases in eastern China linked to low, declining human pressure, steep topography, and climatic conditions favoring tree growth.

Science.gov (United States)

Nüchel, Jonas; Svenning, Jens-Christian

2017-01-01

Globally, the extent of forest continues to decline, however, some countries have increased their forest extent in recent years. China is one of these countries and has managed to increase their tree cover through huge reforestation and afforestation programs during recent decades as well as land abandonment dynamics. This study investigates tree cover change in the eastern half of China between 2000 and 2010 on three different scales, using random forest modeling of remote sensing data for tree cover in relation to environmental and anthropogenic predictor variables. Our results show that between the years 2000 and 2010 2,667,875 km2 experienced an increase in tree cover while 1,854,900 km2 experienced a decline in tree cover. The area experiencing ≥10% increase in tree cover is almost twice as large as the area with ≥10% drop in tree cover. There is a clear relation between topography and tree cover change with steeper and mid-elevation areas having a larger response on tree cover increase than other areas. Furthermore, human influence, change in population density, and actual evapotranspiration are also important factors in explaining where tree cover has changed. This study adds to the understanding of tree cover change in China, as it has focus on the entire eastern half of China on three different scales and how tree cover change is linked to topography and anthropogenic pressure. Though, our results show an increase in tree cover in China, this study emphasizes the importance of incorporating anthropogenic factors together with biodiversity protection into the reforestation and afforestation programs in the future.
AUTOMATIC TREE-CROWN DETECTION IN CHALLENGING SCENARIOS

Directory of Open Access Journals (Sweden)

D. Bulatov

2016-06-01

Full Text Available In this paper, a new procedure for individual tree detection and modeling is presented. The input of this procedure consists of a normalized digital surface model NDSM, and a possibly error-prone classification result. The procedure is modular so that the functionality, the advantages and the disadvantages for every single module will be explained. The most important technical contributions of the paper are: Employing watershed transformation combined with classification results, applying hotspots detectors for identifying treetops in groups of trees, and correcting NDSM by detecting and geometric reconstruction of small anomalies, such as earth walls. Two minor contributions are made up by a detailed literature research on available methods for individual tree detection and estimation of tree-crowns for clearly identified trees in order to reduce arbitrariness by assigning trees to one of the few types in the output model.
Tree-inception in PMMA with a barrier

International Nuclear Information System (INIS)

Gefle, O S; Lebedev, S M; Pokholkov, Y P; Gockenbach, E; Borsi, H

2004-01-01

The experimental results of a study of the tree-inception phenomenon for three-layer dielectrics in a divergent field are presented in this paper. It is shown that the tree-inception time depends on both the position of the high-permittivity barrier in the insulating gap and the ratio of the permittivities of the barrier material and main dielectric, and that it has a maximum at the optimal barrier position. It is found that the tree-inception length has a minimum value at this barrier position. Good agreement between the coefficient of the local field non-uniformity and the tree-inception time or the initial tree length was found
Genomics-assisted breeding in fruit trees.

Science.gov (United States)

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

2016-01-01

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

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
Breaking the fault tree circular logic

International Nuclear Information System (INIS)

Lankin, M.

2000-01-01

Event tree - fault tree approach to model failures of nuclear plants as well as of other complex facilities is noticeably dominant now. This approach implies modeling an object in form of unidirectional logical graph - tree, i.e. graph without circular logic. However, genuine nuclear plants intrinsically demonstrate quite a few logical loops (circular logic), especially where electrical systems are involved. This paper shows the incorrectness of existing practice of circular logic breaking by elimination of part of logical dependencies and puts forward a formal algorithm, which enables the analyst to correctly model the failure of complex object, which involves logical dependencies between system and components, in form of fault tree. (author)
Big data of tree species distributions

DEFF Research Database (Denmark)

Serra-Diaz, Josep M.; Enquist, Brian J.; Maitner, Brian

2018-01-01

are currently available in big databases, several challenges hamper their use, notably geolocation problems and taxonomic uncertainty. Further, we lack a complete picture of the data coverage and quality assessment for open/public databases of tree occurrences. Methods: We combined data from five major...... and data aggregation, especially from national forest inventory programs, to improve the current publicly available data.......Background: Trees play crucial roles in the biosphere and societies worldwide, with a total of 60,065 tree species currently identified. Increasingly, a large amount of data on tree species occurrences is being generated worldwide: from inventories to pressed plants. While many of these data...

Monitoring individual tree-based change with airborne lidar.

Science.gov (United States)

Duncanson, Laura; Dubayah, Ralph

2018-05-01

Understanding the carbon flux of forests is critical for constraining the global carbon cycle and managing forests to mitigate climate change. Monitoring forest growth and mortality rates is critical to this effort, but has been limited in the past, with estimates relying primarily on field surveys. Advances in remote sensing enable the potential to monitor tree growth and mortality across landscapes. This work presents an approach to measure tree growth and loss using multidate lidar campaigns in a high-biomass forest in California, USA. Individual tree crowns were delineated in 2008 and again in 2013 using a 3D crown segmentation algorithm, with derived heights and crown radii extracted and used to estimate individual tree aboveground biomass. Tree growth, loss, and aboveground biomass were analyzed with respect to tree height and crown radius. Both tree growth and loss rates decrease with increasing tree height, following the expectation that trees slow in growth rate as they age. Additionally, our aboveground biomass analysis suggests that, while the system is a net source of aboveground carbon, these carbon dynamics are governed by size class with the largest sources coming from the loss of a relatively small number of large individuals. This study demonstrates that monitoring individual tree-based growth and loss can be conducted with multidate airborne lidar, but these methods remain relatively immature. Disparities between lidar acquisitions were particularly difficult to overcome and decreased the sample of trees analyzed for growth rate in this study to 21% of the full number of delineated crowns. However, this study illuminates the potential of airborne remote sensing for ecologically meaningful forest monitoring at an individual tree level. As methods continue to improve, airborne multidate lidar will enable a richer understanding of the drivers of tree growth, loss, and aboveground carbon flux.
Phytotoxicity of polycyclic aromatic hydrocarbons to willow trees

Energy Technology Data Exchange (ETDEWEB)

Thygesen, R.S.; Trapp, S. [Environment and Resources DTU, Technical Univ. of Denmark, Lyngby (Denmark)

2002-07-01

The toxicity of PAH to willow trees (Salix alba, S. viminalis, S. viminalis x schwerinii) was investigated. Willow cuttings were grown in PAH-saturated hydroponic solution (naphthalene NAP, phenanthrene PHEN and benzo(a)pyrene BaP). Toxicity was related to aqueous solubility and was highest for NAP. PHEN did not show significant effects, except in one case. Exposure of trees to BaP showed no effect in two cases, but increased transpiration and growth in two others. High dosages of NAP were fatal for the trees, the lowest dosage significantly stimulated growth. Soil samples were taken from several PAH contaminated sites, among them gas works sites and a former sludge basin. The PAH contents ranged from 1.76 mg/kg to 1451 mg/kg. None of the soils was lethally toxic to the trees, and difference between growth in control soils and growth in PAH contaminated soils was not apparent. Growth and water use efficiency were positively, but not significantly correlated to the PAH content of the soils. Outdoor growth of willows and poplars on the former sludge basin in Valby was monitored, with willows growing faster than poplars (Populus trichocarpa). Phytotoxic effects could be observed at some willows at the Valby sludge basin, but it is not sure whether these effects can be contributed to PAH. (orig.)
The hydrological vulnerability of western North American boreal tree species based on ground-based observations of tree mortality

Science.gov (United States)

Hember, R. A.; Kurz, W. A.; Coops, N. C.

2017-12-01

Several studies indicate that climate change has increased rates of tree mortality, adversely affecting timber supply and carbon storage in western North American boreal forests. Statistical models of tree mortality can play a complimentary role in detecting and diagnosing forest change. Yet, such models struggle to address real-world complexity, including expectations that hydrological vulnerability arises from both drought stress and excess-water stress, and that these effects vary by species, tree size, and competitive status. Here, we describe models that predict annual probability of tree mortality (Pm) of common boreal tree species based on tree height (H), biomass of larger trees (BLT), soil water content (W), reference evapotranspiration (E), and two-way interactions. We show that interactions among H and hydrological variables are consistently significant. Vulnerability to extreme droughts consistently increases as H approaches maximum observed values of each species, while some species additionally show increasing vulnerability at low H. Some species additionally show increasing vulnerability to low W under high BLT, or increasing drought vulnerability under low BLT. These results suggest that vulnerability of trees to increasingly severe droughts depends on the hydraulic efficiency, competitive status, and microclimate of individual trees. Static simulations of Pm across a 1-km grid (i.e., with time-independent inputs of H, BLT, and species composition) indicate complex spatial patterns in the time trends during 1965-2014 and a mean change in Pm of 42 %. Lastly, we discuss how the size-dependence of hydrological vulnerability, in concert with increasingly severe drought events, may shape future responses of stand-level biomass production to continued warming and increasing carbon dioxide concentration in the region.
Azadirachta indica A. Juss. (English: Margosa or Neem tree; Hindi ...

Indian Academy of Sciences (India)

(English: Margosa or Neem tree; Hindi: Neem) ofMeliaceae a large evergreen tree with spreading crown and brownish bark is either pLanted or se(f-sown. Leaves are compound and the LeafLets are somewhat oblique with toothed margin. Flowers are small and white and borne on branched inflorescence. Fruit is about ...
Users' manual for the FTDRAW (Fault Tree Draw) code

International Nuclear Information System (INIS)

Oikawa, Tetsukuni; Hikawa, Michihiro; Tanabe, Syuichi; Nakamura, Norihiro

1985-02-01

This report provides the information needed to use the FTDRAW (Fault Tree Draw) code, which is designed for drawing a fault tree. The FTDRAW code has several optional functions, such as the overview of a fault tree output, fault tree output in English description, fault tree output in Japanese description and summary tree output. Inputs for the FTDRAW code are component failure rate information and gate information which are filed out by a execution of the FTA-J (Fault Tree Analysis-JAERI) code system and option control data. Using the FTDRAW code, we can get drawings of fault trees which is easy to see, efficiently. (author)
Phenology and growth of European trees in relation to climate change

NARCIS (Netherlands)

Kramer, K.

1996-01-01

Research topics<p>The relationships between climate and both phenology and growth of some important European tree species were studied to evaluate the potential impacts of climate change on trees and forests in Europe. In order to make such assessments, insight is
Boosted decision trees and applications

International Nuclear Information System (INIS)

Coadou, Y.

2013-01-01

Decision trees are a machine learning technique more and more commonly used in high energy physics, while it has been widely used in the social sciences. After introducing the concepts of decision trees, this article focuses on its application in particle physics. (authors)
Potential Nitrification and Nitrogen Mineral of Soil in Coffee Agroforestry System with Various Shading Trees

Directory of Open Access Journals (Sweden)

Purwanto .

2007-05-01

Full Text Available The role of shading trees in coffee farms has been well understood to establish suitable condition for the growth of coffee trees, on the other hand their role in nitrogen cycle in coffee farming is not yet well understood. The objectives of this study are to investigate the influence of various legume shading trees on the concentration of soil mineral N (N-NH4 + and N-NO3-, potential nitrification and to study the controlling factors of nitrification under field conditions. This field explorative research was carried out in Sumberjaya, West Lampung. Twelve observation plots covered four land use systems (LUS, i.e. 1 Coffee agroforestry with Gliricidiasepium as shade trees; 2 Coffee agroforestry with Gliricidiaas shade trees and Arachis pintoias cover crops; 3Coffee agroforestry with Paraserianthes falcataria as shade trees; and 4 Mixed/multistrata coffee agroforestry with Gliricidiaand other fruit crops as shade trees. Measurements of soil mineral-N concentration were carried out every three weeks for three months. Results showed that shade tree species in coffee agroforestry significantly affected concentrations of soil NH4 +, NO3- and potential nitrification. Mixed coffee agroforestry had the highest NH4+/N-mineral ratio (7.16% and the lowest potential nitrification (0.13 mg NO2-kg-1 hour -1 compared to other coffee agroforestry systems using single species of leguminous shade trees. Ratio of NH4 + /N-mineral increased 0.8—21% while potential nitrification decreased 55—79% in mixed coffee agroforestry compared to coffee agroforestry with Gliricidia or P. falcatariaas shade trees. Coffee agroforestry with P. falcatariaas shade trees had potential nitrification 53% lower and ratio of NH4 + /N-mineral concentration 20% higher than that with Gliricidia. Coffee agroforestry with P. falcataria as shade trees also had organic C content 17% higher, total N 40% higher, available P 112% higher than that with Gliricidia. The presence of A. pintoiin
Decision Tree Technique for Particle Identification

International Nuclear Information System (INIS)

Quiller, Ryan

2003-01-01

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

Science.gov (United States)

Suzanne M. Owen; Carolyn Hull Sieg; Catherine A. Gehring; Matthew A. Bowker

2009-01-01

Mechanical mastication is increasingly prescribed for wildfire mitigation, yet little is known about the ecological impacts of this fuels treatment. Mastication shreds trees into woodchips as an alternative to tree thinning and burning the resulting slash, which can create soil disturbances that favor exotic plants. Previous research on mastication has not...
Locating a tree in a phylogenetic network

OpenAIRE

van Iersel, Leo; Semple, Charles; Steel, Mike

2010-01-01

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider t...
Suppression of nighttime sap flux with lower stem photosynthesis in Eucalyptus trees.

Science.gov (United States)

Gao, Jianguo; Zhou, Juan; Sun, Zhenwei; Niu, Junfeng; Zhou, Cuiming; Gu, Daxing; Huang, Yuqing; Zhao, Ping

2016-04-01

It is widely accepted that substantial nighttime sap flux (J s,n) or transpiration (E) occurs in most plants, but the physiological implications are poorly known. It has been hypothesized that J s,n or E serves to enhance nitrogen uptake or deliver oxygen; however, no clear evidence is currently available. In this study, sap flux (J s) in Eucalyptus grandis × urophylla with apparent stem photosynthesis was measured, including control trees which were covered by aluminum foil (approximately 1/3 of tree height) to block stem photosynthesis. We hypothesized that the nighttime water flux would be suppressed in trees with lower stem photosynthesis. The results showed that the green tissue degraded after 3 months, demonstrating a decrease in stem photosynthesis. The daytime J s decreased by 21.47%, while J s,n decreased by 12.03% in covered trees as compared to that of control, and the difference was statistically significant (P photosynthesis in covered trees. Predawn (ψ pd) of covered trees was marginally higher than that of control while lower at predawn stomatal conductance (g s), indicating a suppressed water flux in covered trees. There was no difference in leaf carbon content and δ(13)C between the two groups, while leaf nitrogen content and δ(15)N were significantly higher in covered trees than that of the control (P < 0.05), indicating that J s,n was not used for nitrogen uptake. These results suggest that J s,n may act as an oxygen pathway since green tissue has a higher respiration or oxygen demand than non-green tissue. Thus, this study demonstrated the physiological implications of J s,n and the possible benefits of nighttime water use or E by the tree.
Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

Science.gov (United States)

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

2017-04-01

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

Science.gov (United States)

Goloboff, Pablo A

2014-10-01

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

OpenAIRE

Anton Andriyashin

2008-01-01

Stock picking is the field of financial analysis that is of particular interest for many professional investors and researchers. In this study stock picking is implemented via binary classification trees. Optimal tree size is believed to be the crucial factor in forecasting performance of the trees. While there exists a standard method of tree pruning, which is based on the cost-complexity tradeoff and used in the majority of studies employing binary decision trees, this paper introduces a no...
Flood-promoted vessel formation in Prioria copaifera trees in the Darien Gap, Colombia.

Science.gov (United States)

López, Janeth; Del Valle, Jorge I; Giraldo, Jorge A

2014-10-01

Trees growing in floodplains develop mechanisms by which to overcome anoxic conditions. Prioria copaifera Griseb. grows on the floodplains of the Atrato River, Colombia, and monodominant communities of this species remain flooded for at least 6 months a year. The aims of this study were as follows: (i) to compare variations in tree-ring structure with varying river water levels; and (ii) to reconstruct variations in water levels from the chronology of variations in the porosity of the tree rings. Discs were taken from 12 trees, and the number of vessels along 3-mm-wide radial transects was counted. Standard dendrochronological techniques were used to determine the mean number of vessels over 130 years, between 1877 and 2006; the signal-to-noise ratio was 13.3 and the expressed population signal 0.93. Furthermore, this series of vessel numbers was calibrated against variations in the water levels between 1977 and 2000; positive correlations were found with the mean for both the annual river water level and the level from June to August. The transfer function between the principal components of the mean annual water level and those of chronology allowed us to reconstruct the river levels over 130 years. Our conclusions are as follows: (i) the number of vessels per ring is an appropriate proxy for determining variations in water levels; and (ii) P. copaifera grows thicker and produces more vessels when water levels rise. The probable ecophysiological causes of this interesting behaviour are discussed. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Fruit load governs transpiration of olive trees.

Science.gov (United States)

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. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
SplitDist—Calculating Split-Distances for Sets of Trees

DEFF Research Database (Denmark)

Mailund, T

2004-01-01

We present a tool for comparing a set of input trees, calculating for each pair of trees the split-distances, i.e., the number of splits in one tree not present in the other.......We present a tool for comparing a set of input trees, calculating for each pair of trees the split-distances, i.e., the number of splits in one tree not present in the other....
Robust B+ -Tree-Based Indexing of Moving Objects

DEFF Research Database (Denmark)

Jensen, Christian Søndergaard; Tiesyte, Dalia; Tradisauskas, Nerius

2006-01-01

Bx-tree is based on the B+-tree and is relatively easy to integrate into an existing DBMS. However, the Bx-tree is sensitive to data skew. This paper proposes a new query processing algorithm for the Bx-tree that fully exploits the available data statistics to reduce the query enlargement...
Comparison of event tree, fault tree and Markov methods for probabilistic safety assessment and application to accident mitigation

International Nuclear Information System (INIS)

James, H.; Harris, M.J.; Hall, S.F.

1992-01-01

Probabilistic safety assessment (PSA) is used extensively in the nuclear industry. The main stages of PSA and the traditional event tree method are described. Focussing on hydrogen explosions, an event tree model is compared to a novel Markov model and a fault tree, and unexpected implication for accident mitigation is revealed. (author)

Representing Boolean Functions by Decision Trees

KAUST Repository

Chikalov, Igor

2011-01-01

A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.
Locating a tree in a phylogenetic network

NARCIS (Netherlands)

Iersel, van L.J.J.; Semple, C.; Steel, M.A.

2010-01-01

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster
TREDRA, Minimal Cut Sets Fault Tree Plot Program

International Nuclear Information System (INIS)

Fussell, J.B.

1983-01-01

1 - Description of problem or function: TREDRA is a computer program for drafting report-quality fault trees. The input to TREDRA is similar to input for standard computer programs that find minimal cut sets from fault trees. Output includes fault tree plots containing all standard fault tree logic and event symbols, gate and event labels, and an output description for each event in the fault tree. TREDRA contains the following features: a variety of program options that allow flexibility in the program output; capability for automatic pagination of the output fault tree, when necessary; input groups which allow labeling of gates, events, and their output descriptions; a symbol library which includes standard fault tree symbols plus several less frequently used symbols; user control of character size and overall plot size; and extensive input error checking and diagnostic oriented output. 2 - Method of solution: Fault trees are generated by user-supplied control parameters and a coded description of the fault tree structure consisting of the name of each gate, the gate type, the number of inputs to the gate, and the names of these inputs. 3 - Restrictions on the complexity of the problem: TREDRA can produce fault trees with a minimum of 3 and a maximum of 56 levels. The width of each level may range from 3 to 37. A total of 50 transfers is allowed during pagination
Linking and Cutting Spanning Trees

Directory of Open Access Journals (Sweden)

Luís M. S. Russo

2018-04-01

Full Text Available We consider the problem of uniformly generating a spanning tree for an undirected connected graph. This process is useful for computing statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs, we prove that this approach significantly outperforms existing algorithms. For general graphs, experimental results show that the chain converges quickly. This yields an efficient algorithm due to the use of proper fast data structures. To obtain the mixing time of the chain we describe a coupling, which we analyze for cycle graphs and simulate for other graphs.
Treatment of complementary events in event trees in constructing linked fault trees for level 1 and level 2 PRA

International Nuclear Information System (INIS)

Jo, Y. G.

2008-01-01

Complementary events in the event trees for a PRA model should be treated properly in order to evaluate plant risk correctly. In this study, the characteristics of the following three different cut-set generation methods were investigated first in order to find the best practical way for treating complementary events: 1) exact method which treats complementary events logically, 2) no-delete term method which does not treat complementary events at all, and 3) delete term method which treats complementary events by deleting nonsense cut-sets which are generated as a result of ignoring complementary events. Then, practical methods for treating complementary events in constructing linked fault trees for level 1 and level 2 PRA in EPRI R and R workstation software environment, where CAFTA is the fault tree editor and FORTE is the cut-set engine, were suggested and demonstrated. The suggested methods deal with the following selected four typical cases: Case 1: an event tree event (E) is represented by a fault tree gate whose inputs consist of only fault tree gates, Case 2: E is represented by a single basic event, Case 3: E is represented by an OR fault tree gate which has a single basic event and a fault tree gate as inputs, and Case 4: E is represented by an AND fault tree gate which has a single basic event and a fault tree gate as inputs. In the suggested methods, first the high level logic structures of event tree events are examined and restructured, if needed. Then, the delete term method, the exact method, and the combination of the two methods are applied to Case 1, Case 2, and Cases 3 and 4, respectively. Also, it is recommended to treat complementary events, using the suggested methods, before level 1 and level 2 PRA fault trees are coupled. It should be noted that the selected four typical cases may not cover all different cases encountered in level 1 and level 2 PRA modeling. However, a process similar to the one suggested in this study may be used to find
Nitrous oxide fluxes from forest floor, tree stems and canopies of boreal tree species during spring

Science.gov (United States)

Haikarainen, Iikka; Halmeenmäki, Elisa; Machacova, Katerina; Pihlatie, Mari

2017-04-01

Boreal forests are considered as small sources of atmospheric nitrous oxide (N2O) due to microbial N2O production in the soils. Recent evidence shows that trees may play an important role in N2O exchange of forest ecosystems by offering pathways for soil produced N2O to the atmosphere. To confirm magnitude, variability and the origin of the tree mediated N2O emissions more research is needed, especially in boreal forests which have been in a minority in such investigation. We measured forest floor, tree stem and shoot N2O exchange of three boreal tree species at the beginning of the growing season (13.4.-13.6.2015) at SMEAR II station in Hyytiälä, located in Southern Finland (61˚ 51´N, 24˚ 17´E, 181 a.s.l.). The fluxes were measured in silver birch (Betula pendula), downy birch (B. pubescens) and Norway spruce (Picea abies) on two sites with differing soil type and characteristics (paludified and mineral soil), vegetation cover and forest structure. The aim was to study the vertical profile of N2O fluxes at stem level and to observe temporal changes in N2O fluxes over the beginning of the growing season. The N2O exchange was determined using the static chamber technique and gas chromatographic analyses. Scaffold towers were used for measurements at multiple stem heights and at the canopy level. Overall, the N2O fluxes from the forest floor and trees at both sites were very small and close to the detection limit. The measured trees mainly emitted N2O from their stems and shoots, while the forest floor acted as a sink of N2O at the paludified site and as a small source of N2O at the mineral soil site. Stem emissions from all the trees at both sites were on average below 0.5 μg N2O m-2 of stem area h-1, and the shoot emissions varied between 0.2 and 0.5 ng N2O m-2 g-1 dry biomass. When the N2O fluxes were scaled up to the whole forest ecosystem, based on the tree biomass and stand density, the N2O emissions from birch and spruce trees at the paludified site
GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

Science.gov (United States)

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

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the
Evaluation of the seasonal and annual abortifacient risk of western juniper trees on Oregon rangelands: Abortion risk of western juniper trees

Science.gov (United States)

Western juniper trees can cause late term abortions in cattle, similar to ponderosa pine trees. Analyses of western juniper trees from 35 locations across the state of Oregon suggest that western juniper trees in all areas present an abortion risk in pregnant cattle. Results from this study demonstr...
Isoprene emission from Indian trees

Science.gov (United States)

Varshney, C. K.; Singh, Abhai Pratap

2003-12-01

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

Directory of Open Access Journals (Sweden)

Jill L Edmondson

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

OpenAIRE

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 Mountain...
Univariate decision tree induction using maximum margin classification

OpenAIRE

Yıldız, Olcay Taner

2012-01-01

In many pattern recognition applications, first decision trees are used due to their simplicity and easily interpretable nature. In this paper, we propose a new decision tree learning algorithm called univariate margin tree where, for each continuous attribute, the best split is found using convex optimization. Our simulation results on 47 data sets show that the novel margin tree classifier performs at least as good as C4.5 and linear discriminant tree (LDT) with a similar time complexity. F...
Expressive Power of Tree and String Based Wrappers

OpenAIRE

Ikeda, Daisuke; Yamada, Yasuhiro; Hirokawa, Sachio

2003-01-01

There exist two types of wrappers: the string based wrapper such as the LR wrapper, and the tree based wrapper. A tree based wrapper designates extraction regions by nodes on the trees of semistructured documents. The tree based wrapper seems to be more powerful than the string based one. There exist, however, manyHTML documents on the Web such that a standard tree based wrapper fails to extract contents because they are structured by presentational tags, punctuation symbols, and white spaces...
Constructing phylogenetic trees using interacting pathways.

Science.gov (United States)

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.
Analysis of Logic Programs Using Regular Tree Languages

DEFF Research Database (Denmark)

Gallagher, John Patrick

2012-01-01

The eld of nite tree automata provides fundamental notations and tools for reasoning about set of terms called regular or recognizable tree languages. We consider two kinds of analysis using regular tree languages, applied to logic programs. The rst approach is to try to discover automatically...... a tree automaton from a logic program, approximating its minimal Herbrand model. In this case the input for the analysis is a program, and the output is a tree automaton. The second approach is to expose or check properties of the program that can be expressed by a given tree automaton. The input...... to the analysis is a program and a tree automaton, and the output is an abstract model of the program. These two contrasting abstract interpretations can be used in a wide range of analysis and verication problems....
Estimating Coextinction Risks from Epidemic Tree Death: Affiliate Lichen Communities among Diseased Host Tree Populations of Fraxinus excelsior

Science.gov (United States)

Jönsson, Mari T.; Thor, Göran

2012-01-01

At least 10% of the world’s tree species are threatened with extinction and pathogens are increasingly implicated in tree threats. Coextinction and threats to affiliates as a consequence of the loss or decline of their host trees is a poorly understood phenomenon. Ash dieback is an emerging infectious disease causing severe dieback of common ash Fraxinus excelsior throughout Europe. We utilized available empirical data on affiliate epiphytic lichen diversity (174 species and 17,800 observations) among 20 ash dieback infected host tree populations of F. excelsior on the island Gotland in the Baltic Sea, Sweden. From this, we used structured scenario projections scaled with empirical data of ash dieback disease to generate probabilistic models for estimating local and regional lichen coextinction risks. Average coextinction probabilities (Ā) were 0.38 (95% CI ±0.09) for lichens occurring on F. excelsior and 0.14 (95% CI ±0.03) when considering lichen persistence on all tree species. Ā was strongly linked to local disease incidence levels and generally increasing with lichen host specificity to F. excelsior and decreasing population size. Coextinctions reduced affiliate community viability, with significant local reductions in species richness and shifts in lichen species composition. Affiliates were projected to become locally extirpated before their hosts, illuminating the need to also consider host tree declines. Traditionally managed open wooded meadows had the highest incidence of ash dieback disease and significantly higher proportions of affiliate species projected to go extinct, compared with unmanaged closed forests and semi-open grazed sites. Most cothreatened species were not previously red-listed, which suggest that tree epidemics cause many unforeseen threats to species. Our analysis shows that epidemic tree deaths represent an insidious, mostly overlooked, threat to sessile affiliate communities in forested environments. Current conservation and
Development of tree hollows in pedunculate oak (Quercus robur)

OpenAIRE

Ranius, Thomas; Niklasson, Mats; Berg, Niclas

2009-01-01

Many invertebrates, birds and mammals are dependent on hollow trees. For landscape planning that aims at persistence of species inhabiting hollow trees it is crucial to understand the development of such trees. In this study we constructed an individual-based simulation model to predict diameter distribution and formation of hollows in oak tree populations. Based on tree-ring data from individual trees, we estimated the ages when hollow formation commences for pedunculate oak (Quercus robur) ...
Quantifying environmental limiting factors on tree cover using geospatial data.

Science.gov (United States)

Greenberg, Jonathan A; Santos, Maria J; Dobrowski, Solomon Z; Vanderbilt, Vern C; Ustin, Susan L

2015-01-01

Environmental limiting factors (ELFs) are the thresholds that determine the maximum or minimum biological response for a given suite of environmental conditions. We asked the following questions: 1) Can we detect ELFs on percent tree cover across the eastern slopes of the Lake Tahoe Basin, NV? 2) How are the ELFs distributed spatially? 3) To what extent are unmeasured environmental factors limiting tree cover? ELFs are difficult to quantify as they require significant sample sizes. We addressed this by using geospatial data over a relatively large spatial extent, where the wall-to-wall sampling ensures the inclusion of rare data points which define the minimum or maximum response to environmental factors. We tested mean temperature, minimum temperature, potential evapotranspiration (PET) and PET minus precipitation (PET-P) as potential limiting factors on percent tree cover. We found that the study area showed system-wide limitations on tree cover, and each of the factors showed evidence of being limiting on tree cover. However, only 1.2% of the total area appeared to be limited by the four (4) environmental factors, suggesting other unmeasured factors are limiting much of the tree cover in the study area. Where sites were near their theoretical maximum, non-forest sites (tree cover demand, and closed-canopy forests were not limited by any particular environmental factor. The detection of ELFs is necessary in order to fully understand the width of limitations that species experience within their geographic range.
Enumerating all maximal frequent subtrees in collections of phylogenetic trees

Science.gov (United States)

2014-01-01

Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474
QuickJoin—Fast Neighbour-Joining Tree Reconstruction

DEFF Research Database (Denmark)

Mailund; Pedersen, Christian N. Storm

2004-01-01

We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm—while still constructing the same tree as the original neighbour-joining algorithm—making it possible to construct trees for ~8000 species in less...

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