WorldWideScience

Sample records for efficient likelihood-based tree

  1. An efficient and extensible approach for compressing phylogenetic trees

    KAUST Repository

    Matthews, Suzanne J; Williams, Tiffani L

    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

  2. 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.

  3. 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.

  4. Efficient chaining of seeds in ordered trees

    OpenAIRE

    Allali, Julien; Chauve, Cédric; Ferraro, Pascal; Gaillard, Anne-Laure

    2010-01-01

    International audience; We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe...

  5. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance ($\\ensurem...

  6. Likelihood-based inference for clustered line transect data

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Schweder, Tore

    2006-01-01

    The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference...

  7. Likelihood-based Dynamic Factor Analysis for Measurement and Forecasting

    NARCIS (Netherlands)

    Jungbacker, B.M.J.P.; Koopman, S.J.

    2015-01-01

    We present new results for the likelihood-based analysis of the dynamic factor model. The latent factors are modelled by linear dynamic stochastic processes. The idiosyncratic disturbance series are specified as autoregressive processes with mutually correlated innovations. The new results lead to

  8. Likelihood-based inference for clustered line transect data

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus Plenge; Schweder, Tore

    The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference...

  9. Efficient Bulk Operations on Dynamic R-Trees

    DEFF Research Database (Denmark)

    Arge, Lars Allan; Hinrichs, Klaus; Vahrenhold, Jan

    2002-01-01

    In recent years there has been an upsurge of interest in spatial databases. A major issue is how to manipulate efficiently massive amounts of spatial data stored on disk in multidimensional spatial indexes (data structures). Construction of spatial indexes (bulk loading ) has been studied...... intensively in the database community. The continuous arrival of massive amounts of new data makes it important to update existing indexes (bulk updating ) efficiently. In this paper we present a simple, yet efficient, technique for performing bulk update and query operations on multidimensional indexes. We...... present our technique in terms of the so-called R-tree and its variants, as they have emerged as practically efficient indexing methods for spatial data. Our method uses ideas from the buffer tree lazy buffering technique and fully utilizes the available internal memory and the page size of the operating...

  10. Likelihood-Based Inference in Nonlinear Error-Correction Models

    DEFF Research Database (Denmark)

    Kristensen, Dennis; Rahbæk, Anders

    We consider a class of vector nonlinear error correction models where the transfer function (or loadings) of the stationary relation- ships is nonlinear. This includes in particular the smooth transition models. A general representation theorem is given which establishes the dynamic properties...... and a linear trend in general. Gaussian likelihood-based estimators are considered for the long- run cointegration parameters, and the short-run parameters. Asymp- totic theory is provided for these and it is discussed to what extend asymptotic normality and mixed normaity can be found. A simulation study...

  11. LDR: A Package for Likelihood-Based Sufficient Dimension Reduction

    Directory of Open Access Journals (Sweden)

    R. Dennis Cook

    2011-03-01

    Full Text Available We introduce a new mlab software package that implements several recently proposed likelihood-based methods for sufficient dimension reduction. Current capabilities include estimation of reduced subspaces with a fixed dimension d, as well as estimation of d by use of likelihood-ratio testing, permutation testing and information criteria. The methods are suitable for preprocessing data for both regression and classification. Implementations of related estimators are also available. Although the software is more oriented to command-line operation, a graphical user interface is also provided for prototype computations.

  12. Pareto Efficient Solutions of Attack-Defence Trees

    DEFF Research Database (Denmark)

    Aslanyan, Zaruhi; Nielson, Flemming

    2015-01-01

    Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes, such as proba......Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes......, such as probability or cost of attacks and defences. In case of multiple parameters most analytical methods optimise one parameter at a time, e.g., minimise cost or maximise probability of an attack. Such methods may lead to sub-optimal solutions when optimising conflicting parameters, e.g., minimising cost while...... maximising probability. In order to tackle this challenge, we devise automated techniques that optimise all parameters at once. Moreover, in the case of conflicting parameters our techniques compute the set of all optimal solutions, defined in terms of Pareto efficiency. The developments are carried out...

  13. Dominant clonal Eucalyptus grandis x urophylla trees use water more efficiently

    Science.gov (United States)

    Marina Shinkai Gentil Otto; Robert M. Hubbard; Dan Binkley; Jose Luis Stape

    2014-01-01

    Wood growth in trees depends on the acquisition of resources, and can vary with tree size leading to a variety of stand dynamics. Typically, larger trees obtain more resources and grow faster than smaller trees, but while light has been addressed more often, few case studies have investigated the contributions of water use and water use efficiency (WUE) within stands...

  14. Likelihood-Based Inference of B Cell Clonal Families.

    Directory of Open Access Journals (Sweden)

    Duncan K Ralph

    2016-10-01

    Full Text Available The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets.

  15. Maximum likelihood-based analysis of photon arrival trajectories in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Waligorska, Marta [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland); Molski, Andrzej, E-mail: amolski@amu.edu.pl [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer We study model selection and parameter recovery from single-molecule FRET experiments. Black-Right-Pointing-Pointer We examine the maximum likelihood-based analysis of two-color photon trajectories. Black-Right-Pointing-Pointer The number of observed photons determines the performance of the method. Black-Right-Pointing-Pointer For long trajectories, one can extract mean dwell times that are comparable to inter-photon times. -- Abstract: When two fluorophores (donor and acceptor) are attached to an immobilized biomolecule, anti-correlated fluctuations of the donor and acceptor fluorescence caused by Foerster resonance energy transfer (FRET) report on the conformational kinetics of the molecule. Here we assess the maximum likelihood-based analysis of donor and acceptor photon arrival trajectories as a method for extracting the conformational kinetics. Using computer generated data we quantify the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) in selecting the true kinetic model. We find that the number of observed photons is the key parameter determining parameter estimation and model selection. For long trajectories, one can extract mean dwell times that are comparable to inter-photon times.

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

    Science.gov (United States)

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

    2017-04-01

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

  17. 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

  18. Pareto Efficient Solution of Attack-Defence Trees

    NARCIS (Netherlands)

    Aslanyan, Zaruhi; Nielson, Flemming

    Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes, such as

  19. Sampling strategies for efficient estimation of tree foliage biomass

    Science.gov (United States)

    Hailemariam Temesgen; Vicente Monleon; Aaron Weiskittel; Duncan Wilson

    2011-01-01

    Conifer crowns can be highly variable both within and between trees, particularly with respect to foliage biomass and leaf area. A variety of sampling schemes have been used to estimate biomass and leaf area at the individual tree and stand scales. Rarely has the effectiveness of these sampling schemes been compared across stands or even across species. In addition,...

  20. 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...

  1. Efficient Delaunay Tessellation through K-D Tree Decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Peterka, Tom

    2017-08-21

    Delaunay tessellations are fundamental data structures in computational geometry. They are important in data analysis, where they can represent the geometry of a point set or approximate its density. The algorithms for computing these tessellations at scale perform poorly when the input data is unbalanced. We investigate the use of k-d trees to evenly distribute points among processes and compare two strategies for picking split points between domain regions. Because resulting point distributions no longer satisfy the assumptions of existing parallel Delaunay algorithms, we develop a new parallel algorithm that adapts to its input and prove its correctness. We evaluate the new algorithm using two late-stage cosmology datasets. The new running times are up to 50 times faster using k-d tree compared with regular grid decomposition. Moreover, in the unbalanced data sets, decomposing the domain into a k-d tree is up to five times faster than decomposing it into a regular grid.

  2. Analytical estimates and proof of the scale-free character of efficiency and improvement in Barabasi-Albert trees

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Bermejo, B. [Departamento de Fisica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain)], E-mail: benito.hernandez@urjc.es; Marco-Blanco, J. [Departamento de Fisica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain); Romance, M. [Departamento de Matematica Aplicada, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain)

    2009-02-23

    Estimates for the efficiency of a tree are derived, leading to new analytical expressions for Barabasi-Albert trees efficiency. These expressions are used to investigate the dynamic behaviour of such networks. It is proved that the preferential attachment leads to an asymptotic conservation of efficiency as the Barabasi-Albert trees grow.

  3. Analytical estimates and proof of the scale-free character of efficiency and improvement in Barabasi-Albert trees

    International Nuclear Information System (INIS)

    Hernandez-Bermejo, B.; Marco-Blanco, J.; Romance, M.

    2009-01-01

    Estimates for the efficiency of a tree are derived, leading to new analytical expressions for Barabasi-Albert trees efficiency. These expressions are used to investigate the dynamic behaviour of such networks. It is proved that the preferential attachment leads to an asymptotic conservation of efficiency as the Barabasi-Albert trees grow

  4. Maximum likelihood-based analysis of single-molecule photon arrival trajectories

    Science.gov (United States)

    Hajdziona, Marta; Molski, Andrzej

    2011-02-01

    In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

  5. Maximum likelihood-based analysis of single-molecule photon arrival trajectories.

    Science.gov (United States)

    Hajdziona, Marta; Molski, Andrzej

    2011-02-07

    In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 10(3) photons. When the intensity levels are well-separated and 10(4) photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

  6. Explaining growth of individual trees: Light interception and efficiency of light use by Eucalyptus at four sites in Brazil

    Science.gov (United States)

    Dan Binkley; Jose Luiz Stape; William L. Bauerle; Michael G. Ryan

    2010-01-01

    The growth of wood in trees and forests depends on the acquisition of resources (light, water, and nutrients), the efficiency of using resources for photosynthesis, and subsequent partitioning to woody tissues. Patterns of efficiency over time for individual trees, or between trees at one time, result from changes in rates photosynthesis and shifts in...

  7. Efficient OCR using simple features and decision trees with backtracking

    International Nuclear Information System (INIS)

    Abuhaiba, Ibrahim S.I.

    2006-01-01

    In this paper, it is shown that it is adequate to use simple and easy-to-compute figures such as those we call sliced horizontal and vertical projections to solve the OCR problem for machine-printed documents. Recognition is achieved using a decision tree supported with backtracking, smoothing, row and column cropping, and other additions to increase the success rate. Symbols from Times New Roman type face are used to train our system. Activating backtracking, smoothing and cropping achieved more than 98% successes rate for a recognition time below 30ms per character. The recognition algorithm was exposed to a hard test by polluting the original dataset with additional artificial noise and could maintain a high successes rate and low error rate for highly polluted images, which is a result of backtracking, and smoothing and row and column cropping. Results indicate that we can depend on simple features and hints to reliably recognize characters. The error rate can be decreased by increasing the size of training dataset. The recognition time can be reduced by using some programming optimization techniques and more powerful computers. (author)

  8. Experimental demonstration of the maximum likelihood-based chromatic dispersion estimator for coherent receivers

    DEFF Research Database (Denmark)

    Borkowski, Robert; Johannisson, Pontus; Wymeersch, Henk

    2014-01-01

    We perform an experimental investigation of a maximum likelihood-based (ML-based) algorithm for bulk chromatic dispersion estimation for digital coherent receivers operating in uncompensated optical networks. We demonstrate the robustness of the method at low optical signal-to-noise ratio (OSNR...

  9. 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...

  10. Using an implicit min/max KD-Tree for doing efficient terrain line of sight calculations

    CSIR Research Space (South Africa)

    Duvenhage, B

    2009-02-01

    Full Text Available -dimensional tree (kd-tree) based raytracing approach, to calculating LOS information, is efficient. A new implicit min/max kd-tree algorithm is discussed for evaluating LOS queries on large scale spherical terrain. In particular the value of low resolution boundary...

  11. 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.

  12. treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

    Science.gov (United States)

    Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

    2017-01-07

    Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

  13. Recent trends in the intrinsic water-use efficiency of ringless rainforest trees in Borneo.

    Science.gov (United States)

    Loader, N J; Walsh, R P D; Robertson, I; Bidin, K; Ong, R C; Reynolds, G; McCarroll, D; Gagen, M; Young, G H F

    2011-11-27

    Stable carbon isotope (δ(13)C) series were developed from analysis of sequential radial wood increments from AD 1850 to AD 2009 for four mature primary rainforest trees from the Danum and Imbak areas of Sabah, Malaysia. The aseasonal equatorial climate meant that conventional dendrochronology was not possible as the tree species investigated do not exhibit clear annual rings or dateable growth bands. Chronology was established using radiocarbon dating to model age-growth relationships and date the carbon isotopic series from which the intrinsic water-use efficiency (IWUE) was calculated. The two Eusideroxylon zwageri trees from Imbak yielded ages of their pith/central wood (±1 sigma) of 670 ± 40 and 759 ± 40 years old; the less dense Shorea johorensis and Shorea superba trees at Danum yielded ages of 240 ± 40 and 330 ± 40 years, respectively. All trees studied exhibit an increase in the IWUE since AD 1960. This reflects, in part, a response of the forest to increasing atmospheric carbon dioxide concentration. Unlike studies of some northern European trees, no clear plateau in this response was observed. A change in the IWUE implies an associated modification of the local carbon and/or hydrological cycles. To resolve these uncertainties, a shift in emphasis away from high-resolution studies towards long, well-replicated time series is proposed to develop the environmental data essential for model evaluation. Identification of old (greater than 700 years) ringless trees demonstrates their potential in assessing the impacts of climatic and atmospheric change. It also shows the scientific and applied value of a conservation policy that ensures the survival of primary forest containing particularly old trees (as in Imbak Canyon and Danum).

  14. Enhanced photosynthetic efficiency in trees world-wide by rising atmospheric CO2 levels

    Science.gov (United States)

    Ehlers, Ina; Wieloch, Thomas; Groenendijk, Peter; Vlam, Mart; van der Sleen, Peter; Zuidema, Pieter A.; Robertson, Iain; Schleucher, Jürgen

    2014-05-01

    signals is a fundamental advantage of isotopomer ratios (Augusti et al., Chem. Geol 2008). These results demonstrate that increasing [CO2] has reduced the ratio of photorespiration to photosynthesis on a global scale. Photorespiration is a side reaction that decreases the C gain of plants; the suppression of photorespiration in all analyzed trees indicates that increasing atmospheric [CO2] is enhancing the photosynthetic efficiency of trees world-wide. The consensus response of the trees agrees with the response of annual plants in greenhouse experiments, with three important conclusions. First, the generality of the isotopomer shift confirms that the CO2 response reflects the ratio of photosynthesis to photorespiration, and that it creates a robust signal in tree rings. Second, the agreement between greenhouse-grown plants and trees indicates that there has not been an acclimation response of the trees during the past centuries. Third, the results show that the regulation of tree gas exchange has during past centuries been governed by the same rules as observed in manipulative experiments, in contradiction to recent reports (Keenan et al., Nature 2013).

  15. ldr: An R Software Package for Likelihood-Based Su?cient Dimension Reduction

    Directory of Open Access Journals (Sweden)

    Kofi Placid Adragni

    2014-11-01

    Full Text Available In regression settings, a su?cient dimension reduction (SDR method seeks the core information in a p-vector predictor that completely captures its relationship with a response. The reduced predictor may reside in a lower dimension d < p, improving ability to visualize data and predict future observations, and mitigating dimensionality issues when carrying out further analysis. We introduce ldr, a new R software package that implements three recently proposed likelihood-based methods for SDR: covariance reduction, likelihood acquired directions, and principal fitted components. All three methods reduce the dimensionality of the data by pro jection into lower dimensional subspaces. The package also implements a variable screening method built upon principal ?tted components which makes use of ?exible basis functions to capture the dependencies between the predictors and the response. Examples are given to demonstrate likelihood-based SDR analyses using ldr, including estimation of the dimension of reduction subspaces and selection of basis functions. The ldr package provides a framework that we hope to grow into a comprehensive library of likelihood-based SDR methodologies.

  16. An Efficient Method of Vibration Diagnostics For Rotating Machinery Using a Decision Tree

    Directory of Open Access Journals (Sweden)

    Bo Suk Yang

    2000-01-01

    Full Text Available This paper describes an efficient method to automatize vibration diagnosis for rotating machinery using a decision tree, which is applicable to vibration diagnosis expert system. Decision tree is a widely known formalism for expressing classification knowledge and has been used successfully in many diverse areas such as character recognition, medical diagnosis, and expert systems, etc. In order to build a decision tree for vibration diagnosis, we have to define classes and attributes. A set of cases based on past experiences is also needed. This training set is inducted using a result-cause matrix newly developed in the present work instead of using a conventionally implemented cause-result matrix. This method was applied to diagnostics for various cases taken from published work. It is found that the present method predicts causes of the abnormal vibration for test cases with high reliability.

  17. Query and Update Efficient B+-Tree Based Indexing of Moving Objects

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Lin, Dan; Ooi, Beng Chin

    2004-01-01

    . This motivates the design of a solution that enables the B+-tree to manage moving objects. We represent moving-object locations as vectors that are timestamped based on their update time. By applying a novel linearization technique to these values, it is possible to index the resulting values using a single B...... are streamed to a database. Indexes for moving objects must support queries efficiently, but must also support frequent updates. Indexes based on minimum bounding regions (MBRs) such as the R-tree exhibit high concurrency overheads during node splitting, and each individual update is known to be quite costly......+-tree that partitions values according to their timestamp and otherwise preserves spatial proximity. We develop algorithms for range and k nearest neighbor queries, as well as continuous queries. The proposal can be grafted into existing database systems cost effectively. An extensive experimental study explores...

  18. ERA: Efficient serial and parallel suffix tree construction for very long strings

    KAUST Repository

    Mansour, Essam

    2011-09-01

    The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient. This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory. ERa partitions the tree construction process horizontally and vertically and minimizes I/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERa also groups vertical partitions together to amortize the I/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERa indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.

  19. Prediction of strontium bromide laser efficiency using cluster and decision tree analysis

    Directory of Open Access Journals (Sweden)

    Iliev Iliycho

    2018-01-01

    Full Text Available Subject of investigation is a new high-powered strontium bromide (SrBr2 vapor laser emitting in multiline region of wavelengths. The laser is an alternative to the atom strontium lasers and electron free lasers, especially at the line 6.45 μm which line is used in surgery for medical processing of biological tissues and bones with minimal damage. In this paper the experimental data from measurements of operational and output characteristics of the laser are statistically processed by means of cluster analysis and tree-based regression techniques. The aim is to extract the more important relationships and dependences from the available data which influence the increase of the overall laser efficiency. There are constructed and analyzed a set of cluster models. It is shown by using different cluster methods that the seven investigated operational characteristics (laser tube diameter, length, supplied electrical power, and others and laser efficiency are combined in 2 clusters. By the built regression tree models using Classification and Regression Trees (CART technique there are obtained dependences to predict the values of efficiency, and especially the maximum efficiency with over 95% accuracy.

  20. Efficient, reliable and fast high-level triggering using a bonsai boosted decision tree

    International Nuclear Information System (INIS)

    Gligorov, V V; Williams, M

    2013-01-01

    High-level triggering is a vital component of many modern particle physics experiments. This paper describes a modification to the standard boosted decision tree (BDT) classifier, the so-called bonsai BDT, that has the following important properties: it is more efficient than traditional cut-based approaches; it is robust against detector instabilities, and it is very fast. Thus, it is fit-for-purpose for the online running conditions faced by any large-scale data acquisition system.

  1. Generalized Empirical Likelihood-Based Focused Information Criterion and Model Averaging

    Directory of Open Access Journals (Sweden)

    Naoya Sueishi

    2013-07-01

    Full Text Available This paper develops model selection and averaging methods for moment restriction models. We first propose a focused information criterion based on the generalized empirical likelihood estimator. We address the issue of selecting an optimal model, rather than a correct model, for estimating a specific parameter of interest. Then, this study investigates a generalized empirical likelihood-based model averaging estimator that minimizes the asymptotic mean squared error. A simulation study suggests that our averaging estimator can be a useful alternative to existing post-selection estimators.

  2. Likelihood-based inference for cointegration with nonlinear error-correction

    DEFF Research Database (Denmark)

    Kristensen, Dennis; Rahbek, Anders Christian

    2010-01-01

    We consider a class of nonlinear vector error correction models where the transfer function (or loadings) of the stationary relationships is nonlinear. This includes in particular the smooth transition models. A general representation theorem is given which establishes the dynamic properties...... and a linear trend in general. Gaussian likelihood-based estimators are considered for the long-run cointegration parameters, and the short-run parameters. Asymptotic theory is provided for these and it is discussed to what extend asymptotic normality and mixed normality can be found. A simulation study...

  3. Improving the water use efficiency of olive trees growing in water harvesting systems

    Science.gov (United States)

    Berliner, Pedro; Leake, Salomon; Carmi, Gennady; Agam, Nurit

    2017-04-01

    Water is a primary limiting factor for agricultural development in many arid and semi-arid regions in which a runoff generation is a rather frequent event. If conveyed to dyke surrounded plots and ponded, runoff water can thereafter be used for tree production. One of the most promising runoff collection configurations is that of micro-catchments in which water is collected close to the area in which runoff was generated and stored in adjacent shallow pits. The objective of this work was to assess the effect of the geometry of runoff water collection area (shallow pit or trench) on direct evaporative water losses and on the water use efficiency of olive trees grown in them. The study was conducted during the summer of 2013 and 2014. In this study regular micro-catchments with basins of 9 m2 (3 x 3 m) by 0.1 m deep were compared with trenches of one meter deep and one meter wide. Each configuration was replicated three times. One tree was planted in each shallow basin and the distance between trees in the 12 m long trench was four meters. Access tubes for neutron probes were installed in the micro-catchments and trenches (four and seven, respectively) to depths of 2.5 m. Soil water content in the soil profile was monitored periodically throughout drying periods in between simulated runoff events. Transpiration of the trees was estimated from half-hourly sap flow measurements using a Granier system. Total transpiration fluxes were computed for time intervals corresponding to consecutive soil water measurements. During the first year, a large runoff event was simulated by applying once four cubic meters to each plot; and in the second year the same volume of water was split into four applications, simulating a series of small runoff events. In both geometries, trees received the same amount of water per tree. Evaporation from trenches and micro-catchments was estimated as the difference between evapotranspiration obtained computing the differences in total soil water

  4. An Efficient Distributed Algorithm for Constructing Spanning Trees in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Rosana Lachowski

    2015-01-01

    Full Text Available Monitoring and data collection are the two main functions in wireless sensor networks (WSNs. Collected data are generally transmitted via multihop communication to a special node, called the sink. While in a typical WSN, nodes have a sink node as the final destination for the data traffic, in an ad hoc network, nodes need to communicate with each other. For this reason, routing protocols for ad hoc networks are inefficient for WSNs. Trees, on the other hand, are classic routing structures explicitly or implicitly used in WSNs. In this work, we implement and evaluate distributed algorithms for constructing routing trees in WSNs described in the literature. After identifying the drawbacks and advantages of these algorithms, we propose a new algorithm for constructing spanning trees in WSNs. The performance of the proposed algorithm and the quality of the constructed tree were evaluated in different network scenarios. The results showed that the proposed algorithm is a more efficient solution. Furthermore, the algorithm provides multiple routes to the sensor nodes to be used as mechanisms for fault tolerance and load balancing.

  5. Phosphorus use efficiency of the gum arabi tree (Acacia senegal (L) Willd) in Sudan

    Energy Technology Data Exchange (ETDEWEB)

    Elamin, K H; Mustafa, A F [Gezira Agricultural Research Centre, Wad Medani (Sudan). Forestry Research Section

    1996-07-01

    This study was conducted to identify gum arabic tree (Acacia senegal L. Willd) provenances with high efficiency for phosphorus uptake and use. Thirteen provenances were collected from different habitats with the gum belt of the Sudan. A preliminary trial was conducted during the period 1989-1992 at the Gezira Agricultural Research Station in Wad Medani. This study revealed that there are clear genotypic differences in phosphorus use efficiency, nitrogen yield and dry matter production. All the provenances tested also exhibited a high ability for survival under the dry climatic conditions as prevailing in the gum belt of Sudan. Based on differences in phosphorus use efficiency observed in the preliminary study, 4 provenances were selected for a detailed study. Provenance 11 and 2 represented the highly efficient group, provenance 7 the moderately efficient group and provenance 13 the low efficient group. The detailed study revealed that provenance 11 is superior to all others in terms of biomass production as well as in phosphorus use efficiency. Although the ability to take up phosphorus was low, this was compensated by having a high root length density enabling the tree to take up a quantity of phosphorus similar to that taken up by other provenances. The high ability to convert the absorbed phosphorus into a greater quantity of dry matter made this provenance the best in phosphorus use efficiency. These results suggest that provenance 11 may be a suitable candidate to be introduced into the gum belt of Sudan in support of its rehabilitation programme. (author). 13 refs, 4 figs, 5 tabs.

  6. Phosphorus use efficiency of the gum arabi tree (Acacia senegal (L) Willd) in Sudan

    International Nuclear Information System (INIS)

    Elamin, K.H.; Mustafa, A.F.

    1996-01-01

    This study was conducted to identify gum arabic tree (Acacia senegal L. Willd) provenances with high efficiency for phosphorus uptake and use. Thirteen provenances were collected from different habitats with the gum belt of the Sudan. A preliminary trial was conducted during the period 1989-1992 at the Gezira Agricultural Research Station in Wad Medani. This study revealed that there are clear genotypic differences in phosphorus use efficiency, nitrogen yield and dry matter production. All the provenances tested also exhibited a high ability for survival under the dry climatic conditions as prevailing in the gum belt of Sudan. Based on differences in phosphorus use efficiency observed in the preliminary study, 4 provenances were selected for a detailed study. Provenance 11 and 2 represented the highly efficient group, provenance 7 the moderately efficient group and provenance 13 the low efficient group. The detailed study revealed that provenance 11 is superior to all others in terms of biomass production as well as in phosphorus use efficiency. Although the ability to take up phosphorus was low, this was compensated by having a high root length density enabling the tree to take up a quantity of phosphorus similar to that taken up by other provenances. The high ability to convert the absorbed phosphorus into a greater quantity of dry matter made this provenance the best in phosphorus use efficiency. These results suggest that provenance 11 may be a suitable candidate to be introduced into the gum belt of Sudan in support of its rehabilitation programme. (author). 13 refs, 4 figs, 5 tabs

  7. Increased water-use efficiency does not lead to enhanced tree growth under xeric and mesic conditions

    NARCIS (Netherlands)

    Lévesque, M.; Siegwolf, R.; Saurer, M.; Eilmann, B.; Rigling, A.

    2014-01-01

    Higher atmospheric CO2 concentrations (ca ) can under certain conditions increase tree growth by enhancing photosynthesis, resulting in an increase of intrinsic water-use efficiency (i WUE) in trees. However, the magnitude of these effects and their interactions with changing climatic conditions are

  8. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

    Science.gov (United States)

    Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

    2018-01-01

    Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

  9. MB3-Miner: efficiently mining eMBedded subTREEs using Tree Model Guided candidate generation

    NARCIS (Netherlands)

    Tan, H.; Dillon, T.; Hadzic, F.; Chang, E.; Feng, L.

    2005-01-01

    Tree mining has many useful applications in areas such as Bioinformatics, XML mining, Web mining, etc. In general, most of the formally represented information in these domains is a tree structured form. In this paper we focus on mining frequent embedded subtrees from databases of rooted labeled

  10. Integrating individual trip planning in energy efficiency – Building decision tree models for Danish fisheries

    DEFF Research Database (Denmark)

    Bastardie, Francois; Nielsen, J. Rasmus; Andersen, Bo Sølgaard

    2013-01-01

    efficiency for the value of catch per unit of fuel consumed is analysed by merging the questionnaire, logbook and VMS (vessel monitoring system) information. Logic decision trees and conditional behaviour probabilities are established from the responses of fishermen regarding a range of sequential......-intensive but efficient vessels conducting pelagic or industrial fishing are more inclined to base their decision on fish price only, while numerous smaller and less efficient vessels conducting demersal mixed or crustacean fishery usually consider other flexible factors, e.g., the potential for a large catch, weather...... the adaptations of individual fishermen to resource availability dynamics, increasing fuel prices, changes in regulations, and the consequences of socioeconomic external pressures on harvested stocks. A new methodology is described here to obtain quantitative information on the fishermen’s micro-scale decisions...

  11. Efficient algorithms to assess component and gate importance in fault tree analysis

    International Nuclear Information System (INIS)

    Dutuit, Y.; Rauzy, A.

    2001-01-01

    One of the principal activities of risk assessment is either the ranking or the categorization of structures, systems and components with respect to their risk-significance or their safety-significance. Several measures, so-called importance factors, of such a significance have been proposed for the case where the support model is a fault tree. In this article, we show how binary decision diagrams can be use to assess efficiently a number of classical importance factors. This work completes the preliminary results obtained recently by Andrews and Sinnamon, and the authors. It deals also with the concept of joint reliability importance

  12. The Probabilistic Convolution Tree: Efficient Exact Bayesian Inference for Faster LC-MS/MS Protein Inference

    Science.gov (United States)

    Serang, Oliver

    2014-01-01

    Exact Bayesian inference can sometimes be performed efficiently for special cases where a function has commutative and associative symmetry of its inputs (called “causal independence”). For this reason, it is desirable to exploit such symmetry on big data sets. Here we present a method to exploit a general form of this symmetry on probabilistic adder nodes by transforming those probabilistic adder nodes into a probabilistic convolution tree with which dynamic programming computes exact probabilities. A substantial speedup is demonstrated using an illustration example that can arise when identifying splice forms with bottom-up mass spectrometry-based proteomics. On this example, even state-of-the-art exact inference algorithms require a runtime more than exponential in the number of splice forms considered. By using the probabilistic convolution tree, we reduce the runtime to and the space to where is the number of variables joined by an additive or cardinal operator. This approach, which can also be used with junction tree inference, is applicable to graphs with arbitrary dependency on counting variables or cardinalities and can be used on diverse problems and fields like forward error correcting codes, elemental decomposition, and spectral demixing. The approach also trivially generalizes to multiple dimensions. PMID:24626234

  13. New subsea X tree generation brings innovative features providing efficiency for ultra deep waters

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Gustavo Bellot de Almeida; Labes, Alan Zaragoza [FMC Technologies, Houston, TX (United States)

    2008-07-01

    The EVDT has been developed for global applications. Based upon the widely field proven 10 K Vertical Tree and 15 K HPHT Tree, the system has incorporated the latest technological advancements. The Tubing Hanger System and installation tooling are available up to a 7 inch bore for 10,000 psi applications and a 5 inch bore for 15,000 psi applications. The Tubing Hanger can be installed using a Tubing Head when flexibility for sequencing of events is required during offshore installations. Or it can simply land into the wellhead, eliminating the Tubing Head. This allows for a more efficient installation when completion and drilling operations are conducted without retrieving the Sub sea Blow Out Preventer (BOP) and Riser. The EVDT incorporates a retrievable Flow Module downstream of the wing valve that can be configured to project specific variances such as production, gas injection and water injection service. The Flow Module can also be configured to include Multi-Phase Flow Meters, sensors, and gauges. This allows an upgrade sub sea without having to pull and re-run the entire Tree system. These features allowed the system to hit the mark regarding what the industry needs today and also allowed to accommodate technologies that will arise in the years to come. (author)

  14. Transpiration efficiency of a tropical pioneer tree (Ficus insipida) in relation to soil fertility.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Aranda, Jorge; Turner, Benjamin L; Marshall, John D

    2007-01-01

    The response of whole-plant water-use efficiency, termed transpiration efficiency (TE), to variation in soil fertility was assessed in a tropical pioneer tree, Ficus insipida Willd. Measurements of stable isotope ratios (delta(13)C, delta(18)O, delta(15)N), elemental concentrations (C, N, P), plant growth, instantaneous leaf gas exchange, and whole-plant water use were used to analyse the mechanisms controlling TE. Plants were grown individually in 19 l pots with non-limiting soil moisture. Soil fertility was altered by mixing soil with varying proportions of rice husks, and applying a slow release fertilizer. A large variation was observed in leaf photosynthetic rate, mean relative growth rate (RGR), and TE in response to experimental treatments; these traits were well correlated with variation in leaf N concentration. Variation in TE showed a strong dependence on the ratio of intercellular to ambient CO(2) mole fractions (c(i)/c(a)); both for instantaneous measurements of c(i)/c(a) (R(2)=0.69, P <0.0001, n=30), and integrated estimates based on C isotope discrimination (R(2)=0.88, P <0.0001, n=30). On the other hand, variations in the leaf-to-air humidity gradient, unproductive water loss, and respiratory C use probably played only minor roles in modulating TE in the face of variable soil fertility. The pronounced variation in TE resulted from a combination of the strong response of c(i)/c(a) to leaf N, and inherently high values of c(i)/c(a) for this tropical tree species; these two factors conspired to cause a 4-fold variation among treatments in (1-c(i)/c(a)), the term that actually modifies TE. Results suggest that variation in plant N status could have important implications for the coupling between C and water exchange in tropical forest trees.

  15. Efficient utilization of short rotation tree biomass for cooking in India

    Science.gov (United States)

    Sharma, R.; Chauhan, S. K.

    2012-04-01

    The human as well as livestock population increase is phenomenal in developing world including India. The survival of this huge population certainly depends on the carrying capacity of the natural systems, which is essentially determined by the nature itself. Present state of the forests can satisfy the needs of certain population and the demand for wood has rapidly outstripped the sustainability of forests. The fuelwood requirements in the developing world is approximately 80 per cent of total wood requirements and is the major cause of forest degradation. Therefore, there is need to maximize the productivity on one hand and protection/extention of the area on another hand. Wood substitution is an option including shifting from fuelwood for cooking to fossil fuels but in the changing climatic situation, this option is short term alternative. There is need to produce more and use the same efficiently to reduce the demands. Millions of households across the country are using crude cooking stoves for their daily needs which are not only energy inefficient but detrimental to women health also. It has been the policy of Government to encourage trees outside forests to minimize the pressure from forests through meeting requirements outside forests, which is possible through intensively managed short rotation forestry and also some initiatives have been taken to increase the fuelwood efficiency through improved cooking stove, which are working successfully. Woodfuel remained the most important source of household energy in India but regular attempts have not been made to improve the efficiency in its use. This paper will focus on potential of short rotation forestry plantations for energy consumption and its efficient use at domestic scale. This has three fold interrelated economic, environmental and social impact. Key words: Short Rotation Forestry, trees outside forests, wood energy, cooking stove

  16. Carbon Isotope discrimination in acacia auriculiformis - can it be used to select for higher water-use-efficiency in trees?

    International Nuclear Information System (INIS)

    Montagu, K.D.; Woo, K.C.; Puangchit, L.

    1999-01-01

    Full text: Determining the water-use-efficiency of trees in relation lo wood production is problematic due to the sheer size of the plant and the number of years taken to produce the wood. Indirect measures of water-use-efficiency, such as carbon isotope discrimination (Δ), are therefore attractive to tree breeders wishing to select for increased water-use-efficiency. To begin to evaluate the usefulness of Δ as a selection parameter for the tropical tree Acacia auriculiformis we addressed the following questions: 1. Within the tree canopy, how variable is Δ? 2. Is there any genotypic variation in Δ? and 3. Does water availability affect genotypic variation? To address these questions we sampled foliage from pot trials and field trials of A. auriculiformis ranging in age from 3 months lo 8 years in Australia and Thailand. In 16-18m high 8-year-old trees, canopy variation in Δ was large (P>0.01). Foliage Δ values increased down the tree from 22.0 %o at the top to 24.7 %o at the base. The decrease was rapid in the lop 3 m of the canopy thus considerable care must be taken to sampling foliage from the same position in the canopy. Genotype variations in Δ was observed in seedlings and 2 year-old trees (P>0.01) but not in 8 year-old trees (P=0.60). Where genotypic variation were observed the differences between the lowest and highest values were 2.2 - 3.6 %o. Reduced water availability decreased Δ values in both pot and field studies but not in a consistent way across seedlots. Thus it would appear that the Δ of trees grown under favourable conditions does not give an indication of the Δ value which will be obtained under water-limited conditions. This complicates the use of Δ as a screening method. We have clearly shown that genotype variation occurs in A. auriculiformis in both seedlings and young field-grown trees. Considerable care is required when sampling large trees, as variation in Δ within the tree can be as large as between genotypes. The challenge

  17. Efficiency of Individual Tree Detection Approaches Based on Light-Weight and Low-Cost UAS Imagery in Australian Savannas

    Directory of Open Access Journals (Sweden)

    Grigorijs Goldbergs

    2018-01-01

    Full Text Available The reliability of airborne light detection and ranging (LiDAR for delineating individual trees and estimating aboveground biomass (AGB has been proven in a diverse range of ecosystems, but can be difficult and costly to commission. Point clouds derived from structure from motion (SfM matching techniques obtained from unmanned aerial systems (UAS could be a feasible low-cost alternative to airborne LiDAR scanning for canopy parameter retrieval. This study assesses the extent to which SfM three-dimensional (3D point clouds—obtained from a light-weight mini-UAS quadcopter with an inexpensive consumer action GoPro camera—can efficiently and effectively detect individual trees, measure tree heights, and provide AGB estimates in Australian tropical savannas. Two well-established canopy maxima and watershed segmentation tree detection algorithms were tested on canopy height models (CHM derived from SfM imagery. The influence of CHM spatial resolution on tree detection accuracy was analysed, and the results were validated against existing high-resolution airborne LiDAR data. We found that the canopy maxima and watershed segmentation routines produced similar tree detection rates (~70% for dominant and co-dominant trees, but yielded low detection rates (<35% for suppressed and small trees due to poor representativeness in point clouds and overstory occlusion. Although airborne LiDAR provides higher tree detection rates and more accurate estimates of tree heights, we found SfM image matching to be an adequate low-cost alternative for the detection of dominant and co-dominant tree stands.

  18. An efficient computational method for global sensitivity analysis and its application to tree growth modelling

    International Nuclear Information System (INIS)

    Wu, Qiong-Li; Cournède, Paul-Henry; Mathieu, Amélie

    2012-01-01

    Global sensitivity analysis has a key role to play in the design and parameterisation of functional–structural plant growth models which combine the description of plant structural development (organogenesis and geometry) and functional growth (biomass accumulation and allocation). We are particularly interested in this study in Sobol's method which decomposes the variance of the output of interest into terms due to individual parameters but also to interactions between parameters. Such information is crucial for systems with potentially high levels of non-linearity and interactions between processes, like plant growth. However, the computation of Sobol's indices relies on Monte Carlo sampling and re-sampling, whose costs can be very high, especially when model evaluation is also expensive, as for tree models. In this paper, we thus propose a new method to compute Sobol's indices inspired by Homma–Saltelli, which improves slightly their use of model evaluations, and then derive for this generic type of computational methods an estimator of the error estimation of sensitivity indices with respect to the sampling size. It allows the detailed control of the balance between accuracy and computing time. Numerical tests on a simple non-linear model are convincing and the method is finally applied to a functional–structural model of tree growth, GreenLab, whose particularity is the strong level of interaction between plant functioning and organogenesis. - Highlights: ► We study global sensitivity analysis in the context of functional–structural plant modelling. ► A new estimator based on Homma–Saltelli method is proposed to compute Sobol indices, based on a more balanced re-sampling strategy. ► The estimation accuracy of sensitivity indices for a class of Sobol's estimators can be controlled by error analysis. ► The proposed algorithm is implemented efficiently to compute Sobol indices for a complex tree growth model.

  19. The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction.

    Directory of Open Access Journals (Sweden)

    Ross S Williamson

    2015-04-01

    Full Text Available Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron's probability of spiking. One popular method, known as maximally informative dimensions (MID, uses an information-theoretic quantity known as "single-spike information" to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.

  20. A likelihood-based biostatistical model for analyzing consumer movement in simultaneous choice experiments.

    Science.gov (United States)

    Zeilinger, Adam R; Olson, Dawn M; Andow, David A

    2014-08-01

    Consumer feeding preference among resource choices has critical implications for basic ecological and evolutionary processes, and can be highly relevant to applied problems such as ecological risk assessment and invasion biology. Within consumer choice experiments, also known as feeding preference or cafeteria experiments, measures of relative consumption and measures of consumer movement can provide distinct and complementary insights into the strength, causes, and consequences of preference. Despite the distinct value of inferring preference from measures of consumer movement, rigorous and biologically relevant analytical methods are lacking. We describe a simple, likelihood-based, biostatistical model for analyzing the transient dynamics of consumer movement in a paired-choice experiment. With experimental data consisting of repeated discrete measures of consumer location, the model can be used to estimate constant consumer attraction and leaving rates for two food choices, and differences in choice-specific attraction and leaving rates can be tested using model selection. The model enables calculation of transient and equilibrial probabilities of consumer-resource association, which could be incorporated into larger scale movement models. We explore the effect of experimental design on parameter estimation through stochastic simulation and describe methods to check that data meet model assumptions. Using a dataset of modest sample size, we illustrate the use of the model to draw inferences on consumer preference as well as underlying behavioral mechanisms. Finally, we include a user's guide and computer code scripts in R to facilitate use of the model by other researchers.

  1. Investigation on the efficiency of treated Palm Tree waste for removal of organic pollutants

    Science.gov (United States)

    Azoulay, Karima; El HajjajiI, Souad; Dahchour, Abdelmalek

    2017-04-01

    Development of the industrial sector generates several problems of environmental pollution. This issue rises concern among scientific community and decision makers, in this work; we e interested in water resources polluted by the chemical substances, which can cause various problems of health. As an example, dyes generated by different industrial activities such as textile, cosmetic, metal plating, leather, paper and plastic sectors, constitute an important source of pollution. In this work, we aim at investigating the efficiency of palm tree waste for removal of dyes from polluted solution. Our work presents a double environmental aspect, on one hand it constitutes an attempt for valorization of Palm Tree waste, and on the other hand it provides natural adsorbent. The study focuses on the effectiveness of the waste in removing Methylene Bleu and Methyl Orange taken as models of pollutants from aqueous solution. Kinetics and isotherm experiments were conducted in order to determine the sorption behavior of the examined dye. The effects of initial dye and adsorbent concentrations are considered. The results indicate that the correlation coefficient calculated from pseudo-second order equation was higher than the other kinetic equations, indicating that equilibrium data fitted well with pseudo-second order model where adsorption process was chemisorption. The adsorption equilibrium was well described by Langmuir isotherm model.

  2. ERA: Efficient serial and parallel suffix tree construction for very long strings

    KAUST Repository

    Mansour, Essam; Allam, Amin; Skiadopoulos, Spiros G.; Kalnis, Panos

    2011-01-01

    The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree

  3. A likelihood-based framework for the analysis of discussion threads

    NARCIS (Netherlands)

    Gómez, Vincenc; Kappen, Hilbert J.; Litvak, Nelli; Kaltenbrunner, Andreas

    2013-01-01

    Online discussion threads are conversational cascades in the form of posted messages that can be generally found in social systems that comprise many-to-many interaction such as blogs, news aggregators or bulletin board systems. We propose a framework based on generative models of growing trees to

  4. Efficient Dynamic Adaptation Strategies for Object Tracking Tree in Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    CHEN, M.

    2012-12-01

    Full Text Available Most object tracking trees are established using the predefined mobility profile. However, when the real object's movement behaviors and query rates are different from the predefined mobility profile and query rates, the update cost and query cost of object tracking tree may increase. To upgrade the object tracking tree, the sink needs to send very large messages to collect the real movement information from the network, introducing a very large message overhead, which is referred to as adaptation cost. The Sub Root Message-Tree Adaptive procedure was proposed to dynamically collect the real movement information under the sub-tree and reconstruct the sub-tree to provide good performance based on the collected information. The simulation results indicates that the Sub Root Message-Tree Adaptive procedure is sufficient to achieve good total cost and lower adaptation cost.

  5. Effects of species-specific leaf characteristics and reduced water availability on fine particle capture efficiency of trees

    International Nuclear Information System (INIS)

    Räsänen, Janne V.; Holopainen, Toini; Joutsensaari, Jorma; Ndam, Collins; Pasanen, Pertti; Rinnan, Åsmund; Kivimäenpää, Minna

    2013-01-01

    Trees can improve air quality by capturing particles in their foliage. We determined the particle capture efficiencies of coniferous Pinus sylvestris and three broadleaved species: Betula pendula, Betula pubescens and Tilia vulgaris in a wind tunnel using NaCl particles. The importance of leaf surface structure, physiology and moderate soil drought on the particle capture efficiencies of the trees were determined. The results confirm earlier findings of more efficient particle capture by conifers compared to broadleaved plants. The particle capture efficiency of P. sylvestris (0.21%) was significantly higher than those of B. pubescens, T. vulgaris and B. pendula (0.083%, 0.047%, 0.043%, respectively). The small leaf size of P. sylvestris was the major characteristic that increased particle capture. Among the broadleaved species, low leaf wettability, low stomatal density and leaf hairiness increased particle capture. Moderate soil drought tended to increase particle capture efficiency of P. sylvestris. -- Highlights: • Coniferous Scots pine was the most efficient particle collector. • Decreasing single leaf size increases particle deposition of the total leaf area. • Hairiness of the leaf increases particle deposition. -- Trees can improve air quality by removing PM 2.5 pollutants carried on the wind at a velocity of 3 m s −1 , the efficiency of which depends on species leaf characteristics and physical factors

  6. Efficient reduction and modularization for large fault trees stored by pages

    International Nuclear Information System (INIS)

    Chen, Shanqi; Wang, Jin; Wang, Jiaqun; Wang, Fang; Hu, Liqin

    2016-01-01

    Highlights: • New fault tree pre-processing methods used in RiskA are presented. • Including the fault tree paging storage, simplification and modularization. • For getting MCS for fault trees containing more than 10,000 gates and events. • Reduce computer resources needs (RAM) and improve computation speed. - Abstract: Fault Tree Analysis (FTA), an indispensable tool used in Probabilistic Risk Assessment (PRA), has been used throughout the commercial nuclear power industry for safety and reliability analyses. However, large fault tree analysis, such as those used in nuclear power plant requires significant computer resources, which makes the analysis of PRA model inefficient and time consuming. This paper describes a fault tree pre-processing method used in the reliability and probabilistic safety assessment program RiskA that is capable of generating minimal cutsets for fault trees containing more than 10,000 gates and basic events. The novel feature of this method is not only that Boolean reduction rules are used but also that a new objective of simplification is proposed. Moreover, since the method aims to find more fault tree modules by the linear-time algorithm, it can optimize fault tree modularization, which further reduces the computational time of large fault tree analysis.

  7. Energy-efficient multicast traffic grooming strategy based on light-tree splitting for elastic optical networks

    Science.gov (United States)

    Liu, Huanlin; Yin, Yarui; Chen, Yong

    2017-07-01

    In order to address the problem of optimizing the spectrum resources and power consumption in elastic optical networks (EONs), we investigate the potential gains by jointly employing the light-tree splitting and traffic grooming for multicast requests. An energy-efficient multicast traffic grooming strategy based on light-tree splitting (EED-MTGS-LS) is proposed in this paper. Firstly, we design a traffic pre-processing mechanism to decide the multicast requests' routing order, which considers the request's bandwidth requirement and physical hops synthetically. Then, by dividing a light-tree to some sub-light-trees and grooming the request to these sub-light-trees, the light-tree sharing ratios of multicast requests can be improved. What's more, a priority scheduling vector is constructed, which aims to improve the success rate of spectrum assignment for grooming requests. Finally, a grooming strategy is designed to optimize the total power consumption by reducing the use of transponders and IP routers during routing. Simulation results show that the proposed strategy can significantly improve the spectrum utilization and save the power consumption.

  8. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

    Directory of Open Access Journals (Sweden)

    Kodner Robin B

    2010-10-01

    Full Text Available Abstract Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

  9. Plant delta 15N correlates with the transpiration efficiency of nitrogen acquisition in tropical trees.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Turner, Benjamin L

    2009-11-01

    Based upon considerations of a theoretical model of (15)N/(14)N fractionation during steady-state nitrate uptake from soil, we hypothesized that, for plants grown in a common soil environment, whole-plant delta(15)N (deltaP) should vary as a function of the transpiration efficiency of nitrogen acquisition (F(N)/v) and the difference between deltaP and root delta(15)N (deltaP - deltaR). We tested these hypotheses with measurements of several tropical tree and liana species. Consistent with theoretical expectations, both F(N)/v and deltaP - deltaR were significant sources of variation in deltaP, and the relationship between deltaP and F(N)/v differed between non-N(2)-fixing and N(2)-fixing species. We interpret the correlation between deltaP and F(N)/v as resulting from variation in mineral nitrogen efflux-to-influx ratios across plasma membranes of root cells. These results provide a simple explanation of variation in delta(15)N of terrestrial plants and have implications for understanding nitrogen cycling in ecosystems.

  10. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

    Science.gov (United States)

    Wan, Shixiang; Zou, Quan

    2017-01-01

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

  11. Mineralization and N-use efficiency of tree legume prunings from ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... There is substantial evidence that fertilizer tree systems are capable of maintaining increased and sustainable crop ... of N immobilized early in the season by the low quality organic materials is stimulated by well distributed rainfall. .... and 10 months old sesbania trees were cut and incorporated on.

  12. Long-term CO2 rise has increased photosynthetic efficiency and water use efficiency but did not stimulate diameter growth of tropical trees

    Science.gov (United States)

    Groenendijk, P.; Zuidema, P.; Sleen, P. V. D.; Vlam, M.; Ehlers, I.; Schleucher, J.

    2014-12-01

    Tropical forests are a crucial component of the global carbon cycle, and their responses to atmospheric changes may shift carbon cycling and climate systems. Dynamic Global Vegetation Models (DGVMs) are the major tools to simulate tropical forest responses to climate change. One of the main determinants of these simulated responses is the effect of CO2 on tropical tree physiology and growth, the 'CO2 fertilization effect'. The paucity of CO2 enrichment experiments in the tropics importantly limits insights into the CO2 fertilization effect as well as the validation of DGVMs. However, use can be made of the 40% rise in atmospheric CO2 concentration since the onset of the Industrial Revolution. The effects of the historical CO2 rise on tree physiology and growth can be obtained from stable isotopes, isotopomers and tree diameter increments obtained in tree-ring studies. We studied the physiological and growth responses of 12 tree species in Bolivia, Cameroon and Thailand to 150 years of CO2 enrichment. Analyses of 13C of wood cellulose revealed strong, long-term increases in leaf intercellular CO2 concentrations for all study species and a marked improvement of intrinsic water use efficiency (iWUE). For a subset of one species per site, we studied the Deuterium isotopomers (isomers with isotopic atoms) of glucose in wood to obtain a direct estimate of the photorespiration-to-photosynthesis ratio. We found that this ratio consistently and strongly decreased over the past century, thus increasing the effeciency and rate of photosynthesis. In spite of these strong physiological responses to increased CO2levels, we did not find evidence for increased tree diameter growth for any of the sites, or for sites combined. Possible reasons for the lack of a growth stimulation include increased (leaf) temperature, insufficient availability of nutrients or a shift in biomass investment in trees. Our results suggest that the strong CO2 fertilization of tropical tree growth often

  13. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    DEFF Research Database (Denmark)

    Wang, X.; Heimann, T.; Lo, P.

    2012-01-01

    to their robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures...... with ringlike cross-sections. Domain-specific knowledge is learned from training data sets and integrated into the tracking process by simple adaption of parameters. In addition, an efficient branching detection algorithm is presented. This approach was evaluated by extracting coronary arteries from 32 CTA data...... for the tracking of coronary arteries were achieved. For the extraction of airway trees, 51.3% of the total tree length, 53.6% of the total number of branches and a 4.98% false positive rate were attained. In both experiments, our approach is comparable to state-of-the-art methods....

  14. Uptake and distribution of soil applied zinc by citrus trees-addressing fertilizer use efficiency with 68Zn labeling.

    Science.gov (United States)

    Hippler, Franz Walter Rieger; Boaretto, Rodrigo Marcelli; Quaggio, José Antônio; Boaretto, Antonio Enedi; Abreu-Junior, Cassio Hamilton; Mattos, Dirceu

    2015-01-01

    The zinc (Zn) supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay) that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff) and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays.

  15. Uptake and distribution of soil applied zinc by citrus trees-addressing fertilizer use efficiency with 68Zn labeling.

    Directory of Open Access Journals (Sweden)

    Franz Walter Rieger Hippler

    Full Text Available The zinc (Zn supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays.

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

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2010-06-01

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

  17. Resource-use efficiencies of three indigenous tree species planted in resource islands created by shrubs: implications for reforestation of subtropical degraded shrublands

    Science.gov (United States)

    Nan Liu; Qinfeng Guo

    2012-01-01

    Shrub resource islands are characterized by resources accumulated shrubby areas surrounded by relative barren soils. This research aims to determine resource-use efficiency of native trees species planted on shrub resource islands, and to determine how the planted trees may influence the resource islands in degraded shrublands in South China. Shrub (Rhodomyrtus...

  18. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    International Nuclear Information System (INIS)

    Wang, X; Heimann, T; Meinzer, H P; Wegner, I; Lo, P; Sumkauskaite, M; Puderbach, M; De Bruijne, M

    2012-01-01

    The segmentation of tree-like tubular structures such as coronary arteries and airways is an essential step for many 3D medical imaging applications. Statistical tracking techniques for the extraction of elongated structures have received considerable attention in recent years due to their robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures with ringlike cross-sections. Domain-specific knowledge is learned from training data sets and integrated into the tracking process by simple adaption of parameters. In addition, an efficient branching detection algorithm is presented. This approach was evaluated by extracting coronary arteries from 32 CTA data sets and distal airways from 20 CT scans. These data sets were provided by the organizers of the workshop ‘3D Segmentation in the Clinic: A Grand Challenge II-Coronary Artery Tracking (CAT08)’ and ‘Extraction of Airways from CT 2009 (EXACT’09)’. On average, 81.5% overlap and 0.51 mm accuracy for the tracking of coronary arteries were achieved. For the extraction of airway trees, 51.3% of the total tree length, 53.6% of the total number of branches and a 4.98% false positive rate were attained. In both experiments, our approach is comparable to state-of-the-art methods. (paper)

  19. New efficient utility upper bounds for the fully adaptive model of attack trees

    NARCIS (Netherlands)

    Buldas, Ahto; Lenin, Aleksandr

    2013-01-01

    We present a new fully adaptive computational model for attack trees that allows attackers to repeat atomic attacks if they fail and to play on if they are caught and have to pay penalties. The new model allows safer conclusions about the security of real-life systems and is somewhat

  20. Weighted profile likelihood-based confidence interval for the difference between two proportions with paired binomial data.

    Science.gov (United States)

    Pradhan, Vivek; Saha, Krishna K; Banerjee, Tathagata; Evans, John C

    2014-07-30

    Inference on the difference between two binomial proportions in the paired binomial setting is often an important problem in many biomedical investigations. Tang et al. (2010, Statistics in Medicine) discussed six methods to construct confidence intervals (henceforth, we abbreviate it as CI) for the difference between two proportions in paired binomial setting using method of variance estimates recovery. In this article, we propose weighted profile likelihood-based CIs for the difference between proportions of a paired binomial distribution. However, instead of the usual likelihood, we use weighted likelihood that is essentially making adjustments to the cell frequencies of a 2 × 2 table in the spirit of Agresti and Min (2005, Statistics in Medicine). We then conduct numerical studies to compare the performances of the proposed CIs with that of Tang et al. and Agresti and Min in terms of coverage probabilities and expected lengths. Our numerical study clearly indicates that the weighted profile likelihood-based intervals and Jeffreys interval (cf. Tang et al.) are superior in terms of achieving the nominal level, and in terms of expected lengths, they are competitive. Finally, we illustrate the use of the proposed CIs with real-life examples. Copyright © 2014 John Wiley & Sons, Ltd.

  1. Likelihood-based methods for evaluating principal surrogacy in augmented vaccine trials.

    Science.gov (United States)

    Liu, Wei; Zhang, Bo; Zhang, Hui; Zhang, Zhiwei

    2017-04-01

    There is growing interest in assessing immune biomarkers, which are quick to measure and potentially predictive of long-term efficacy, as surrogate endpoints in randomized, placebo-controlled vaccine trials. This can be done under a principal stratification approach, with principal strata defined using a subject's potential immune responses to vaccine and placebo (the latter may be assumed to be zero). In this context, principal surrogacy refers to the extent to which vaccine efficacy varies across principal strata. Because a placebo recipient's potential immune response to vaccine is unobserved in a standard vaccine trial, augmented vaccine trials have been proposed to produce the information needed to evaluate principal surrogacy. This article reviews existing methods based on an estimated likelihood and a pseudo-score (PS) and proposes two new methods based on a semiparametric likelihood (SL) and a pseudo-likelihood (PL), for analyzing augmented vaccine trials. Unlike the PS method, the SL method does not require a model for missingness, which can be advantageous when immune response data are missing by happenstance. The SL method is shown to be asymptotically efficient, and it performs similarly to the PS and PL methods in simulation experiments. The PL method appears to have a computational advantage over the PS and SL methods.

  2. Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

    Science.gov (United States)

    Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

    2008-03-01

    Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

  3. 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...

  4. Main-Memory Operation Buffering for Efficient R-Tree Update

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Saltenis, Simonas; Biveinis, Laurynas

    2007-01-01

    the buffering of update operations in main memory as well as the grouping of operations to reduce disk I/O. In particular, operations are performed in bulk so that multiple operations are able to share I/O. The paper presents an analytical cost model that is shown to be accurate by empirical studies...... the main memory that is indeed available, or do not support some of the standard index operations. Assuming a setting where the index updates need not be written to disk immediately, we propose an R-tree-based indexing technique that does not exhibit any of these drawbacks. This technique exploits...

  5. Development of K-bioassay for the efficient potassium fertilization of citrus tree

    Energy Technology Data Exchange (ETDEWEB)

    U, Jang Kual [Cheju National University, Cheju (Korea, Republic of); Han, Hae Ryong [Cheju National University, Cheju (Korea, Republic of); Moon, Duk Young; Kim, Chang Myung; Lim, Han Cheol; Moon, Do Kyung [Cheju Citrus Research Institute, Cheju (Korea, Republic of); Song, Sung Jun [Cheju National Univerisity, Cheju (Korea, Republic of)

    1994-12-31

    a Similar to the {sup 42} K uptake, {sup 86} Rb uptake by the roots of Hordeum distichum grown in the hydroponic culture was negatively correlated with the concentration of K supplied previously, showing that {sup 86} Rb can be used for the K-bioassay. {sup 86} Rb having longer half life(18.86 day) than {sup 42} K(12.36 hr) allowed the use of larger number of root samples. {sup 86} Rb uptake of 3 years old Citrus unshiu Marc. grown in water culture decreased drastically with the increase of K concentration of the culture solution, thus demonstrating that the nutrition status of K for citrus trees can be diagnosed by K-bioassay using {sup 86} Rb tracer. {sup 86} Rb uptake by the excised roots of Hordeum distichum correlated with the exchangeable K in soil. The amount of exchangeable K in soil for the optimal plant growth can be determined by its relationship. {sup 42} K- and {sup 86} Rb-uptake by the Hordeum distichum roots were markedly inhibited by 5 x 10{sup -3} M KCN in the bioassay solution, indicating that uptake is metabolically controlled. There was no significant relationship between K content in citrus leaves and K concentration in the water-culture medium. It is concluded that K-bioassay is a potentially useful tool for determining of K requirement in citrus trees. (author)

  6. Solar energy efficiency of cocoa clones cultivated under three species of shade trees.

    Directory of Open Access Journals (Sweden)

    Oscar Regazzoni

    2015-04-01

    Full Text Available This experiment aims to know the solar energy efficiency of four clones of cocoa that cultivated under three different shading plants. This experiment has been done from September until December 2013 located at Kaliwining Experiment Farm with characteristic 45 m above sea level, soil type is low humic gley, soil texture is silty clay loam, and climate classification type D based on Scmidht and Fergusson Classification. This experiment used Nested Design as Experimental Design with species of shading plant as main plot which are Teak (Tectona grandis L., Krete (Cassia surattensis (Burm. F., Lamtoro (Leucaena leucocephala L. and Cocoa clones as sub plot which are Sulawesi 1, Sulawesi 2, KKM 22, KW 165. The observation of solar energy efficiency consists of daily solar radiation intensity, solar radiation intensity above plant, solar radiation intensity under plant, and also plant total dry weight. The experimental result showed that there is differences (heterogenity between shading location based on homogenity test by Bartlett Method. There are some interaction between the kind of shading plant and clones in parameter of interception efficiency, absorbtion efficiency, the efficiency of solar energy that caught by plant, and solar energy conversion efficiency. The efficiency of solar energy that caught by plant will affect the solar energy conversion efficiency with R2 = 0,86.

  7. Nitrogen release, tree uptake, and ecosystem retention in a mid-rotation loblolly pine plantation following fertilization with 15N-enriched enhanced efficiency fertilizers.

    OpenAIRE

    Werner, Amy

    2013-01-01

    Nitrogen is the most frequently limiting nutrient in southern pine plantations.  Previous studies found that only 10 to 25% of applied urea fertilizer N is taken up by trees.  Enhanced efficiency fertilizers could increase tree uptake efficiency by controlling the release of N and/or stabilize N.  Three enhanced efficiency fertilizers were selected as a representation of fertilizers that could be used in forestry: 1) NBPT treated urea (NBPT urea), 2) polymer coated urea (PC urea), and 3) mono...

  8. CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

    International Nuclear Information System (INIS)

    Wang Jianyong; Wang Tianzhi; Zuiderweg, Erik R. P.; Crippen, Gordon M.

    2005-01-01

    Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

  9. Relationship between photosynthetic phosphorus-use efficiency and foliar phosphorus fractions in tropical tree species

    OpenAIRE

    Hidaka, Amane; Kitayama, Kanehiro

    2013-01-01

    How plants develop adaptive strategies to efficiently use nutrients on infertile soils is an important topic in plant ecology. It has been suggested that, with decreasing phosphorus (P) availability, plants increase photosynthetic P-use efficiency (PPUE) (i.e., the ratio of instantaneous photosynthetic carbon assimilation rate per unit foliar P). However, the mechanism to increase PPUE remains unclear. In this study, we tested whether high PPUE is explained by an optimized allocation of P in ...

  10. Long-term tree growth rate, water use efficiency, and tree ring nitrogen isotope composition of Pinus massoniana L. in response to global climate change and local nitrogen deposition in Southern China

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Fangfang [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Graduate Univ. of Chinese Academy of Sciences, Beijing (China); Griffith Univ., Nathan, QLD (Australia). Environmental Future Centre; Kuang, Yuanwen; Wen, Dazhi [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Chinese Academy of Sciences, Guangzhou (China). Pearl River Delta Research Centre of Environmental Pollution and Control; Xu, Zhihong [Griffith Univ., Nathan, QLD (Australia). Environmental Future Centre; Li, Jianli; Zuo, Weidong [Agriculture and Forestry Technology Extension Centre, Nanhai District, Guangdong (China); Hou, Enqing [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Graduate Univ. of Chinese Academy of Sciences, Beijing (China)

    2010-12-15

    We aimed to investigate long-term tree growth rates, water use efficiencies (WUE), and tree ring nitrogen (N) isotope compositions ({delta}{sup 15}N) of Masson pine (Pinus massoniana L.) in response to global climate change and local N deposition in Southern China. Tree annual growth rings of Masson pine were collected from four forest sites, viz. South China Botanical Garden (SBG), Xi Qiao Shan (XQS) Forest Park, Ding Hu Shan (DHS) Natural Reserve, and Nan Kun Shan (NKS) Natural Reserve in Southern China. The mean annual basal area increment (BAI), WUE, and {delta}{sup 15}N at every 5-year intervals of Masson pine during the last 50 years were determined. Regression analyses were used to quantify the relationships of BAI and WUE with atmospheric carbon dioxide concentration ([CO{sub 2}]), temperature, rainfall, and tree ring elemental concentrations at the four study sites. Tree BAI showed a quadratic relationship with rising [CO{sub 2}]. The tipping points of [CO{sub 2}] for BAI, the peaks of BAI when the critical [CO{sub 2}] was reached, occurred earlier at the sites of SBG, XQS, and DHS which were exposed to higher temperature, N deposition, and lower mineral nutrient availability, as compared with the tipping points of [CO{sub 2}] for BAI at the site of NKS which had higher rainfall, lower temperature, and better nutritional status. The average tipping point of [CO{sub 2}] at the four sites for the BAI response curves was 356 ppm, after which, the BAI would be expected to decrease quadratically with rising [CO{sub 2}]. The multiple regressions of BAI confirmed the relationships of long-term tree growth rate with rainfall, tree WUE, and nutrients and {delta}{sup 15}N in tree rings. Nonlinear relationships between BAI and tree ring {delta}{sup 15}N at DHS and negatively linear one at NKS reflected the fertilization effect of N deposition on tree growth rate initially, but this effect peaked or became negative once the forest approached or passed the N saturation

  11. Transpiration and water-use efficiency in mixed-species forests versus monocultures: effects of tree size, stand density and season.

    Science.gov (United States)

    Forrester, David I

    2015-03-01

    Mixtures can be more productive than monocultures and may therefore use more water, which may make them more susceptible to droughts. The species interactions that influence growth, transpiration and water-use efficiency (WUE, tree growth per unit transpiration) within a given mixture vary with intra- and inter-annual climatic variability, stand density and tree size, but these effects remain poorly quantified. These relationships were examined in mixtures and monocultures of Eucalyptus globulus Labill. and Acacia mearnsii de Wildeman. Growth and transpiration were measured between ages 14 and 15 years. All E. globulus trees in mixture that were growing faster than similar sized trees in monocultures had higher WUE, while trees with similar growth rates had similar WUE. By the age of 14 years A. mearnsii trees were beginning to senesce and there were no longer any relationships between tree size and growth or WUE. The relationship between transpiration and tree size did not differ between treatments for either species, so stand-level increases in transpiration simply reflected the larger mean tree size in mixtures. Increasing neighbourhood basal area increased the complementarity effect on E. globulus growth and transpiration. The complementarity effect also varied throughout the year, but this was not related to the climatic seasonality. This study shows that stand-level responses can be the net effect of a much wider range of individual tree-level responses, but at both levels, if growth has not increased for a given species, it appears unlikely that there will be differences in transpiration or WUE for that species. Growth data may provide a useful initial indication of whether mixtures have higher transpiration or WUE, and which species and tree sizes contribute to this effect. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Influence of Drought on Mesophyll Resistance to CO2 Diffusion and its Impact on Water-Use Efficiency in Trees

    Science.gov (United States)

    Guo, J.; Beverly, D.; Cook, C.; Ewers, B. E.; Williams, D. G.

    2015-12-01

    The resistance to CO2 diffusion inside leaves (mesophyll resistance; rm) during photosynthesis is often comparable in magnitude to stomatal diffusion resistance, and varies among species and across environmental conditions. Consequently, photosynthesis is strongly limited by rm at low internal CO2 partial pressures, such that its variation may determine patterns of leaf water-use efficiency (WUE). Reduction in stomatal conductance with drought typically increases WUE, but also decreases photosynthesis. In theory, the decrease in photosynthesis could be countered by reduction in rm while maintaining high WUE. It is still uncertain how drought-related changes in rm affect short- and long-term WUE strategies of different tree species. We conducted field observations of instantaneous WUE and 13C discrimination in two dominant conifer species (Pinus contorta and Picea engelmannii) in SE Wyoming over the seasonal dry-down period in the summer of 2015. rm was examined by on-line 13C discrimination using isotope laser spectroscopy. Controlled environment studies on three conifer species (P. contorta, P. engelmannii, and Abies lasiocarpa) and one angiosperm (Populus tremuloides) are in progress. We hypothesize that the plasticity of rm in response to drought accounts for significant adjustments in photosynthetic capacity and WUE. Needle leaf conifers are known to have relatively high rm, and we expect them to show greater improvements in photosynthesis and WUE when rm is decreased compared to angiosperm tree species.

  13. Transpiration efficiency over an annual cycle, leaf gas exchange and wood carbon isotope ratio of three tropical tree species.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Aranda, Jorge; Virgo, Aurelio; Garcia, Milton

    2009-09-01

    Variation in transpiration efficiency (TE) and its relationship with the stable carbon isotope ratio of wood was investigated in the saplings of three tropical tree species. Five individuals each of Platymiscium pinnatum (Jacq.) Dugand, Swietenia macrophylla King and Tectona grandis Linn. f. were grown individually in large (760 l) pots over 16 months in the Republic of Panama. Cumulative transpiration was determined by repeatedly weighing the pots with a pallet truck scale. Dry matter production was determined by destructive harvest. The TE, expressed as experiment-long dry matter production divided by cumulative water use, averaged 4.1, 4.3 and 2.9 g dry matter kg(-1) water for P. pinnatum, S. macrophylla and T. grandis, respectively. The TE of T. grandis was significantly lower than that of the other two species. Instantaneous measurements of the ratio of intercellular to ambient CO(2) partial pressures (c(i)/c(a)), taken near the end of the experiment, explained 66% of variation in TE. Stomatal conductance was lower in S. macrophylla than in T. grandis, whereas P. pinnatum had similar stomatal conductance to T. grandis, but with a higher photosynthetic rate. Thus, c(i)/c(a) and TE appeared to vary in response to both stomatal conductance and photosynthetic capacity. Stem-wood delta(13)C varied over a relatively narrow range of just 2.2 per thousand, but still explained 28% of variation in TE. The results suggest that leaf-level processes largely determined variation among the three tropical tree species in whole-plant water-use efficiency integrated over a full annual cycle.

  14. A review and comparison of Bayesian and likelihood-based inferences in beta regression and zero-or-one-inflated beta regression.

    Science.gov (United States)

    Liu, Fang; Eugenio, Evercita C

    2018-04-01

    Beta regression is an increasingly popular statistical technique in medical research for modeling of outcomes that assume values in (0, 1), such as proportions and patient reported outcomes. When outcomes take values in the intervals [0,1), (0,1], or [0,1], zero-or-one-inflated beta (zoib) regression can be used. We provide a thorough review on beta regression and zoib regression in the modeling, inferential, and computational aspects via the likelihood-based and Bayesian approaches. We demonstrate the statistical and practical importance of correctly modeling the inflation at zero/one rather than ad hoc replacing them with values close to zero/one via simulation studies; the latter approach can lead to biased estimates and invalid inferences. We show via simulation studies that the likelihood-based approach is computationally faster in general than MCMC algorithms used in the Bayesian inferences, but runs the risk of non-convergence, large biases, and sensitivity to starting values in the optimization algorithm especially with clustered/correlated data, data with sparse inflation at zero and one, and data that warrant regularization of the likelihood. The disadvantages of the regular likelihood-based approach make the Bayesian approach an attractive alternative in these cases. Software packages and tools for fitting beta and zoib regressions in both the likelihood-based and Bayesian frameworks are also reviewed.

  15. Cross-scale interactions affect tree growth and intrinsic water use efficiency and highlight the importance of spatial context in managing forests under global change

    Science.gov (United States)

    Kenneth J. Ruzicka; Klaus J. Puettmann; J. Renée Brooks

    2017-01-01

    Summary1. We investigated the potential of cross-scale interactions to affect the outcome of density reduction in a large-scale silvicultural experiment to better understand options for managing forests under climate change. 2. We measured tree growth and intrinsic water-use efficiency (iWUE) based on stable carbon isotopes (δ...

  16. TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.

    Science.gov (United States)

    Höhna, Sebastian; May, Michael R; Moore, Brian R

    2016-03-01

    Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation-extinction) that are modeled using birth-death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models-where rates are constant, vary continuously, or change episodically through time-and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. We enable both statistical inference and efficient simulation under these models. We also provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification. The source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/ CONTACT: Sebastian.Hoehna@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Identification of Influence of Part Tolerances of 3PWR-SE Pump On Its Total Efficiency Taking Into Consideration Multi-Valued Logic Trees

    Directory of Open Access Journals (Sweden)

    Deptuła Adam

    2017-03-01

    Full Text Available This paper presents the way of identifying the influence of the tolerance of model pumps (TYPE 3PWR-SE construction on the total efficiency. The identification of sensitive control dimensions (Value/Tolerance of examined pumps has been made by means of the multi-valued logic and inductive decision trees. In order to confirm the obtained results, multiple-valued logic trees have been used in the paper according to algorithms for the minimization of individual logic functions. What is more, a specific monotonicity of values of the most key parameters has been determined for the investigated set of pumps having individual specification numbers.

  18. Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering

    Science.gov (United States)

    Sethi, Suresh; Linden, Daniel; Wenburg, John; Lewis, Cara; Lemons, Patrick R.; Fuller, Angela K.; Hare, Matthew P.

    2016-01-01

    Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark–recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark–recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark–recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark–recapture studies. Moderately sized SNP (64+) and MSAT (10–15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding.

  19. An investigation of the leaf retention capacity, efficiency and mechanism for atmospheric particulate matter of five greening tree species in Beijing, China.

    Science.gov (United States)

    Liu, Jinqiang; Cao, Zhiguo; Zou, Songyan; Liu, Huanhuan; Hai, Xiao; Wang, Shihua; Duan, Jie; Xi, Benye; Yan, Guangxuan; Zhang, Shaowei; Jia, Zhongkui

    2018-03-01

    Urban trees have the potential to reduce air pollution, but the retention capacity and efficiency of different tree species for atmospheric particulate matter (PM) accumulation and the underlying mechanism hasn't been well understood. To select tree species with high air purification abilities, the supplementing ultrasonic cleaning (UC) procedure was first introduced into the conventional leaf cleaning methods [single water cleaning (WC) or plus brush cleaning (BC)] for eluting the leaf-retained PM. Further updates to the methodology were applied to investigate the retention capacity, efficiency, and mechanism for PM of five typical greening tree species in Beijing, China. Meanwhile, the particle size distribution of PM on the leaves, the PM retention efficiencies of easily removable (ERP), difficult-to-remove (DRP) and totally removable (TRP) particles on the leaf (AE leaf ), and the individual tree scales were estimated. The experimental leaf samples were collected from trees with similar sizes 4 (SDR) and 14days (LDR) after rainfall. When the leaves were cleaned by WC+BC, there was, on average, 29%-46% of the PM remaining on the leaves of different species, which could be removed almost completely if UC was supplemented. From SDR to LDR, the mass of the leaf-retained PM increased greatly, and the particle size distribution changed markedly for all species except for Sophorajaponica. Pinus tabuliformis retains particles with the largest average diameter (34.2μm), followed by Ginkgo biloba (20.5μm), Sabina chinensis (16.4μm), Salix babylonica (16.0μm), and S. japonica (13.1μm). S. japonica and S. chinensis had the highest AE leaf to retain the TRP and ERP of both PM 1 and PM 1-2.5 , respectively. Conversely, S. babylonica and P. tabuliformis could retain both TRP and ERP of PM 2.5-5 and PM 5-10 , and PM >10 and TSP with the highest AE leaf , respectively. In conclusion, our results could be useful in selecting greening tree species with high air purification

  20. Competition for light and light use efficiency for Acacia mangium and Eucalyptus grandis trees in mono-specific and mixed-species plantations in Brazil

    Science.gov (United States)

    Le Maire, G.; Nouvellon, Y.; Gonçalves, J.; Bouillet, J.; Laclau, J.

    2010-12-01

    Mixed plantations with N-fixing species might be an attractive option for limiting the use of fertilizer in highly productive Eucalyptus plantations. A randomized block design was set up in southern Brazil, including a replacement series and an additive series design, as well as a nitrogen fertilization treatment, and conducted during a full 6 years rotation. The gradient of competition between Eucalyptus and Acacia in this design resulted in very different conditions of growth of Acacia, from totally dominated up to dominant canopies. We used the MAESTRA model to estimate the amount of absorbed photosynthetically active radiation (APAR) at tree level. This model requires the description of the scene and distinct structural variables of the two species, and their evolution with time. The competition for light is analysed by comparing the inter-specific values of APAR during a period of 2 years at the end of the rotation. APAR is further compared to the measured increment in stem wood biomass of the tree, and their ratio is an estimation of the light use efficiency for stemwood production at tree-scale. Variability of these LUE are analysed in respect to the species, the size of the tree, and at plot scale (competition level). Stemwood production was 3400, 3900 and 2400 gDM/m2 while APAR was 1640, 2280 and 2900 MJ/y for the pure Eucalyptus, pure Acacia and 50/50 mixed plantation, respectively, for an average LAI of 3.7, 3.3 and 4.5, respectively. Individual LUE for stemwood was estimated at an average value of 1.72 and 1.41 gDM/MJ/tree for Eucalyptus and Acacia, respectively, and at 0.92 and 0.40 gDM/MJ/tree when they were planted in mixed 50/50 plantations. LUE was highly dependant on tree size for both species. At the plot scale, LUE for stemwood were 2.1 gDM/MJ and 1.75 for Eucalyptus and Acacias, respectively, and 0.85 for the mixed 50/50 plantation. These results suggest that the mixed 50/50 plantation, which absorbed a higher amount of light, produce less

  1. Evaluation of hedgerow trees in alley cropping for phosphorus use efficiency and N{sub 2} fixation in low P soils in moist savanna in Nigeria

    Energy Technology Data Exchange (ETDEWEB)

    Sanginga, N [International Inst. of Tropical Agriculture, Ibadan (Nigeria); Danso, S K.A. [Joint FAO/IAEA Div. of Nuclear Techniques in Food and Agriculture, Vienna (Austria). Soil Fertility and Crop Production Section; Zapata, F [FAO/IAEA Agriculture and Biotechnology Lab., Seibersdorf (Austria). Soils Science Unit; Bowen, G D [Commonwealth Scientific and Industrial Research Organization, Glen Osmond (Australia). Div. of Soils

    1996-07-01

    Soils low in P and N are common in the moist savanna climatic zones and consequently growth of hedgerow trees in alley cropping systems might require addition of N and P fertilizers. This is difficult for small scale farmers who have limited access to fertilizers and therefore depend only on limited input cropping systems. Exploiting genetic differences in P use efficiency and using hedgerow trees selected for high N{sub 2} fixation ability can improve tree establishment and growth on N and P-poor soils, restore soil fertility and preserve soil from degradation. Field experiments carried out at Fashola (moist savanna) have shown that large differences in growth and P use efficiency occurred between N{sub 2} fixing trees such as Gliricidia sepium, and non N{sub 2}-fixing trees such as Senna siamea and Senna spectabilis. Provenances or isoline differences in P use efficiency also occurred within species and was also influenced by level of P and period of growth. Differences between species and provenances in P uptake and growth were largely related to differences in physiological P-use efficiency (PPUE), root length and VAM infection rate, especially at low P. In general, nodulation was improved by P application, but varied among provenances. Gliricidia Sepium fixed about 61% of its N from atmospheric N{sub 2} in the pot experiment and 40% in the field. The percentage of N fixed was not affected by rate of P application. Differences in P and N accumulation and use efficiency were also influenced by management practices such as pruning. The distribution of total P followed the same trend as that of dry matter yield, while no significant correlations were found between partitioning of dry matter and total N. Uncut and cut G. Sepium derived 35 and 54% respectively of their N from atmospheric N{sub 2}. About 54% of the fixed N{sub 2} was partitioned to shoots and roots and this was not proportional to the size of these organs relative the whole plant. 17refs,2figs,2tabs.

  2. Comparison of water-use efficiency estimates based on tree-ring carbon isotopes with simulations of a dynamic vegetation model

    Science.gov (United States)

    Saurer, Matthias; Renato, Spahni; Fortunat, Joos; David, Frank; Kerstin, Treydte; Rolf, Siegwolf

    2015-04-01

    Tree-ring d13C-based estimates of intrinsic water-use efficiency (iWUE, reflecting the ratio of assimilation A to stomatal conductance gs) generally show a strong increase during the industrial period, likely associated with the increase in atmospheric CO2. However, it is not clear, first, if tree-ring d13C-derived iWUE-values indeed reflect actual plant and ecosystem-scale variability in fluxes and, second, what physiological changes were the drivers of the observed iWUE increase, changes in A or gs or both. To address these questions, we used a complex dynamic vegetation model (LPX) that combines process-based vegetation dynamics with land-atmosphere carbon and water exchange. The analysis was conducted for three functional types, representing conifers, oaks, larch, and various sites in Europe, where tree-ring isotope data are available. The increase in iWUE over the 20th century was comparable in LPX-simulations as in tree-ring-estimates, strengthening confidence in these results. Furthermore, the results from the LPX model suggest that the cause of the iWUE increase was reduced stomatal conductance during recent decades rather than increased assimilation. High-frequency variation reflects the influence of climate, like for example the 1976 summer drought, resulting in strongly reduced A and g in the model, particularly for oak.

  3. Growth, water use efficiency, and adaptive features of the tree legume tagasaste (Chamaecytisus proliferus Link.) on deep sands in south-western Australia

    International Nuclear Information System (INIS)

    Lefroy, E. C.; Pate, J. S.

    2001-01-01

    Four-year-old tagasaste trees in dense plantation and wide-spaced alley cropping layouts at Moora, Western Australia, were cut back to 0.6 m high and their patterns of coppice regrowth and water use monitored over 3 years. Trees reached a permanent fresh watertable at 5 m depth by means of deeply penetrating sinker roots. Dry matter (DM) accumulation and transpiration loss were closely similar at the 2 planting densities despite higher soil water contents in alley plots. Yearly transpiration at plantation density amounted to 0.55 and 0.63 of Penman-Montieth potential evapotranspiration (E 0 ) in the second and third years, respectively. Mean water use efficiency over the 3 years was 247 L/kg DM, compared with values in the range 186-320 L/kg for younger pot-and column-grown trees. Using a combination of neutron moisture metre (NMM) assays of soil moisture and deuterium: hydrogen ratios of groundwater and xylem water of tagasaste and annual weeds, it was shown that trees became increasingly dependent on groundwater over time and had the capacity to switch rapidly between soil and groundwater sources. Seasonal changes in carbon isotope composition of new shoot tip dry matter indicated that plantation trees were less stressed than alley trees by the third summer as they adapted to heavy dependence on groundwater. In the third season, when plantation trees were transpiring at rates equivalent to 2.3 times annual rainfall, NMM profiles and time domain reflectometry (TDR) assays indicated that no free drainage occurred and that trees were capable of hydraulically lifting groundwater to near surface soil in the dry season. Additional adaptive features of importance to this environment included heat stress induced leaf shedding, development of perennial root nodules on lower parts of tap roots, and an ability to respond in summer to artificial irrigation or a seasonal rainfall by rapidly increasing transpiration 2-3-fold to values equalling E 0 . Copyright (2001) CSIRO

  4. Earthworms in tropical tree plantations: effects of management and relations with soil carbon and nutrient use efficiency

    Science.gov (United States)

    X Zou; Grizelle Gonzalez

    2001-01-01

    With the vast amount of abandoned tropical land due to non- sustainable farming practices, tropical tree-plantations become an effective means in restoring soil productivity and preserving ecosystem biodiversity. Because earthworms are the dominant soil fauna in moist tropical regions and play an important role in improving soil fertility, understanding the mechanisms...

  5. An efficient connected dominating set algorithm in WSNs based on the induced tree of the crossed cube

    Directory of Open Access Journals (Sweden)

    Zhang Jing

    2015-06-01

    Full Text Available The connected dominating set (CDS has become a well-known approach for constructing a virtual backbone in wireless sensor networks. Then traffic can forwarded by the virtual backbone and other nodes turn off their radios to save energy. Furthermore, a smaller CDS incurs fewer interference problems. However, constructing a minimum CDS is an NP-hard problem, and thus most researchers concentrate on how to derive approximate algorithms. In this paper, a novel algorithm based on the induced tree of the crossed cube (ITCC is presented. The ITCC is to find a maximal independent set (MIS, which is based on building an induced tree of the crossed cube network, and then to connect the MIS nodes to form a CDS. The priority of an induced tree is determined according to a new parameter, the degree of the node in the square of a graph. This paper presents the proof that the ITCC generates a CDS with a lower approximation ratio. Furthermore, it is proved that the cardinality of the induced trees is a Fibonacci sequence, and an upper bound to the number of the dominating set is established. The simulations show that the algorithm provides the smallest CDS size compared with some other traditional algorithms.

  6. Sudden Exposure to Solar UV-B Radiation Reduces Net CO2 Uptake and Photosystem I Efficiency in Shade-Acclimated Tropical Tree Seedlings1

    Science.gov (United States)

    Krause, G. Heinrich; Grube, Esther; Virgo, Aurelio; Winter, Klaus

    2003-01-01

    Tree seedlings developing in the understory of the tropical forest have to endure short periods of high-light stress when tree-fall gaps are formed, and direct solar radiation, including substantial UV light, reaches the leaves. In experiments simulating the opening of a tree-fall gap, the response of photosynthesis in leaves of shade-acclimated seedlings (Anacardium excelsum, Virola surinamensis, and Calophyllum longifolium) to exposure to direct sunlight (for 20–50 min) was investigated in Panama (9°N). To assess the effects of solar UV-B radiation (280–320 nm), the sunlight was filtered through plastic films that selectively absorbed UV-B or transmitted the complete spectrum. The results document a strong inhibition of CO2 assimilation by sun exposure. Light-limited and light-saturated rates of photosynthetic CO2 uptake by the leaves were affected, which apparently occurred independently of a simultaneous inhibition of potential photosystem (PS) II efficiency. The ambient UV-B light substantially contributed to these effects. The photochemical capacity of PSI, measured as absorbance change at 810 nm in saturating far-red light, was not significantly affected by sun exposure of the seedlings. However, a decrease in the efficiency of P700 photooxidation by far-red light was observed, which was strongly promoted by solar UV-B radiation. The decrease in PSI efficiency may result from enhanced charge recombination in the reaction center, which might represent an incipient inactivation of PSI, but contributes to thermal dissipation of excessive light energy and thereby to photoprotection. PMID:12586898

  7. Uptake and Distribution of Soil Applied Zinc by Citrus Trees?Addressing Fertilizer Use Efficiency with 68Zn Labeling

    OpenAIRE

    Hippler, Franz Walter Rieger; Boaretto, Rodrigo Marcelli; Quaggio, Jos? Ant?nio; Boaretto, Antonio Enedi; Abreu-Junior, Cassio Hamilton; Mattos, Dirceu

    2015-01-01

    The zinc (Zn) supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citru...

  8. Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements.

    Science.gov (United States)

    Xu, Jason; Guttorp, Peter; Kato-Maeda, Midori; Minin, Vladimir N

    2015-12-01

    Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements-important genetic markers in molecular epidemiology. Estimation of the effects of individual covariates on the birth, death, and shift rates of the process can be accomplished by analyzing patient data, but inferring these rates in a discretely and unevenly observed setting presents computational challenges. We propose a multi-type branching process approximation to BDS processes and develop a corresponding expectation maximization algorithm, where we use spectral techniques to reduce calculation of expected sufficient statistics to low-dimensional integration. These techniques yield an efficient and robust optimization routine for inferring the rates of the BDS process, and apply broadly to multi-type branching processes whose rates can depend on many covariates. After rigorously testing our methodology in simulation studies, we apply our method to study intrapatient time evolution of IS6110 transposable element, a genetic marker frequently used during estimation of epidemiological clusters of Mycobacterium tuberculosis infections. © 2015, The International Biometric Society.

  9. Evaluation of efficient glucose release using sodium hydroxide and phosphoric acid as pretreating agents from the biomass of Sesbania grandiflora (L.) Pers.: A fast growing tree legume.

    Science.gov (United States)

    Mund, Nitesh K; Dash, Debabrata; Barik, Chitta R; Goud, Vaibhav V; Sahoo, Lingaraj; Mishra, Prasannajit; Nayak, Nihar R

    2017-07-01

    Sesbania grandiflora (L.) Pers. is one of the fast growing tree legumes having the efficiency to produce around 50tha -1 above ground dry matters in a year. In this study, biomass of 2years old S. grandiflora was selected for the chemical composition, pretreatments and enzymatic hydrolysis studies. The stem biomass with a wood density of 3.89±0.01gmcm -3 contains about 38% cellulose, 12% hemicellulose and 28% lignin. Enzymatic hydrolysis of pretreated biomass revealed that phosphoric acid (H 3 PO 4 ) pretreated samples even at lower cellulase loadings [1 Filter Paper Units (FPU)], could efficiently convert about 86% glucose, while, even at higher cellulase loadings (60FPU) alkali pretreated biomass could convert only about 58% glucose. The effectiveness of phosphoric acid pretreatment was also supported by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM) and Fourier transform infrared spectroscopy (FTIR) analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Empirical likelihood-based confidence intervals for the sensitivity of a continuous-scale diagnostic test at a fixed level of specificity.

    Science.gov (United States)

    Gengsheng Qin; Davis, Angela E; Jing, Bing-Yi

    2011-06-01

    For a continuous-scale diagnostic test, it is often of interest to find the range of the sensitivity of the test at the cut-off that yields a desired specificity. In this article, we first define a profile empirical likelihood ratio for the sensitivity of a continuous-scale diagnostic test and show that its limiting distribution is a scaled chi-square distribution. We then propose two new empirical likelihood-based confidence intervals for the sensitivity of the test at a fixed level of specificity by using the scaled chi-square distribution. Simulation studies are conducted to compare the finite sample performance of the newly proposed intervals with the existing intervals for the sensitivity in terms of coverage probability. A real example is used to illustrate the application of the recommended methods.

  11. An efficient viral vector for functional genomic studies of Prunus fruit trees and its induced resistance to Plum pox virus via silencing of a host factor gene.

    Science.gov (United States)

    Cui, Hongguang; Wang, Aiming

    2017-03-01

    RNA silencing is a powerful technology for molecular characterization of gene functions in plants. A commonly used approach to the induction of RNA silencing is through genetic transformation. A potent alternative is to use a modified viral vector for virus-induced gene silencing (VIGS) to degrade RNA molecules sharing similar nucleotide sequence. Unfortunately, genomic studies in many allogamous woody perennials such as peach are severely hindered because they have a long juvenile period and are recalcitrant to genetic transformation. Here, we report the development of a viral vector derived from Prunus necrotic ringspot virus (PNRSV), a widespread fruit tree virus that is endemic in all Prunus fruit production countries and regions in the world. We show that the modified PNRSV vector, harbouring the sense-orientated target gene sequence of 100-200 bp in length in genomic RNA3, could efficiently trigger the silencing of a transgene or an endogenous gene in the model plant Nicotiana benthamiana. We further demonstrate that the PNRSV-based vector could be manipulated to silence endogenous genes in peach such as eukaryotic translation initiation factor 4E isoform (eIF(iso)4E), a host factor of many potyviruses including Plum pox virus (PPV). Moreover, the eIF(iso)4E-knocked down peach plants were resistant to PPV. This work opens a potential avenue for the control of virus diseases in perennial trees via viral vector-mediated silencing of host factors, and the PNRSV vector may serve as a powerful molecular tool for functional genomic studies of Prunus fruit trees. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  12. Studies on 13C isotope discrimination for identifying tree provenances efficient in water use under water deficit conditions in Kenya

    International Nuclear Information System (INIS)

    Nyamai, D.O.; Juma, P.O.

    1996-01-01

    Screening for drought resistance traits was conducted in a semi-arid site in Machakos using 11 provenances of Acacia tortilis, 6 provenances of Prosopis juliflora and 4 provenances of Casuarina equisetifolia. Tolerance to drought was assessed by the 13 C isotope discrimination (Δ) technique as well as by determining the waster use efficiency (WUE). Measurements of dry matter and early growth performance were also taken as indicators of drought resistance. The results showed significant differences in the 13 C Isotope discrimination, water use efficiency and dry matter yields by the different provenances tested. Generally, the results indicated that there were significant linear negative relationships between 13 C discrimination with water use efficiency as well as dry matter yield. The results further showed highly significant positive relationship between dry matter yield and water use efficiency. Acacia tortilis provenances from middle East and neighbouring North Eastern Africa region appear to possess the greatest abilities for drought resistance in comparison with those from sub-saharan Africa as indicated by their 13 C Isotope discrimination levels, dry matter yield and water use efficiency. However, Acacia provenance from Israel had the highest drought resistance trail. Prosopis provenance from Costa Rica and Casuarina from Dakar region in Senegal also emerged as the best provenances in terms of drought tolerance as shown by the 13 C isotope discrimination and dry matter traits. (author). 8 refs, 4 figs, 3 tabs

  13. 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.

  14. The Efficiency of Mycorrhizal Fungi on Growth Characteristics and some Nutrients Uptake of Plane tree Seedling (Platanus orientalis L.

    Directory of Open Access Journals (Sweden)

    H. Alipour

    2016-07-01

    Full Text Available Introduction: Drought stress is one of the most important abiotic stresses which significantly reduce yield and growth of most of plants. Plane tree is one of the important trees planted in the urban landscapes of Iran. One of the major limiting factors of landscapes development is providing water for plants. Deficit irrigation is a desirable method for saving water use in water deficit conditions and ultimately reducing necessary cost of water securement to landscape plants. Moreover, inoculation of plant root with mycorrhizal fungi can be considered as a method to reduce water demand of plants. In addition, mycorrhiza can increase plant resistance against environmental stress, such as salinity, temperature stress, drought stress and etc. Mycorrhiza can improve drought stress through enhancing water uptake as result of extra radical hyphae and stomatal regulation or transpiration. Increasing P concentration by mycorrhiza inoculation can be another mechansim for drought resistance in plants. The purpose of the present study was to evaluate two Glomus species in combination together on plane tree under water deficit for growth characteristics and nutrients uptake such as P, Fe and Zn concentration. Materials and Methods: This outdoor experiment was conducted at - Isfahan University of Technology, Isfahan, Iran, with average temperature 14.2 ºC and 27.9 ºC night/day, respectively and relative humidity 35-70% between Mar and Aug 2012 and repeated under the same condition in 2013. This experiment was carried out to evaluate the effect of inoculation with mycorrhizal fungus on plane saplings response to different applicable water levels (50 and 100% of water needs based on a completely randomized design with 3 replications. The treatments were control (without fertilizer, Germans peat + fertilizer, Germans peat + fertilizer + mycorrhiza in 50% of field capacity and Germans peat + fertilizer + mycorrhizain 100% of field capacity. The Mycorrhiza

  15. Herbivory mitigation through increased water-use efficiency in a leaf-mining moth-apple tree relationship.

    Science.gov (United States)

    Pincebourde, Sylvain; Frak, Ela; Sinoquet, Hervé; Regnard, Jean Luc; Casas, Jérôme

    2006-12-01

    Herbivory alters plant gas exchange but the effects depend on the type of leaf damage. In contrast to ectophagous insects, leaf miners, by living inside the leaf tissues, do not affect the integrity of the leaf surface. Thus, the effect of leaf miners on CO2 uptake and water-use efficiency by leaves remains unclear. We explored the impacts of the leaf-mining moth Phyllonorycter blancardella (Lepidoptera: Gracillariidae) on light responses of the apple leaf gas exchanges to determine the balance between the negative effects of reduced photosynthesis and potential positive impacts of increased water-use efficiency (WUE). Gas exchange in intact and mined leaf tissues was measured using an infrared gas analyser. The maximal assimilation rate was slightly reduced but the light response of net photosynthesis was not affected in mined leaf tissues. The transpiration rate was far more affected than the assimilation rate in the mine integument as a result of stomatal closure from moderate to high irradiance level. The WUE was about 200% higher in the mined leaf tissues than in intact leaf portions. Our results illustrate a novel mechanism by which plants might minimize losses from herbivore attacks; via trade-offs between the negative impacts on photosynthesis and the positive effects of increased WUE.

  16. Laser Direct Writing of Tree-Shaped Hierarchical Cones on a Superhydrophobic Film for High-Efficiency Water Collection.

    Science.gov (United States)

    Wang, Meng; Liu, Qian; Zhang, Haoran; Wang, Chuang; Wang, Lei; Xiang, Bingxi; Fan, Yongtao; Guo, Chuan Fei; Ruan, Shuangchen

    2017-08-30

    Directional water collection has stimulated a great deal of interest because of its potential applications in the field of microfluidics, liquid transportation, fog harvesting, and so forth. There have been some bio or bioinspired structures for directional water collection, from one-dimensional spider silk to two-dimensional star-like patterns to three-dimensional Nepenthes alata. Here we present a simple way for the accurate design and highly controllable driving of tiny droplets: by laser direct writing of hierarchical patterns with modified wettability and desired geometry on a superhydrophobic film, the patterned film can precisely and directionally drive tiny water droplets and dramatically improve the efficiency of water collection with a factor of ∼36 compared with the original superhydrophobic film. Such a patterned film might be an ideal platform for water collection from humid air and for planar microfluidics without tunnels.

  17. Improving yield and water use efficiency of apple trees through intercrop-mulch of crown vetch (Coronilla varia L.) combined with different fertilizer treatments in the Loess Plateau

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, W.; Li, Y.; Gong, Q.; Zhang, H.; Zhao, Z.; Zheng, Z.; Zhai, B.; Wang, Z.

    2016-07-01

    Improving water use efficiency (WUE) and soil fertility is relevant for apple production in drylands. The effects of intercrop-mulch (IM) of crown vetch (Coronilla varia L.) combined with different fertilizer treatments on WUE of apple trees and soil fertility of apple orchards were assessed over three years (2011, 2013 and 2014). A split-plot design was adopted, in which the main treatments were IM and no intercrop-mulch (NIM). Five sub-treatments were established: no fertilization (CK); nitrogen and phosphorus fertilizer (NP); manure (M); N, P and potassium fertilizer (NPK); and NPK fertilizer combined with manure (NPKM). Due to mowing and mulching each month during July–September, the evapotranspiration for IM was 17.3% lower than that of NIM in the dry year of 2013. Additionally, the soil water storage of NPKM treatment was higher than that of CK during the experimental period. Thus, single fruit weight and fruit number per tree increased with IM and NPKM application. Moreover, applying NPKM with IM resulted in the highest yield (on average of three years), which was 73.25% and 130.51% greater than that of CK in IM and NIM, respectively. The WUE of NPKM combined with IM was also the highest in 2013 and 2014 (47.69 and 56.95% greater than applying IM alone). In addition, due to application of IM combined with NPKM, soil organic matter was increased by 25.8% compared with that of CK (in NIM). Additionally, application of IM combined with NPKM obtained more economic net return, compared to other combinations. Therefore, applying NPKM with IM is recommended for improving apple production in this rain-fed agricultural area.

  18. 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....

  19. 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.

  20. Tradeoff between Stem Hydraulic Efficiency and Mechanical Strength Affects Leaf–Stem Allometry in 28 Ficus Tree Species

    Directory of Open Access Journals (Sweden)

    Ze-Xin Fan

    2017-09-01

    Full Text Available Leaf–stem allometry is an important spectrum that linked to biomass allocation and life history strategy in plants, although the determinants and evolutionary significance of leaf–stem allometry remain poorly understood. Leaf and stem architectures – including stem area/mass, petiole area/mass, lamina area/mass, leaf number, specific leaf area (LA, and mass-based leafing intensity (LI – were measured on the current-year branches for 28 Ficus species growing in a common garden in SW China. The leaf anatomical traits, stem wood density (WD, and stem anatomical and mechanical properties of these species were also measured. We analyzed leaf–stem allometric relationships and their associations with stem hydraulic ad mechanical properties using species-level data and phylogenetically independent contrasts. We found isometric relationship between leaf lamina area/mass and stem area/mass, suggesting that the biomass allocation to leaf was independent to stem size. However, allometric relationship between LA/mass and petiole mass was found, indicating large leaves invest a higher fractional of biomass in petiole than small ones. LI, i.e., leaf numbers per unit of stem mass, was negatively related with leaf and stem size. Species with larger terminal branches tend to have larger vessels and theoretical hydraulic conductivity, but lower WD and mechanical strength. The size of leaf lamina, petiole, and stem was correlated positively with stem theoretical hydraulic conductivity, but negatively with stem WD and mechanical strength. Our results suggest that leaf–stem allometry in Ficus species was shaped by the trade-off between stem hydraulic efficiency and mechanical stability, supporting a functional interpretation of the relationship between leaf and stem dimensions.

  1. A likelihood-based time series modeling approach for application in dendrochronology to examine the growth-climate relations and forest disturbance history

    Science.gov (United States)

    A time series intervention analysis (TSIA) of dendrochronological data to infer the tree growth-climate-disturbance relations and forest disturbance history is described. Maximum likelihood is used to estimate the parameters of a structural time series model with components for ...

  2. 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.

  3. 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 ...

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. 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...

  9. 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 ...

  10. 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 ...

  11. 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 ...

  12. 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 ...

  13. 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.

  14. 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.

  15. 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…

  16. 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...

  17. 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.

  18. 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.

  19. 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

  20. Single-tree water use and water-use efficiencies of selected indigenous and introduced species in the Southern Cape region of South Africa

    CSIR Research Space (South Africa)

    Mapeto, P

    2017-03-01

    Full Text Available In South Africa, the development of a plantation tree industry using fast-growing introduced species was accelerated by the limited extent of indigenous forests. However, concerns about the impacts of plantations on the country’s limited water...

  1. 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.

  2. Flexible and efficient estimating equations for variogram estimation

    KAUST Repository

    Sun, Ying; Chang, Xiaohui; Guan, Yongtao

    2018-01-01

    Variogram estimation plays a vastly important role in spatial modeling. Different methods for variogram estimation can be largely classified into least squares methods and likelihood based methods. A general framework to estimate the variogram through a set of estimating equations is proposed. This approach serves as an alternative approach to likelihood based methods and includes commonly used least squares approaches as its special cases. The proposed method is highly efficient as a low dimensional representation of the weight matrix is employed. The statistical efficiency of various estimators is explored and the lag effect is examined. An application to a hydrology dataset is also presented.

  3. Flexible and efficient estimating equations for variogram estimation

    KAUST Repository

    Sun, Ying

    2018-01-11

    Variogram estimation plays a vastly important role in spatial modeling. Different methods for variogram estimation can be largely classified into least squares methods and likelihood based methods. A general framework to estimate the variogram through a set of estimating equations is proposed. This approach serves as an alternative approach to likelihood based methods and includes commonly used least squares approaches as its special cases. The proposed method is highly efficient as a low dimensional representation of the weight matrix is employed. The statistical efficiency of various estimators is explored and the lag effect is examined. An application to a hydrology dataset is also presented.

  4. 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....

  5. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    shaped corolla. Fruit is large, ellipsoidal, green with a hard and smooth shell containing numerous flattened seeds, which are embedded in fleshy pulp. Calabash tree is commonly grown in the tropical gardens of the world as a botanical oddity.

  6. 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.

  7. Efficiency of a new strategy involving a new class of natural hetero-ligand iron(III) chelates (Fe(III)-NHL) to improve fruit tree growth in alkaline/calcareous soils.

    Science.gov (United States)

    Fuentes, Marta; Ortuño, María F; Pérez-Sarmiento, Francisco; Bacaicoa, Eva; Baigorri, Roberto; Conejero, Wenceslao; Torrecillas, Arturo; García-Mina, José M

    2012-12-01

    Iron (Fe) chlorosis is a serious problem affecting the yield and quality of numerous crops and fruit trees cultivated in alkaline/calcareous soils. This paper describes the efficiency of a new class of natural hetero-ligand Fe(III) chelates (Fe-NHL) to provide available Fe for chlorotic lemon trees grown in alkaline/calcareous soils. These chelates involve the participation in the reaction system of a partially humified lignin-based natural polymer and citric acid. First results showed that Fe-NHL was adsorbed on the soil matrix while maintaining available Fe for plants in alkaline/calcareous solution. The effects of using three different sources as Fe fertilisers were also compared: two Fe-NHL formulations (NHL1, containing 100% of Fe as Fe-NHL, and NHL2, containing 80% of Fe as Fe-NHL and 20% of Fe as Fe-ethylenediamine-N,N'-bis-(o-hydroxyphenylacetic) acid (Fe-EDDHA)) and Fe-EDDHA. Both Fe-NHL formulations increased fruit yield without negative effects on fruit quality in comparison with Fe-EDDHA. In the absence of the Fe-starter fraction (NHL1), trees seemed to optimise Fe assimilation and translocation from Fe-NHL, directing it to those parts of the plant more involved in development. The field assays confirmed that Fe-NHL-based fertilisers are able to provide Fe to chlorotic trees, with results comparable to Fe-EDDHA. Besides, this would imply a more sustainable and less expensive remediation than synthetic chelates. Copyright © 2012 Society of Chemical Industry.

  8. Eficiência da poda em cafeeiros no controle da Xylella fastidiosa Prune efficiency in the control of Xylella fastidiosa in coffee trees

    Directory of Open Access Journals (Sweden)

    Rachel Benetti Queiroz-Voltan

    2006-01-01

    management procedures have attenuated the disease incidence, such as the use of bacteria-free seedlings and insect vector control. Pruning is an important practice for optimization of coffee orchard production. Coffee growers refer to pruning as training; coffee tree training depends on the coffee plant type and environment, using traditional or drastic trimming. This research aimed at evaluating the efficiency of different prune procedures in the control of X. fastidiosa incidence in coffee commercial cultivars Acaiá IAC 474-19 and Catuaí Vermelho IAC 81. Eight plants of each cultivar were submitted to three pruning types (traditional, "skeleton cut" and trunking; and eight plants were not pruned (controls. Prior to pruning, five plant branches were collected for anatomical studies. Thereafter, five other branches from all treatments were collected in October/2004 (rainy period and June/2005 (dry period for the anatomical studies. No significant differences were observed for `Acaiá IAC 474-19' that presented lower proportion of xylem vessel obstruction independent of the prune treatment. Prune treatments in `Catuaí Vermelho IAC 81' were also not significantly different; however, plants submitted to dramatic trimmings such as the "skeleton cut" and trunking showed a trend for lower proportion of xylem vessel obstruction by the bacteria, in both rainy and dry periods. It was suggested that the drastic pruning procedures ("skeleton cut" and trunking might be advantageous for the Xyllela control in situations of high disease incidence.

  9. 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)

  10. 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

  11. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tree with irregularly-shaped trunk, greyish-white scaly bark and milky latex. Leaves in opposite pairs are simple, oblong and whitish beneath. Flowers that occur in branched inflorescence are white, 2–. 3cm across and fragrant. Calyx is glandular inside. Petals bear numerous linear white scales, the corollary.

  12. Flowering Trees

    Indian Academy of Sciences (India)

    Berrya cordifolia (Willd.) Burret (Syn. B. ammonilla Roxb.) – Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading ...

  13. Flowering Trees

    Indian Academy of Sciences (India)

    Canthium parviflorum Lam. of Rubiaceae is a large shrub that often grows into a small tree with conspicuous spines. Leaves are simple, in pairs at each node and are shiny. Inflorescence is an axillary few-flowered cymose fascicle. Flowers are small (less than 1 cm across), 4-merous and greenish-white. Fruit is ellipsoid ...

  14. Flowering Trees

    Indian Academy of Sciences (India)

    sriranga

    Hook.f. ex Brandis (Yellow. Cadamba) of Rubiaceae is a large and handsome deciduous tree. Leaves are simple, large, orbicular, and drawn abruptly at the apex. Flowers are small, yellowish and aggregate into small spherical heads. The corolla is funnel-shaped with five stamens inserted at its mouth. Fruit is a capsule.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Celtis tetrandra Roxb. of Ulmaceae is a moderately large handsome deciduous tree with green branchlets and grayish-brown bark. Leaves are simple with three to four secondary veins running parallel to the mid vein. Flowers are solitary, male, female and bisexual and inconspicuous. Fruit is berry-like, small and globose ...

  16. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Aglaia elaeagnoidea (A.Juss.) Benth. of Meliaceae is a small-sized evergreen tree of both moist and dry deciduous forests. The leaves are alternate and pinnately compound, terminating in a single leaflet. Leaflets are more or less elliptic with entire margin. Flowers are small on branched inflorescence. Fruit is a globose ...

  17. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowers are borne on stiff bunches terminally on short shoots. They are 2-3 cm across, white, sweet-scented with light-brown hairy sepals and many stamens. Loquat fruits are round or pear-shaped, 3-5 cm long and are edible. A native of China, Loquat tree is grown in parks as an ornamental and also for its fruits.

  18. Flowering Trees

    Indian Academy of Sciences (India)

    mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off in large shreds. Leaves are thick, oblong, leathery and bright red when young. The female flowers are drooping and are larger than male flowers. Fruit is large, red in color and velvety.

  19. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  20. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  1. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  2. ~{owering 'Trees

    Indian Academy of Sciences (India)

    . Stamens are fused into a purple staminal tube that is toothed. Fruit is about 0.5 in. across, nearly globose, generally 5-seeded, green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening.

  3. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  4. Flowering Trees

    Indian Academy of Sciences (India)

    Guaiacum officinale L. (LIGNUM-VITAE) of Zygophyllaceae is a dense-crowned, squat, knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5.

  5. 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.

  6. 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.)

  7. Studies on {sup 13}C isotope discrimination for identifying tree provenances efficient in water use under water deficit conditions in Kenya

    Energy Technology Data Exchange (ETDEWEB)

    Nyamai, D O; Juma, P O [Kenya Forestry Research Inst., Nairobi (Kenya). Agroforestry Research Programme

    1996-07-01

    Screening for drought resistance traits was conducted in a semi-arid site in Machakos using 11 provenances of Acacia tortilis, 6 provenances of Prosopis juliflora and 4 provenances of Casuarina equisetifolia. Tolerance to drought was assessed by the {sup 13}C isotope discrimination ({Delta}) technique as well as by determining the waster use efficiency (WUE). Measurements of dry matter and early growth performance were also taken as indicators of drought resistance. The results showed significant differences in the {sup 13}C Isotope discrimination, water use efficiency and dry matter yields by the different provenances tested. Generally, the results indicated that there were significant linear negative relationships between {sup 13}C discrimination with water use efficiency as well as dry matter yield. The results further showed highly significant positive relationship between dry matter yield and water use efficiency. Acacia tortilis provenances from middle East and neighbouring North Eastern Africa region appear to possess the greatest abilities for drought resistance in comparison with those from sub-saharan Africa as indicated by their {sup 13}C Isotope discrimination levels, dry matter yield and water use efficiency. However, Acacia provenance from Israel had the highest drought resistance trail. Prosopis provenance from Costa Rica and Casuarina from Dakar region in Senegal also emerged as the best provenances in terms of drought tolerance as shown by the {sup 13}C isotope discrimination and dry matter traits. (author). 8 refs, 4 figs, 3 tabs.

  8. Likelihood based testing for no fractional cointegration

    DEFF Research Database (Denmark)

    Lasak, Katarzyna

    . The standard cointegration analysis only considers the assumption that deviations from equilibrium can be integrated of order zero, which is very restrictive in many cases and may imply an important loss of power in the fractional case. We consider the alternative hypotheses with equilibrium deviations...... that can be mean reverting with order of integration possibly greater than zero. Moreover, the degree of fractional cointegration is not assumed to be known, and the asymptotic null distribution of both tests is found when considering an interval of possible values. The power of the proposed tests under...

  9. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

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

    Science.gov (United States)

    2013-01-01

    well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

  11. Quantification of tannins in tree foliage. A laboratory manual for the FAO/IAEA co-ordinated research project on 'Use of nuclear and related techniques to develop simple tannin assays for predicting and improving the safety and efficiency of feeding ruminants on tanniniferous tree foliage'

    International Nuclear Information System (INIS)

    2000-01-01

    Tanniniferous trees and shrubs are of importance in animal production because they can provide significant protein supplements, but unfortunately the amounts of tannins that they contain vary widely and largely unpredictably, and their effects on animals range from beneficial to toxicity and death. The toxic or antinutritional effects tend to occur in times of stress when a very large proportion of the diet is tanniniferous. With a better understanding of tannin properties and proper management, they could become an invaluable source of protein for strategic supplementation. As the demand for food rises, tanniniferous plants must play an increasingly important part in the diet of animals, in particular for ruminants in smallholder subsistence farming in developing countries. It is therefore critical that techniques be developed to measure and manage the anti-nutritional components that they contain. Keeping the above in mind, a Joint FAO/IAEA Co-ordinated Research Project (CRP) on 'Use of Nuclear and Related Techniques to Develop Simple Tannin Assays for Predicting and Improving the Safety and Efficiency of Feeding Ruminants on Tanniniferous Tree Foliage' has been initiated. In order to provide sound basis for this CRP, an FAO/IAEA Consultants Meeting was held in August 1997 in Vienna, at which the tanniniferous plants to be studied, the analytical methods, the test animals and the animal response evaluation techniques were defined. This publication contains methodologies for the analysis of tannins using chemical-, protein precipitation/binding- and bio-assays recommended by the consultants

  12. 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.

  13. 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.

  14. Tree-level formalism

    International Nuclear Information System (INIS)

    Brandhuber, Andreas; Spence, Bill; Travaglini, Gabriele

    2011-01-01

    We review two novel techniques used to calculate tree-level scattering amplitudes efficiently: MHV diagrams, and on-shell recursion relations. For the MHV diagrams, we consider applications to tree-level amplitudes and focus in particular on the N=4 supersymmetric formulation. We also briefly describe the derivation of loop amplitudes using MHV diagrams. For the recursion relations, after presenting their general proof, we discuss several applications to massless theories with and without supersymmetry, to theories with massive particles, and to graviton amplitudes in general relativity. This article is an invited review for a special issue of Journal of Physics A: Mathematical and Theoretical devoted to 'Scattering amplitudes in gauge theories'. (review)

  15. 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....

  16. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

    We know that “trees are good,” 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 individual’s 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...

  17. 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...

  18. ELB-trees - Efficient Lock-free B+trees

    DEFF Research Database (Denmark)

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

    2014-01-01

    As computer systems scale in the number of processors, data structures with good parallel performance become increasingly important. Lock-free data structures promise improved parallel performance at the expense of higher complexity and sequential execution time.We present ELBtrees, a new lock-fr...

  19. 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...

  20. RBT—A Tool for Building Refined Buneman Trees

    DEFF Research Database (Denmark)

    Besenbacher, Søren; Mailund; Westh-Nielsen, Lasse

    2005-01-01

    We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm—which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction—enables refined Buneman tree reconstruction on large taxa sets....

  1. A hierarchical scheme for geodesic anatomical labeling of airway trees

    DEFF Research Database (Denmark)

    Feragen, Aasa; Petersen, Jens; Owen, Megan

    2012-01-01

    We present a fast and robust supervised algorithm for label- ing anatomical airway trees, based on geodesic distances in a geometric tree-space. Possible branch label configurations for a given unlabeled air- way tree are evaluated based on the distances to a training set of labeled airway trees....... In tree-space, the airway tree topology and geometry change continuously, giving a natural way to automatically handle anatomical differences and noise. The algorithm is made efficient using a hierarchical approach, in which labels are assigned from the top down. We only use features of the airway...

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

    Science.gov (United States)

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

    2017-08-01

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

  3. On Chinese and Western Family Trees: Mechanism and Performance

    Directory of Open Access Journals (Sweden)

    Elton S SIQUEIRA

    2016-10-01

    Full Text Available Family tree is an efficient data structure to store the kinship information in a family. There are basically two kinds of trees: Western Family Tree (WFT and Oriental Family Tree such as Chinese Family Tree (CFT. To get an insight of their efficiency in the context of family kinship presentation and information extraction, in this paper we develop WFT and CFT presentation models and search algorithms, comparing their search performance and inherent mechanism. The study reveals that the computational cost is higher in CFT model, but it provides a greater gain in information retrieval and produces more details of the kinship between individuals in the family.

  4. 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.

  5. 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...

  6. 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,...

  7. 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.

  8. Efficient Representation for Online Suffix Tree Construction

    DEFF Research Database (Denmark)

    Larsson, N. Jesper; Fuglsang, Kasper; Karlsson, Kenneth

    2014-01-01

    of branch lookup operations (known to be a bottleneck in construction time) with some additional techniques to reduce construction cost. We discuss various effects of our approach and compare it to previous techniques. An experimental evaluation shows that we are able to reduce construction time to around...

  9. Efficient Tree Search in Encrypted Data

    NARCIS (Netherlands)

    Brinkman, R.; Feng, L.; Doumen, J.M.; Hartel, P.H.; Jonker, W.

    Sometimes there is a need to store sensitive data on an untrusted database server. Song, Wagner and Perrig have introduced a way to search for the existence of a word in an encrypted textual document. The search speed is linear in the size of the document. It does not scale well for a large

  10. 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.

  11. 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.

  12. 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

  13. 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...

  14. Conifers, angiosperm trees, and lianas: growth, whole-plant water and nitrogen use efficiency, and stable isotope composition ({delta}13C and {delta}18O) of seedlings grown in a tropical environment.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Aranda, Jorge; Turner, Benjamin L

    2008-09-01

    Seedlings of several species of gymnosperm trees, angiosperm trees, and angiosperm lianas were grown under tropical field conditions in the Republic of Panama; physiological processes controlling plant C and water fluxes were assessed across this functionally diverse range of species. Relative growth rate, r, was primarily controlled by the ratio of leaf area to plant mass, of which specific leaf area was a key component. Instantaneous photosynthesis, when expressed on a leaf-mass basis, explained 69% of variation in r (P physiological models of tropical forest trees.

  15. 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...

  16. 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.

  17. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sören

    2017-11-22

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical attributes that drive the kinetic behavior of a plant and the exothermic reaction of the combustion. Coupled with realistic physics for rods, the particles enable dynamic branch motions. We model material properties, such as moisture and charring behavior, and associate them with individual particles. The combustion is efficiently processed in the surface domain of the tree model on a polygonal mesh. A user can dynamically interact with the model by initiating fires and by inducing stress on branches. The flames realistically propagate through the tree model by consuming the available resources. Our method runs at interactive rates and supports multiple tree instances in parallel. We demonstrate the effectiveness of our approach through numerous examples and evaluate its plausibility against the combustion of real wood samples.

  18. Design of data structures for mergeable trees

    DEFF Research Database (Denmark)

    Georgiadis, Loukas; Tarjan, Robert Endre; Werneck, Renato Fonseca F.

    2006-01-01

    merge operation can change many arcs. In spite of this, we develop a data structure that supports merges and all other standard tree operations in O(log2 n) amortized time on an n-node forest. For the special case that occurs in the motivating application, in which arbitrary arc deletions...... are not allowed, we give a data structure with an O(log n) amortized time bound per operation, which is asymptotically optimal. The analysis of both algorithms is not straightforward and requires ideas not previously used in the study of dynamic trees. We explore the design space of algorithms for the problem......Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant allows an operation that merges two tree paths. In contrast to the standard problem, in which only one tree arc at a time changes, a single...

  19. 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.

  20. 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...

  1. The decision tree approach to classification

    Science.gov (United States)

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

    1975-01-01

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

  2. A review of pruning fruit trees

    Science.gov (United States)

    Zhang, L.; Koc, A. B.; Wang, X. N.; Jiang, Y. X.

    2018-05-01

    The focus of this review is to present the results of studies and articles about ways to prune fruit trees. Pruning should be done in late winter or early spring so that the infection risk can be significantly decreased. This review will also offer an overview of methods to prevent infections and speed up recovery on the trees. The following is an interpretation of why high-power ultrasonic assisted pruning in the fruits trees is needed and will elaborate on the efficiency, labor costs, and safety, as well as space, location, and some environmental issues.

  3. Genomics-assisted breeding in fruit trees

    OpenAIRE

    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 pl...

  4. 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.

  5. 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…

  6. 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...

  7. 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 ...

  8. 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…

  9. 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....

  10. 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

  11. Deterministic Automata for Unordered Trees

    Directory of Open Access Journals (Sweden)

    Adrien Boiret

    2014-08-01

    Full Text Available Automata for unordered unranked trees are relevant for defining schemas and queries for data trees in Json or Xml format. While the existing notions are well-investigated concerning expressiveness, they all lack a proper notion of determinism, which makes it difficult to distinguish subclasses of automata for which problems such as inclusion, equivalence, and minimization can be solved efficiently. In this paper, we propose and investigate different notions of "horizontal determinism", starting from automata for unranked trees in which the horizontal evaluation is performed by finite state automata. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers from coNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending on the choice of the order, we obtain different classes of automata, each of which has the same expressiveness as CMso.

  12. 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.

  13. Accurate phylogenetic tree reconstruction from quartets: a heuristic approach.

    Science.gov (United States)

    Reaz, Rezwana; Bayzid, Md Shamsuzzoha; Rahman, M Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A 'quartet' is an unrooted tree over 4 taxa, hence the quartet-based supertree methods combine many 4-taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets.

  14. 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.

  15. Introduction to parallel algorithms and architectures arrays, trees, hypercubes

    CERN Document Server

    Leighton, F Thomson

    1991-01-01

    Introduction to Parallel Algorithms and Architectures: Arrays Trees Hypercubes provides an introduction to the expanding field of parallel algorithms and architectures. This book focuses on parallel computation involving the most popular network architectures, namely, arrays, trees, hypercubes, and some closely related networks.Organized into three chapters, this book begins with an overview of the simplest architectures of arrays and trees. This text then presents the structures and relationships between the dominant network architectures, as well as the most efficient parallel algorithms for

  16. Efficient computation of hashes

    International Nuclear Information System (INIS)

    Lopes, Raul H C; Franqueira, Virginia N L; Hobson, Peter R

    2014-01-01

    The sequential computation of hashes at the core of many distributed storage systems and found, for example, in grid services can hinder efficiency in service quality and even pose security challenges that can only be addressed by the use of parallel hash tree modes. The main contributions of this paper are, first, the identification of several efficiency and security challenges posed by the use of sequential hash computation based on the Merkle-Damgard engine. In addition, alternatives for the parallel computation of hash trees are discussed, and a prototype for a new parallel implementation of the Keccak function, the SHA-3 winner, is introduced.

  17. 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.

  18. 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...

  19. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  20. Examining the influences of tree-to-tree competition and climate on size-growth relationships in hydric, multi-aged Fraxinus nigra stands

    Science.gov (United States)

    Christopher E. Looney; Anthony W. D' Amato; Shawn Fraver; Brian J. Palik; Michael R. Reinikainen

    2016-01-01

    Most research on tree-tree competition and size-growth relationship (SGR – a stand-level metric that infers the relative efficiency with which different sized trees utilize available resources) has focused on upland systems. It is unclear if inferences from these studies extend to wetland forests. Moreover, no study to date has thoroughly investigated the relationship...

  1. Eficiência de fungos micorrízicos arbusculares sobre o crescimento do porta-enxerto de pessegueiro 'aldrighi Efficiency of arbuscular mycorrhizal fungi on growth of 'aldrighi' peach tree rootstock

    Directory of Open Access Journals (Sweden)

    José Luis da Silva Nunes

    2009-01-01

    Full Text Available Este trabalho visou avaliar a eficiência de diferentes espécies de fungos micorrízicos arbusculares (FMAs sobre o crescimento vegetativo e o conteúdo de nutrientes de plantas do porta-enxerto de pessegueiro (Prunus persica cv. Aldrighi. O experimento foi realizado no município de Eldorado do Sul (RS, entre 2004 e 2005. Foram utilizados quatro tratamentos de inoculação de estirpes de FMAs (Acaulospora sp. Trappe, Glomus clarum Nicol. & Schenck, Glomus etunicatum Becker & Gerd e Scutellospora heterogama Nicol. & Gerd. e um tratamento testemunha, sem inoculação. O delineamento experimental utilizado foi o de blocos casualizados, com 20 plantas por parcela e quatro repetições. A altura das plantas, o diâmetro do colo, a área foliar, as biomassas fresca e seca, o conteúdo em nutrientes e em substâncias da parte aérea e das raízes e a colonização das raízes foram avaliados aos 180 dias após a semeadura. O uso das espécies de FMAs beneficia o desenvolvimento de plantas do porta-enxerto cv. Aldrighi, e a eficiência da simbiose planta-FMAs é variável com a espécie de FMAs inoculada. As plantas submetidas à inoculação com S. heterogama e G. etunicatum destacaram-se das demais, com maior crescimento vegetativo e maiores teores de nitrogênio, fósforo e potássio nos tecidos.This work aimed to evaluate the eficiency of four species of arbuscular mycorrhizal fungi (AMF on the vegetative growth and the nutrient contents of peach tree rootstocks (Prunus persica cv. Aldrighi. The experiment was conducted at the Estação Experimental Agronômica (EEA of the Universidade Federal do Rio Grande do Sul (UFRGS, Eldorado do Sul, RS, during 2004 and 2005. Four treatments of AMF inoculation strains (Acaulospora sp. Trappe, Glomus clarum Nicol. & Schenck, Glomus etunicatum Becker & Gerd e Scutellospora heterogama Nicol. & Gerd. and one with non-inoculated plants were used. A randomized block design was used, with 20 plants per plot and four

  2. 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...

  3. Helping to increase tree crops

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1970-07-01

    Tree crops such as coffee, coconuts, palm oil, citrus fruits and cocoa are of major importance to the economies of countries in Africa, Asia and Latin America, and may be a prime source of foreign exchange earnings. The search for ways to improve efficiently the yields of crops like these - now being aided by the Division of Atomic Energy in Food and Agriculture operated jointly with the Food and Agriculture Organization - thus has a clearly defined practical goal. D. Nethsinghe deals here with some of the work. (author)

  4. Helping to increase tree crops

    International Nuclear Information System (INIS)

    1970-01-01

    Tree crops such as coffee, coconuts, palm oil, citrus fruits and cocoa are of major importance to the economies of countries in Africa, Asia and Latin America, and may be a prime source of foreign exchange earnings. The search for ways to improve efficiently the yields of crops like these - now being aided by the Division of Atomic Energy in Food and Agriculture operated jointly with the Food and Agriculture Organization - thus has a clearly defined practical goal. D. Nethsinghe deals here with some of the work. (author)

  5. 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

  6. 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)

  7. 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...

  8. 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-...

  9. 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 ...

  10. 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

  11. 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...

  12. 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...

  13. 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.

  14. 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…

  15. 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...

  16. Event tree analysis using artificial intelligence techniques

    International Nuclear Information System (INIS)

    Dixon, B.W.; Hinton, M.F.

    1985-01-01

    Artificial Intelligence (AI) techniques used in Expert Systems and Object Oriented Programming are discussed as they apply to Event Tree Analysis. A SeQUence IMPortance calculator, SQUIMP, is presented to demonstrate the implementation of these techniques. Benefits of using AI methods include ease of programming, efficiency of execution, and flexibility of application. The importance of an appropriate user interface is stressed. 5 figs

  17. Building Very Large Neighbour-Joining Trees

    DEFF Research Database (Denmark)

    Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm

    2010-01-01

    , and the NJ method in general, becomes a problem when inferring phylogenies with 10000+ taxa. In this paper we present two extentions of RapidNJ which reduce memory requirements and enable RapidNJ to infer very large phylogenetic trees efficiently. We also present an improved search heuristic for Rapid...

  18. 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)

  19. 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....

  20. Efficient Spatial Data Structure for Multiversion Management of Engineering Drawings

    Directory of Open Access Journals (Sweden)

    Yasuaki Nakamura

    2004-08-01

    Full Text Available In the engineering database system, multiple versions of a design including engineering drawings should be managed efficiently. The paper proposes an extended spatial data structure for efficient management of multiversion engineering drawings. The R-tree is adapted as a basic data structure. The efficient mechanism to manage the difference between drawings is introduced to the R-tree to eliminate redundant duplications and to reduce the amount of storage required for the data structure. The extended data structures of the R-tree, MVR and MVR* trees, are developed and the performances of these trees are evaluated. A series of simulation tests shows that, compared with the basic R-tree, the amounts of storage required for the MVR and MVR* trees are reduced to 50% and 30%, respectively. The search efficiencies of the R, MVR, and MVR* trees are almost the same.

  1. 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.

  2. Fast Image Texture Classification Using Decision Trees

    Science.gov (United States)

    Thompson, David R.

    2011-01-01

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

  3. 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.

  4. 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.

  5. 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...

  6. Learning Type Extension Trees for Metal Bonding State Prediction

    DEFF Research Database (Denmark)

    Frasconi, Paolo; Jaeger, Manfred; Passerini, Andrea

    2008-01-01

    Type Extension Trees (TET) have been recently introduced as an expressive representation language allowing to encode complex combinatorial features of relational entities. They can be efficiently learned with a greedy search strategy driven by a generalized relational information gain and a discr......Type Extension Trees (TET) have been recently introduced as an expressive representation language allowing to encode complex combinatorial features of relational entities. They can be efficiently learned with a greedy search strategy driven by a generalized relational information gain...

  7. Decision tree methods: applications for classification and prediction.

    Science.gov (United States)

    Song, Yan-Yan; Lu, Ying

    2015-04-25

    Decision tree methodology is a commonly used data mining method for establishing classification systems based on multiple covariates or for developing prediction algorithms for a target variable. This method classifies a population into branch-like segments that construct an inverted tree with a root node, internal nodes, and leaf nodes. The algorithm is non-parametric and can efficiently deal with large, complicated datasets without imposing a complicated parametric structure. When the sample size is large enough, study data can be divided into training and validation datasets. Using the training dataset to build a decision tree model and a validation dataset to decide on the appropriate tree size needed to achieve the optimal final model. This paper introduces frequently used algorithms used to develop decision trees (including CART, C4.5, CHAID, and QUEST) and describes the SPSS and SAS programs that can be used to visualize tree structure.

  8. 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)

  9. New weighting methods for phylogenetic tree reconstruction using multiple loci.

    Science.gov (United States)

    Misawa, Kazuharu; Tajima, Fumio

    2012-08-01

    Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima-Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima-Takezaki and by the modified least-squares method.

  10. Architecture of 53 rain forest tree species differing in adult stature and shade tolerance

    NARCIS (Netherlands)

    Poorter, L.; Bongers, F.J.J.M.; Sterck, F.J.; Wöll, H.

    2003-01-01

    Tree architecture determines a tree's light capture, stability, and efficiency of crown growth. The hypothesis that light demand and adult stature of tree species within a community, independently of each other, determine species' architectural traits was tested by comparing 53 Liberian rain forest

  11. Two related algorithms for root-to-frontier tree pattern matching

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Hemerik, C.; Zwaan, G.

    2006-01-01

    Tree pattern matching (TPM) algorithms on ordered, ranked trees play an important role in applications such as compilers and term rewriting systems. Many TPM algorithms appearing in the literature are based on tree automata. For efficiency, these automata should be deterministic, yet deterministic

  12. A Hybrid Shared-Memory Parallel Max-Tree Algorithm for Extreme Dynamic-Range Images

    NARCIS (Netherlands)

    Moschini, Ugo; Meijster, Arnold; Wilkinson, Michael

    Max-trees, or component trees, are graph structures that represent the connected components of an image in a hierarchical way. Nowadays, many application fields rely on images with high-dynamic range or floating point values. Efficient sequential algorithms exist to build trees and compute

  13. 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.

  14. 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.

  15. 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...

  16. 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

  17. 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...

  18. 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.

  19. 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...

  20. NLCD 2001 - Tree Canopy

    Data.gov (United States)

    Minnesota Department of Natural Resources — The National Land Cover Database 2001 tree canopy layer for Minnesota (mapping zones 39-42, 50-51) was produced through a cooperative project conducted by the...

  1. 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...

  2. 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

  3. 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....

  4. 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....

  5. 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

  6. 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...

  7. 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

  8. 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

  9. Use of nuclear and related techniques to develop simple tannin assays for predicting and improving the safety and efficiency of feeding ruminants on tanniniferous tree foliage: Achievements, result implications, and future research

    Energy Technology Data Exchange (ETDEWEB)

    Makkar, H.P.S. [Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna (Austria)]. E-mail: h.makkar@iaea.org

    2005-08-19

    The utilization of unconventional feed resources holds great relevance to developing countries, where the main constraint to livestock development is the scarcity and fluctuation of the quality and quantity of the year-around animal feed supply. There is a serious shortage in concentrated animal feeds such as soybean, cottonseed and groundnut meals, etc. In addition, the human population is increasingly rapidly and arable land is decreasing, due to solid degradation, urbanization and industrialization. Production of grain in developing countries is mostly for human consumption. Novel approaches through the utilization of tree leaves, agro-industrial by-products, aquatic sources are required to bridge the gap between supply and demand of feeds. As the demand for food rises, including that of animal origin, unconventional feed resources including tanninferous plants must play an increasingly important part in the diet of animals, in particular for ruminants in smallholder farming systems in developing countries.

  10. Use of nuclear and related techniques to develop simple tannin assays for predicting and improving the safety and efficiency of feeding ruminants on tanniniferous tree foliage: Achievements, result implications, and future research

    International Nuclear Information System (INIS)

    Makkar, H.P.S.

    2005-01-01

    The utilization of unconventional feed resources holds great relevance to developing countries, where the main constraint to livestock development is the scarcity and fluctuation of the quality and quantity of the year-around animal feed supply. There is a serious shortage in concentrated animal feeds such as soybean, cottonseed and groundnut meals, etc. In addition, the human population is increasingly rapidly and arable land is decreasing, due to solid degradation, urbanization and industrialization. Production of grain in developing countries is mostly for human consumption. Novel approaches through the utilization of tree leaves, agro-industrial by-products, aquatic sources are required to bridge the gap between supply and demand of feeds. As the demand for food rises, including that of animal origin, unconventional feed resources including tanninferous plants must play an increasingly important part in the diet of animals, in particular for ruminants in smallholder farming systems in developing countries

  11. Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

    Science.gov (United States)

    Kordi, Misagh; Bansal, Mukul S

    2017-06-01

    Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.

  12. 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...

  13. Failure diagnosis and fault tree analysis

    International Nuclear Information System (INIS)

    Weber, G.

    1982-07-01

    In this report a methodology of failure diagnosis for complex systems is presented. Systems which can be represented by fault trees are considered. This methodology is based on switching algebra, failure diagnosis of digital circuits and fault tree analysis. Relations between these disciplines are shown. These relations are due to Boolean algebra and Boolean functions used throughout. It will be shown on this basis that techniques of failure diagnosis and fault tree analysis are useful to solve the following problems: 1. describe an efficient search of all failed components if the system is failed. 2. Describe an efficient search of all states which are close to a system failure if the system is still operating. The first technique will improve the availability, the second the reliability and safety. For these problems, the relation to methods of failure diagnosis for combinational circuits is required. Moreover, the techniques are demonstrated for a number of systems which can be represented by fault trees. (orig./RW) [de

  14. Computer aided fault tree synthesis

    International Nuclear Information System (INIS)

    Poucet, A.

    1983-01-01

    Nuclear as well as non-nuclear organisations are showing during the past few years a growing interest in the field of reliability analysis. This urges for the development of powerful, state of the art methods and computer codes for performing such analysis on complex systems. In this report an interactive, computer aided approach is discussed, based on the well known fault tree technique. The time consuming and difficut task of manually constructing a system model (one or more fault trees) is replaced by an efficient interactive procedure in which the flexibility and the learning process inherent to the manual approach are combined with the accuracy in the modelling and the speed of the fully automatical approach. The method presented is based upon the use of a library containing component models. The possibility of setting up a standard library of models of general use and the link with a data collection system are discussed. The method has been implemented in the CAFTS-SALP software package which is described shortly in the report

  15. 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...

  16. New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

    Science.gov (United States)

    Whelan, Simon

    2007-10-01

    Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.

  17. 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....

  18. Decision-Tree Formulation With Order-1 Lateral Execution

    Science.gov (United States)

    James, Mark

    2007-01-01

    A compact symbolic formulation enables mapping of an arbitrarily complex decision tree of a certain type into a highly computationally efficient multidimensional software object. The type of decision trees to which this formulation applies is that known in the art as the Boolean class of balanced decision trees. Parallel lateral slices of an object created by means of this formulation can be executed in constant time considerably less time than would otherwise be required. Decision trees of various forms are incorporated into almost all large software systems. A decision tree is a way of hierarchically solving a problem, proceeding through a set of true/false responses to a conclusion. By definition, a decision tree has a tree-like structure, wherein each internal node denotes a test on an attribute, each branch from an internal node represents an outcome of a test, and leaf nodes represent classes or class distributions that, in turn represent possible conclusions. The drawback of decision trees is that execution of them can be computationally expensive (and, hence, time-consuming) because each non-leaf node must be examined to determine whether to progress deeper into a tree structure or to examine an alternative. The present formulation was conceived as an efficient means of representing a decision tree and executing it in as little time as possible. The formulation involves the use of a set of symbolic algorithms to transform a decision tree into a multi-dimensional object, the rank of which equals the number of lateral non-leaf nodes. The tree can then be executed in constant time by means of an order-one table lookup. The sequence of operations performed by the algorithms is summarized as follows: 1. Determination of whether the tree under consideration can be encoded by means of this formulation. 2. Extraction of decision variables. 3. Symbolic optimization of the decision tree to minimize its form. 4. Expansion and transformation of all nested conjunctive

  19. 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....

  20. Index of efficiency of macronutrients in tree species in a mixed araucaria forest/Paraná State/ Índice de eficiência de macronutrientes em espécies arbóreas – floresta ombrófila mista montana/Paraná

    Directory of Open Access Journals (Sweden)

    Luciano Farinha Watzlawick

    2006-06-01

    Full Text Available The main objective of this research work was to study the Efficiency Index of Macronutrients in tree biomass in a Mixed Araucaria Forest through 20 primary sample plots of 12 m x 12 m. The efficiency indexes of macronutrients (EIMacronutrients varied between the tree species, and between the biomass up ground components (stem = wood stem + bark; leaves and total = stem + branch + leaves. The species that showed hight EIMacronutrients to the stem production were the same that showed hight EIMacronutrients to the woody components production (stem + branches, excetp Myrsine ferruginea; Schinus terebinthifolius and Calyptranthes concinna.O trabalho aqui apresentado teve como objetivo principal caracterizar o Índice de Eficiência de Macronutrientes (IEMacronutrientes = Biomassa Produzida/Nutriente Utilizado nos componentes da biomassa acima do solo (DAP ³ 10,0 cm das espécies arbóreas da Floresta Ombrofila Mista Montana, General Carneiro/PR, utilizando 20 unidades amostrais primárias (UAPs de 12 m x 12 m. Os índices de eficiência de macronutrientes (IEMacronutrientes entre as espécies arbóreas, bem como entre os componentes da biomassa acima do solo (fuste = madeira do fuste + casca; folhas e total = fuste + galhos + folhas variaram. As espécies que apresentaram altos IEMacronutrientes para a produção de fuste foram as mesmas que apresentaram altos IEMacronutrientes para a produção de componentes lenhosos (fuste + galhos, exceto Myrsine ferruginea; Schinus terebinthifolius e Calyptranthes concinna.

  1. Evaluation of geocast routing trees on random and actual networks

    NARCIS (Netherlands)

    Meijerink, Berend Jan; Baratchi, Mitra; Heijenk, Geert; Koucheryavy, Yevgeni; Mamatas, Lefteris; Matta, Ibrahim; Ometov, Aleksandr; Papadimitriou, Panagiotis

    2017-01-01

    Efficient geocast routing schemes are needed to transmit messages to mobile networked devices in geographically scoped areas. To design an efficient geocast routing algorithm a comprehensive evaluation of different routing tree approaches is needed. In this paper, we present an analytical study

  2. 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

  3. Portraits of Tree Families

    NARCIS (Netherlands)

    Balgooy, van M.M.J.

    1998-01-01

    With the publication of the second volume of the series ‘Malesian Seed Plants’, entitled ‘Portraits of Tree Families’, I would like to refer to the Introduction of the first volume, ‘Spot-characters’ for a historical background and an explanation of the aims of this series. The present book treats

  4. 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 ...

  5. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    transducers can be concisely represented in Haskell, and demonstrate the benefits of utilising such an approach with a number of examples. In particular, tree transducers afford a modular programming style as they can be easily composed and manipulated. Our Haskell representation generalises the original...

  6. Chapter 5 - Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2014-01-01

    Tree mortality is a natural process in all forest ecosystems. Extremely high mortality, however, can also be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  7. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

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

  8. Base tree property

    Czech Academy of Sciences Publication Activity Database

    Balcar, B.; Doucha, Michal; Hrušák, M.

    2015-01-01

    Roč. 32, č. 1 (2015), s. 69-81 ISSN 0167-8094 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : forcing * Boolean algebras * base tree Subject RIV: BA - General Mathematics Impact factor: 0.614, year: 2015 http://link.springer.com/article/10.1007/s11083-013-9316-2

  9. Multiquarks and Steiner trees

    International Nuclear Information System (INIS)

    Richard, Jean-Marc

    2010-01-01

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

  10. PL-MOD: a computer code for modular fault tree analysis and evaluation

    International Nuclear Information System (INIS)

    Olmos, J.; Wolf, L.

    1978-01-01

    The computer code PL-MOD has been developed to implement the modular methodology to fault tree analysis. In the modular approach, fault tree structures are characterized by recursively relating the top tree event to all basic event inputs through a set of equations, each defining an independent modular event for the tree. The advantages of tree modularization lie in that it is a more compact representation than the minimal cut-set description and in that it is well suited for fault tree quantification because of its recursive form. In its present version, PL-MOD modularizes fault trees and evaluates top and intermediate event failure probabilities, as well as basic component and modular event importance measures, in a very efficient way. Thus, its execution time for the modularization and quantification 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 the computer code MOCUS

  11. The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees

    DEFF Research Database (Denmark)

    Sand, Andreas; Steel, Mike

    2013-01-01

    Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer...... species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent; however, for lateral gene transfers it was recently shown that a zone...... of inconsistency exists for a specific four-taxon tree topology, and it was posed as an open question whether inconsistencies could exist for other four-taxon tree topologies? In this letter we analyze all remaining four-taxon topologies and show that no other inconsistencies exist....

  12. Likelihood-Based Clustering of Meta-Analytic SROC Curves

    Science.gov (United States)

    Holling, Heinz; Bohning, Walailuck; Bohning, Dankmar

    2012-01-01

    Meta-analysis of diagnostic studies experience the common problem that different studies might not be comparable since they have been using a different cut-off value for the continuous or ordered categorical diagnostic test value defining different regions for which the diagnostic test is defined to be positive. Hence specificities and…

  13. Likelihood based inference for partially observed renewal processes

    NARCIS (Netherlands)

    van Lieshout, Maria Nicolette Margaretha

    2016-01-01

    This paper is concerned with inference for renewal processes on the real line that are observed in a broken interval. For such processes, the classic history-based approach cannot be used. Instead, we adapt tools from sequential spatial point process theory to propose a Monte Carlo maximum

  14. 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.

  15. 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.

  16. Increased spruce tree growth in Central Europe since 1960s.

    Science.gov (United States)

    Cienciala, Emil; Altman, Jan; Doležal, Jiří; Kopáček, Jiří; Štěpánek, Petr; Ståhl, Göran; Tumajer, Jan

    2018-04-01

    Tree growth response to recent environmental changes is of key interest for forest ecology. This study addressed the following questions with respect to Norway spruce (Picea abies, L. Karst.) in Central Europe: Has tree growth accelerated during the last five decades? What are the main environmental drivers of the observed tree radial stem growth and how much variability can be explained by them? Using a nationwide dendrochronological sampling of Norway spruce in the Czech Republic (1246 trees, 266 plots), novel regional tree-ring width chronologies for 40(±10)- and 60(±10)-year old trees were assembled, averaged across three elevation zones (break points at 500 and 700m). Correspondingly averaged drivers, including temperature, precipitation, nitrogen (N) deposition and ambient CO 2 concentration, were used in a general linear model (GLM) to analyze the contribution of these in explaining tree ring width variability for the period from 1961 to 2013. Spruce tree radial stem growth responded strongly to the changing environment in Central Europe during the period, with a mean tree ring width increase of 24 and 32% for the 40- and 60-year old trees, respectively. The indicative General Linear Model analysis identified CO 2 , precipitation during the vegetation season, spring air temperature (March-May) and N-deposition as the significant covariates of growth, with the latter including interactions with elevation zones. The regression models explained 57% and 55% of the variability in the two tree ring width chronologies, respectively. Growth response to N-deposition showed the highest variability along the elevation gradient with growth stimulation/limitation at sites below/above 700m. A strong sensitivity of stem growth to CO 2 was also indicated, suggesting that the effect of rising ambient CO 2 concentration (direct or indirect by increased water use efficiency) should be considered in analyses of long-term growth together with climatic factors and N

  17. WAMCUT, a computer code for fault tree evaluation. Final report

    International Nuclear Information System (INIS)

    Erdmann, R.C.

    1978-06-01

    WAMCUT is a code in the WAM family which produces the minimum cut sets (MCS) for a given fault tree. The MCS are useful as they provide a qualitative evaluation of a system, as well as providing a means of determining the probability distribution function for the top of the tree. The program is very efficient and will produce all the MCS in a very short computer time span. 22 figures, 4 tables

  18. 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

  19. 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

    complexity of the problem: A linear work array is used to adjust storage capacity depending on the size of trees. The dimension of the array limits the complexity of the tree to be processed. The array bounds may be altered by changing the following two FORTRAN statements: COMMON IA (50000), DATA IASIZE /50000/. The value of 50000 is suitable for trees with about 100 components. FTAP2 is the more efficient version and is recommended normally. FTAP1 differs in internal data storage format and should be used for large trees

  20. Optimal tree design for daylighting in residential buildings

    Energy Technology Data Exchange (ETDEWEB)

    Hongbing, Wang [College of Landscape Architecture, Beijing Forestry University, 35, East Qinghua Rd., Beijing (China); Shanghai Botanical Garden, 1111, Longwu Rd., Shanghai (China); Jun, Qin; Yonghong, Hu [Shanghai Botanical Garden, 1111, Longwu Rd., Shanghai (China); Li, Dong [College of Landscape Architecture, Beijing Forestry University, 35, East Qinghua Rd., Beijing (China)

    2010-12-15

    Urban reforestation is advocated as an efficient countermeasure to the intensification of urban heat islands. The greening and beautification of residential quarters is one of the main concerns of residents, while lighting and ventilation are two main energy-consuming building services. Hence, the tree layout in green space between buildings is important, and it is necessary to determine the relationships between trees and buildings. This study takes Shanghai as a case study to optimize tree design between residential buildings and meet good daylighting requirements. Models were made using software such as AutoCAD and SketchUp. The relationships between maximum tree height and building separation were determined. For the same building layout, there were different tree height limits according to crown shape; the order of decreasing height limits was cylindrical, conical, spherical, and inverted conical crowns. Three cases having different green space between building layouts were studied. Their maximum tree heights differed. Overall, our model helps us realize good daylighting of a building environment. The formula allows us to determine which trees to plant between buildings in that we can predict the effects of future tree growth on building daylighting. (author)

  1. 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.

  2. 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)

  3. 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…

  4. 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...

  5. 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...

  6. 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, ...

  7. Steiner tree heuristic in the Euclidean d-space using bottleneck distances

    DEFF Research Database (Denmark)

    Lorenzen, Stephan Sloth; Winter, Pawel

    2016-01-01

    Some of the most efficient heuristics for the Euclidean Steiner minimal tree problem in the d-dimensional space, d ≥2, use Delaunay tessellations and minimum spanning trees to determine small subsets of geometrically close terminals. Their low-cost Steiner trees are determined and concatenated...... in a greedy fashion to obtain a low cost tree spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To avoid this and to obtain even better solutions, bottleneck distances are utilized to determine good subsets of terminals...

  8. Load Balancing Issues with Constructing Phylogenetic Trees using Neighbour-Joining Algorithm

    International Nuclear Information System (INIS)

    Al Mamun, S M

    2012-01-01

    Phylogenetic tree construction is one of the most important and interesting problems in bioinformatics. Constructing an efficient phylogenetic tree has always been a research issue. It needs to consider both the correctness and the speed of the tree construction. In this paper, we implemented the neighbour-joining algorithm, using Message Passing Interface (MPI) for constructing the phylogenetic tree. Performance is efficacious, comparing to the best sequential algorithm. From this paper, it would be clear to the researchers that how load balance can make a great effect for constructing phylogenetic trees using neighbour-joining algorithm.

  9. 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.

  10. 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.

  11. PROVIDING R-TREE SUPPORT FOR MONGODB

    Directory of Open Access Journals (Sweden)

    L. Xiang

    2016-06-01

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

  12. Providing R-Tree Support for Mongodb

    Science.gov (United States)

    Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

    2016-06-01

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

  13. 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.

  14. 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.

  15. Mapping trees outside forests using high-resolution aerial imagery: a comparison of pixel- and object based classification approaches

    Science.gov (United States)

    Dacia M. Meneguzzo; Greg C. Liknes; Mark D. Nelson

    2013-01-01

    Discrete trees and small groups of trees in nonforest settings are considered an essential resource around the world and are collectively referred to as trees outside forests (ToF). ToF provide important functions across the landscape, such as protecting soil and water resources, providing wildlife habitat, and improving farmstead energy efficiency and aesthetics....

  16. Fault tree analysis

    International Nuclear Information System (INIS)

    1981-09-01

    Suggestion are made concerning the method of the fault tree analysis, the use of certain symbols in the examination of system failures. This purpose of the fault free analysis is to find logical connections of component or subsystem failures leading to undesirable occurrances. The results of these examinations are part of the system assessment concerning operation and safety. The objectives of the analysis are: systematical identification of all possible failure combinations (causes) leading to a specific undesirable occurrance, finding of reliability parameters such as frequency of failure combinations, frequency of the undesirable occurrance or non-availability of the system when required. The fault tree analysis provides a near and reconstructable documentation of the examination. (orig./HP) [de

  17. 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…

  18. 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.

  19. 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.

  20. 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

  1. 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....

  2. 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...

  3. 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.

  4. 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.

  5. 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...

  6. A fault tree analysis strategy using binary decision diagrams

    International Nuclear Information System (INIS)

    Reay, Karen A.; Andrews, John D.

    2002-01-01

    The use of binary decision diagrams (BDDs) in fault tree analysis provides both an accurate and efficient means of analysing a system. There is a problem, however, with the conversion process of the fault tree to the BDD. The variable ordering scheme chosen for the construction of the BDD has a crucial effect on its resulting size and previous research has failed to identify any scheme that is capable of producing BDDs for all fault trees. This paper proposes an analysis strategy aimed at increasing the likelihood of obtaining a BDD for any given fault tree, by ensuring the associated calculations are as efficient as possible. The method implements simplification techniques, which are applied to the fault tree to obtain a set of 'minimal' subtrees, equivalent to the original fault tree structure. BDDs are constructed for each, using ordering schemes most suited to their particular characteristics. Quantitative analysis is performed simultaneously on the set of BDDs to obtain the top event probability, the system unconditional failure intensity and the criticality of the basic events

  7. Real Time Animation of Trees Based on BBSC in Computer Games

    Directory of Open Access Journals (Sweden)

    Xuefeng Ao

    2009-01-01

    Full Text Available That researchers in the field of computer games usually find it is difficult to simulate the motion of actual 3D model trees lies in the fact that the tree model itself has very complicated structure, and many sophisticated factors need to be considered during the simulation. Though there are some works on simulating 3D tree and its motion, few of them are used in computer games due to the high demand for real-time in computer games. In this paper, an approach of animating trees in computer games based on a novel tree model representation—Ball B-Spline Curves (BBSCs are proposed. By taking advantage of the good features of the BBSC-based model, physical simulation of the motion of leafless trees with wind blowing becomes easier and more efficient. The method can generate realistic 3D tree animation in real-time, which meets the high requirement for real time in computer games.

  8. Distribution of total nitrogen and N-15 labelled nitrogen applied to apple trees

    International Nuclear Information System (INIS)

    Calvache, Marcelo.

    1990-01-01

    The efficiency of nitrogen fertilization from one year's application was studied in apple trees. Urea enriched with 1,5% N-15 a.e. was applied to 2 years old apple trees. Two irrigation treatments were studied, Al approx. 200mm/week and A2 approx. 100 mm/week. The distribution of N in the different parts of the trees was determined after 2 months of fertilization and after the experimental trees were excavated. The recovery of labelled fertilizer N was different in the trees in both treatments (Al = 1,2% and A2 = 3,1%). However, the distribution in the tree's parts was similar: 46% in leaves, 34% in branches and 20% in roots. We also determined that sampling only 20% of leaves at the beginning and the end of the experiment it is possible to know the quantity of nitrogen from fertilizer, without the excavation trees

  9. 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.

  10. 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

  11. Tree cover changes in- and ouside protected areas in China

    DEFF Research Database (Denmark)

    Nüchel, Jonas; Bøcher, Peder Klith; Svenning, J.-C.

    Protected areas (PAs) are one of the main tools in the global conservation of biodiversity and ecosystems. This is also the case for China. However, only few studies have investigated protected areas´ efficiency in maintaining ecosystems and biodiversity. One way to investigate this is to look...... at tree cover changes inside the PAs and on the surrounding areas. Using MODIS Vegetation Continuous Fields we mapped tree-cover changes between 2000-2010 in- and outside PAs in China. The PAs were extracted from the World Database on Protected Areas. Our aim were to investigated the following four...... between tree cover change and general human pressure. We did not find a significant correlation between tree cover change inside and outside PAs with increasing general human pressures. The lack of correlation could be due to the huge reforestation China has carried out the last years, mainly to stop...

  12. Fruit tree model for uptake of organic compounds from soil

    DEFF Research Database (Denmark)

    Trapp, Stefan; Rasmussen, D.; Samsoe-Petersen, L.

    2003-01-01

    -state, and an example calculation is given. The Fruit Tree Model is compared to the empirical equation of Travis and Arms (T&A), and to results from fruits, collected in contaminated areas. For polar compounds, both T&A and the Fruit Tree Model predict bioconcentration factors fruit to soil (BCF, wet weight based......) of > 1. No empirical data are available to support this prediction. For very lipophilic compounds (log K-OW > 5), T&A overestimates the uptake. The conclusion from the Fruit Tree Model is that the transfer of lipophilic compounds into fruits is not relevant. This was also found by an empirical study...... with PCDD/F. According to the Fruit Tree Model, polar chemicals are transferred efficiently into fruits, but empirical data to verify these predictions are lacking....

  13. An overview of decision tree applied to power systems

    DEFF Research Database (Denmark)

    Liu, Leo; Rather, Zakir Hussain; Chen, Zhe

    2013-01-01

    The corrosive volume of available data in electric power systems motivate the adoption of data mining techniques in the emerging field of power system data analytics. The mainstream of data mining algorithm applied to power system, Decision Tree (DT), also named as Classification And Regression...... Tree (CART), has gained increasing interests because of its high performance in terms of computational efficiency, uncertainty manageability, and interpretability. This paper presents an overview of a variety of DT applications to power systems for better interfacing of power systems with data...... analytics. The fundamental knowledge of CART algorithm is also introduced which is then followed by examples of both classification tree and regression tree with the help of case study for security assessment of Danish power system....

  14. 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.

  15. 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.

  16. Sweet orange trees grafted on selected rootstocks fertilized with nitrogen, phosphorus and potassium

    OpenAIRE

    Quaggio,José Antônio; Mattos Junior,Dirceu; Cantarella,Heitor; Stuchi,Eduardo Sanches; Sempionato,Otávio Ricardo

    2004-01-01

    The majority of citrus trees in Brazil are grafted on 'Rangpur lime' (Citrus limonia Osb.) rootstock. Despite its good horticultural performance, search for disease tolerant rootstock varieties to improve yield and longevity of citrus groves has increased. The objective of this work was to evaluate yield efficiency of sweet oranges on different rootstocks fertilized with N, P, and potassium. Tree growth was affected by rootstock varieties; trees on 'Swingle' citrumelo [Poncirus trifoliata (L....

  17. 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.

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. The Steiner tree problem

    CERN Document Server

    Hwang, FK; Winter, P

    1992-01-01

    The Steiner problem asks for a shortest network which spans a given set of points. Minimum spanning networks have been well-studied when all connections are required to be between the given points. The novelty of the Steiner tree problem is that new auxiliary points can be introduced between the original points so that a spanning network of all the points will be shorter than otherwise possible. These new points are called Steiner points - locating them has proved problematic and research has diverged along many different avenues. This volume is devoted to the assimilation of the rich field of intriguing analyses and the consolidation of the fragments. A section has been given to each of the three major areas of interest which have emerged. The first concerns the Euclidean Steiner Problem, historically the original Steiner tree problem proposed by Jarník and Kössler in 1934. The second deals with the Steiner Problem in Networks, which was propounded independently by Hakimi and Levin and has enjoyed the most...

  3. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  4. Distributed Merge Trees

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

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

  5. 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.

  6. An enhanced component connection method for conversion of fault trees to binary decision diagrams

    International Nuclear Information System (INIS)

    Remenyte-Prescott, R.; Andrews, J.D.

    2008-01-01

    Fault tree analysis (FTA) is widely applied to assess the failure probability of industrial systems. Many computer packages are available, which are based on conventional kinetic tree theory methods. When dealing with large (possibly non-coherent) fault trees, the limitations of the technique in terms of accuracy of the solutions and the efficiency of the processing time become apparent. Over recent years, the binary decision diagram (BDD) method has been developed that solves fault trees and overcomes the disadvantages of the conventional FTA approach. First of all, a fault tree for a particular system failure mode is constructed and then converted to a BDD for analysis. This paper analyses alternative methods for the fault tree to BDD conversion process. For most fault tree to BDD conversion approaches, the basic events of the fault tree are placed in an ordering. This can dramatically affect the size of the final BDD and the success of qualitative and quantitative analyses of the system. A set of rules is then applied to each gate in the fault tree to generate the BDD. An alternative approach can also be used, where BDD constructs for each of the gate types are first built and then merged to represent a parent gate. A powerful and efficient property, sub-node sharing, is also incorporated in the enhanced method proposed in this paper. Finally, a combined approach is developed taking the best features of the alternative methods. The efficiency of the techniques is analysed and discussed

  7. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

    Science.gov (United States)

    Pyron, R Alexander; Hendry, Catriona R; Chou, Vincent M; Lemmon, Emily M; Lemmon, Alan R; Burbrink, Frank T

    2014-12-01

    Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Analysis of large fault trees based on functional decomposition

    International Nuclear Information System (INIS)

    Contini, Sergio; Matuzas, Vaidas

    2011-01-01

    With the advent of the Binary Decision Diagrams (BDD) approach in fault tree analysis, a significant enhancement has been achieved with respect to previous approaches, both in terms of efficiency and accuracy of the overall outcome of the analysis. However, the exponential increase of the number of nodes with the complexity of the fault tree may prevent the construction of the BDD. In these cases, the only way to complete the analysis is to reduce the complexity of the BDD by applying the truncation technique, which nevertheless implies the problem of estimating the truncation error or upper and lower bounds of the top-event unavailability. This paper describes a new method to analyze large coherent fault trees which can be advantageously applied when the working memory is not sufficient to construct the BDD. It is based on the decomposition of the fault tree into simpler disjoint fault trees containing a lower number of variables. The analysis of each simple fault tree is performed by using all the computational resources. The results from the analysis of all simpler fault trees are re-combined to obtain the results for the original fault tree. Two decomposition methods are herewith described: the first aims at determining the minimal cut sets (MCS) and the upper and lower bounds of the top-event unavailability; the second can be applied to determine the exact value of the top-event unavailability. Potentialities, limitations and possible variations of these methods will be discussed with reference to the results of their application to some complex fault trees.

  9. Analysis of large fault trees based on functional decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Contini, Sergio, E-mail: sergio.contini@jrc.i [European Commission, Joint Research Centre, Institute for the Protection and Security of the Citizen, 21020 Ispra (Italy); Matuzas, Vaidas [European Commission, Joint Research Centre, Institute for the Protection and Security of the Citizen, 21020 Ispra (Italy)

    2011-03-15

    With the advent of the Binary Decision Diagrams (BDD) approach in fault tree analysis, a significant enhancement has been achieved with respect to previous approaches, both in terms of efficiency and accuracy of the overall outcome of the analysis. However, the exponential increase of the number of nodes with the complexity of the fault tree may prevent the construction of the BDD. In these cases, the only way to complete the analysis is to reduce the complexity of the BDD by applying the truncation technique, which nevertheless implies the problem of estimating the truncation error or upper and lower bounds of the top-event unavailability. This paper describes a new method to analyze large coherent fault trees which can be advantageously applied when the working memory is not sufficient to construct the BDD. It is based on the decomposition of the fault tree into simpler disjoint fault trees containing a lower number of variables. The analysis of each simple fault tree is performed by using all the computational resources. The results from the analysis of all simpler fault trees are re-combined to obtain the results for the original fault tree. Two decomposition methods are herewith described: the first aims at determining the minimal cut sets (MCS) and the upper and lower bounds of the top-event unavailability; the second can be applied to determine the exact value of the top-event unavailability. Potentialities, limitations and possible variations of these methods will be discussed with reference to the results of their application to some complex fault trees.

  10. 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.

  11. 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.

  12. 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.

  13. 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…

  14. 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%; ...

  15. Sparse suffix tree construction in small space

    DEFF Research Database (Denmark)

    Bille, Philip; Fischer, Johannes; Gørtz, Inge Li

    2013-01-01

    the correct tree with high probability. We then give a Las-Vegas algorithm which also uses O(b) space and runs in the same time bounds with high probability when b = O(√n). Furthermore, additional tradeoffs between the space usage and the construction time for the Monte-Carlo algorithm are given......., which may be of independent interest, that allows to efficiently answer b longest common prefix queries on suffixes of T, using only O(b) space. We expect that this technique will prove useful in many other applications in which space usage is a concern. Our first solution is Monte-Carlo and outputs...

  16. Crop tree release options for young hardwood stands in North Carolina

    Science.gov (United States)

    Jamie L. Schuler; Daniel J. Robison

    2006-01-01

    Harvesting southern hardwood forests using even-aged reproduction methods commonly regenerate new stands with 20,000 to 50,000 stems per acre. Overstocking and an overabundance of non-commercial tree species are considered major constraints to growing productive and valuable hardwoods. Crop tree release practices have been promoted as an efficient way of thinning young...

  17. A structurally based analytic model for estimation of biomass and fuel loads of woodland trees

    Science.gov (United States)

    Robin J. Tausch

    2009-01-01

    Allometric/structural relationships in tree crowns are a consequence of the physical, physiological, and fluid conduction processes of trees, which control the distribution, efficient support, and growth of foliage in the crown. The structural consequences of these processes are used to develop an analytic model based on the concept of branch orders. A set of...

  18. Learning decision trees with flexible constraints and objectives using integer optimization

    NARCIS (Netherlands)

    Verwer, S.; Zhang, Y.

    2017-01-01

    We encode the problem of learning the optimal decision tree of a given depth as an integer optimization problem. We show experimentally that our method (DTIP) can be used to learn good trees up to depth 5 from data sets of size up to 1000. In addition to being efficient, our new formulation allows

  19. Spray deposition inside multiple-row nursery trees with a laser-guided sprayer

    Science.gov (United States)

    Multiple-row container-grown trees require specially designed sprayers to achieve efficient spray delivery quality. A five-port air-assisted sprayer with both automatic and manual control modes was developed to discharge adequate spray deposition inside multiple-row tree plants. The sprayer resulted...

  20. NDE of logs and standing trees using new acoustic tools : technical application and results

    Science.gov (United States)

    Peter Carter; Xiping Wang; Robert J. Ross; David Briggs

    2005-01-01

    The new Director ST300 provides a means to efficiently assess stands for stiffness and related wood properties based on standing tree acoustic velocily measures, and can be easily integrated with pre-harvest and earlier stand assessments. This provides for effective valuation for forest sale, stumpage purchase, harvest planning, and ranking of progeny or clones in tree...

  1. 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.

  2. YBYRÁ facilitates comparison of large phylogenetic trees.

    Science.gov (United States)

    Machado, Denis Jacob

    2015-07-01

    The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

  3. 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

  4. New approaches to evaluating fault trees

    International Nuclear Information System (INIS)

    Sinnamon, R.M.; Andrews, J.D.

    1997-01-01

    Fault Tree Analysis is now a widely accepted technique to assess the probability and frequency of system failure in many industries. For complex systems an analysis may produce hundreds of thousands of combinations of events which can cause system failure (minimal cut sets). The determination of these cut sets can be a very time consuming process even on modern high speed digital computers. Computerised methods, such as bottom-up or top-down approaches, to conduct this analysis are now so well developed that further refinement is unlikely to result in vast reductions in computer time. It is felt that substantial improvement in computer utilisation will only result from a completely new approach. This paper describes the use of a Binary Decision Diagram for Fault Tree Analysis and some ways in which it can be efficiently implemented on a computer. In particular, attention is given to the production of a minimum form of the Binary Decision Diagram by considering the ordering that has to be given to the basic events of the fault tree

  5. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    Science.gov (United States)

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  6. 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.

  7. Better trees through systematic breeding

    Science.gov (United States)

    Robert Z. Callaham

    1957-01-01

    Today I would like to tell you briefly about the efforts of forest geneticists to improve the quality of forest trees. What do we mean by quality? Here, the consumer has the first word. The trees we produce are primarily for timber production, and the timber growing and wood-using industries give us our guidelines. Nevertheless, many of the characteristics sought by...

  8. Tree physiology and bark beetles

    Science.gov (United States)

    Michael G. Ryan; Gerard Sapes; Anna Sala; Sharon Hood

    2015-01-01

    Irruptive bark beetles usually co-occur with their co-evolved tree hosts at very low (endemic) population densities. However, recent droughts and higher temperatures have promoted widespread tree mortality with consequences for forest carbon, fire and ecosystem services (Kurz et al., 2008; Raffa et al., 2008; Jenkins et al., 2012). In this issue of New Phytologist,...

  9. Tree Hydraulics: How Sap Rises

    Science.gov (United States)

    Denny, Mark

    2012-01-01

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

  10. 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)

  11. Who pays for tree improvement?

    Science.gov (United States)

    Tom D. Byram; E. M. Raley

    2011-01-01

    Tree improvement has been one of the most successful collaborative research efforts in history, eliciting participation from a wide variety of players. This effort has included state forestry agencies, research universities, integrated forest industries, and the USDA Forest Service. Tree improvement was organized through cooperatives whose objectives were to distribute...

  12. 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

  13. Tree Simulation Techniques for Integrated Safety Assessment

    International Nuclear Information System (INIS)

    Melendez Asensio, E.; Izquierdo Rocha, J.M.; Sanchez Perez, M.; Hortal Reymundo, J.; Perez Mulas, A.

    1999-01-01

    In the development of a PSA a central role is played by the construction of the event trees that, stemming from each initiating event considered, will finally lead to the calculation of the core damage frequency (CDF). This construction is extensively done by means of expert judgement, performing simulation of the sequences only when some doubt arises (typically for small break LOCAs) using integrated codes. Transient analysis done within the framework of the PSA has important simplifications that affect the transient simulation, specially in relation with the control and protection systems, and may not identify complicated sequences. Specialised simulation tools such as RELAP5 have been used only at very specific points of the PSAs due to time and model complexity constraints. On the other hand, a large amount of work and expertise has been laid in the development of simulation tools, independently of the PSA effort. Tools simplified in the phenomena they consider, but complete in the treatment of automatic and manual control and protection systems are now available for automatic generation and testing of the sequences appearing in the Event Trees. Additionally, an increasing effort and interest has been spent in the development of efficient means for the representation of the Emergency Operating Procedures, which, incorporated into the simulating tool would make a more realistic picture of the real plant performance. At present; both types of analyses - transient and probabilistic - can converge to be able to dynamically generate an Event Tree while taking into account the actual performance of the control and protection systems of the plant and the operator actions. Such a tool would allow for an assessment of the Event Trees, and, if fed with probabilistic data, can provide results of the same nature. Key aspects of this approach that imply new theoretical as well as practical developments in addition to those traditionally covered by classical simulation

  14. 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

  15. Two intelligent spraying systems developed for tree crop production

    Science.gov (United States)

    Precision pesticide application technologies are needed to achieve efficient and effective spray deposition on target areas and minimize off-target losses. Two variable-rate intelligent sprayers were developed as an introduction of new generation sprayers for tree crop applications. The first spraye...

  16. Most Recent Match Queries in On-Line Suffix Trees

    DEFF Research Database (Denmark)

    Larsson, N. Jesper

    2014-01-01

    A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the problem of locating a most recent match: supporting queries...

  17. An improved apparatus for pressure-injecting fluid into trees

    Science.gov (United States)

    Garold F. Gregory; Thomas W. Jones

    1975-01-01

    Our original tree-injection apparatus was modified to be more convenient and efficient. The fluid reservoir consists of high-pressure plastic plumbing components. Quick couplers are used for all hose connections. Most important, the injector heads were modified for a faster and more convenient and secure attachment with double-headed nails.

  18. Hyper-parameter tuning of a decision tree induction algorithm

    NARCIS (Netherlands)

    Mantovani, R.G.; Horváth, T.; Cerri, R.; Vanschoren, J.; de Carvalho, A.C.P.L.F.

    2017-01-01

    Supervised classification is the most studied task in Machine Learning. Among the many algorithms used in such task, Decision Tree algorithms are a popular choice, since they are robust and efficient to construct. Moreover, they have the advantage of producing comprehensible models and satisfactory

  19. ADTool: Security Analysis with Attack-Defense Trees

    NARCIS (Netherlands)

    Kordy, Barbara; Kordy, P.T.; Mauw, Sjouke; Schweitzer, Patrick; Joshi, Kaustubh; Siegle, Markus; Stoelinga, Mariëlle Ida Antoinette; d' Argenio, P.R.

    ADTool is free, open source software assisting graphical modeling and quantitative analysis of security, using attack–defense trees. The main features of ADTool are easy creation, efficient editing, and automated bottom-up evaluation of security-relevant measures. The tool also supports the usage of

  20. 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.

  1. 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.

  2. 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

  3. TreeBASIS Feature Descriptor and Its Hardware Implementation

    Directory of Open Access Journals (Sweden)

    Spencer Fowers

    2014-01-01

    Full Text Available This paper presents a novel feature descriptor called TreeBASIS that provides improvements in descriptor size, computation time, matching speed, and accuracy. This new descriptor uses a binary vocabulary tree that is computed using basis dictionary images and a test set of feature region images. To facilitate real-time implementation, a feature region image is binary quantized and the resulting quantized vector is passed into the BASIS vocabulary tree. A Hamming distance is then computed between the feature region image and the effectively descriptive basis dictionary image at a node to determine the branch taken and the path the feature region image takes is saved as a descriptor. The TreeBASIS feature descriptor is an excellent candidate for hardware implementation because of its reduced descriptor size and the fact that descriptors can be created and features matched without the use of floating point operations. The TreeBASIS descriptor is more computationally and space efficient than other descriptors such as BASIS, SIFT, and SURF. Moreover, it can be computed entirely in hardware without the support of a CPU for additional software-based computations. Experimental results and a hardware implementation show that the TreeBASIS descriptor compares well with other descriptors for frame-to-frame homography computation while requiring fewer hardware resources.

  4. A new fast method for inferring multiple consensus trees using k-medoids.

    Science.gov (United States)

    Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

    2018-04-05

    Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant. We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Caliński-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms. The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while

  5. Leaf development and photosynthetic properties of three tropical tree species with delayed greening

    NARCIS (Netherlands)

    Cai, Z.Q.; Slot, M.; Fan, Z.X.

    2005-01-01

    Leaf developmental patterns were characterized for three tropical tree species with delayed greening. Changes in the pigment contents, photosynthetic capacity, stomata development, photosystem 2 efficiency, rate of energy dissipation, and the activity of partial protective enzymes were followed in

  6. CARBON ISOTOPE DISCRIMINATION AND GROWTH RESPONSE TO STAND DENSITY REDUCTIONS IN OLD PINUS PONDEROSA TREES

    Science.gov (United States)

    Carbon isotope ratios ( 13C) of tree rings are commonly used for paleoclimatic reconstruction and for inferring canopy water-use efficiency (WUE). However, the responsiveness of carbon isotope discrimination ( ) to site disturbance and resource availability has only rarely been ...

  7. 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.)

  8. 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.

  9. Predicting gene function using hierarchical multi-label decision tree ensembles

    Directory of Open Access Journals (Sweden)

    Kocev Dragi

    2010-01-01

    Full Text Available Abstract Background S. cerevisiae, A. thaliana and M. musculus are well-studied organisms in biology and the sequencing of their genomes was completed many years ago. It is still a challenge, however, to develop methods that assign biological functions to the ORFs in these genomes automatically. Different machine learning methods have been proposed to this end, but it remains unclear which method is to be preferred in terms of predictive performance, efficiency and usability. Results We study the use of decision tree based models for predicting the multiple functions of ORFs. First, we describe an algorithm for learning hierarchical multi-label decision trees. These can simultaneously predict all the functions of an ORF, while respecting a given hierarchy of gene functions (such as FunCat or GO. We present new results obtained with this algorithm, showing that the trees found by it exhibit clearly better predictive performance than the trees found by previously described methods. Nevertheless, the predictive performance of individual trees is lower than that of some recently proposed statistical learning methods. We show that ensembles of such trees are more accurate than single trees and are competitive with state-of-the-art statistical learning and functional linkage methods. Moreover, the ensemble method is computationally efficient and easy to use. Conclusions Our results suggest that decision tree based methods are a state-of-the-art, efficient and easy-to-use approach to ORF function prediction.

  10. Assessing the predictive capability of randomized tree-based ensembles in streamflow modelling

    Science.gov (United States)

    Galelli, S.; Castelletti, A.

    2013-07-01

    Combining randomization methods with ensemble prediction is emerging as an effective option to balance accuracy and computational efficiency in data-driven modelling. In this paper, we investigate the prediction capability of extremely randomized trees (Extra-Trees), in terms of accuracy, explanation ability and computational efficiency, in a streamflow modelling exercise. Extra-Trees are a totally randomized tree-based ensemble method that (i) alleviates the poor generalisation property and tendency to overfitting of traditional standalone decision trees (e.g. CART); (ii) is computationally efficient; and, (iii) allows to infer the relative importance of the input variables, which might help in the ex-post physical interpretation of the model. The Extra-Trees potential is analysed on two real-world case studies - Marina catchment (Singapore) and Canning River (Western Australia) - representing two different morphoclimatic contexts. The evaluation is performed against other tree-based methods (CART and M5) and parametric data-driven approaches (ANNs and multiple linear regression). Results show that Extra-Trees perform comparatively well to the best of the benchmarks (i.e. M5) in both the watersheds, while outperforming the other approaches in terms of computational requirement when adopted on large datasets. In addition, the ranking of the input variable provided can be given a physically meaningful interpretation.

  11. 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.

  12. Reconstructing 3D Tree Models Using Motion Capture and Particle Flow

    Directory of Open Access Journals (Sweden)

    Jie Long

    2013-01-01

    Full Text Available Recovering tree shape from motion capture data is a first step toward efficient and accurate animation of trees in wind using motion capture data. Existing algorithms for generating models of tree branching structures for image synthesis in computer graphics are not adapted to the unique data set provided by motion capture. We present a method for tree shape reconstruction using particle flow on input data obtained from a passive optical motion capture system. Initial branch tip positions are estimated from averaged and smoothed motion capture data. Branch tips, as particles, are also generated within a bounding space defined by a stack of bounding boxes or a convex hull. The particle flow, starting at branch tips within the bounding volume under forces, creates tree branches. The forces are composed of gravity, internal force, and external force. The resulting shapes are realistic and similar to the original tree crown shape. Several tunable parameters provide control over branch shape and arrangement.

  13. 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.

  14. Tree Coding of Bilevel Images

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    Presently, sequential tree coders are the best general purpose bilevel image coders and the best coders of halftoned images. The current ISO standard, Joint Bilevel Image Experts Group (JBIG), is a good example. A sequential tree coder encodes the data by feeding estimates of conditional...... is one order of magnitude slower than JBIG, obtains excellent and highly robust compression performance. A multipass free tree coding scheme produces superior compression results for all test images. A multipass free template coding scheme produces significantly better results than JBIG for difficult...... images such as halftones. By utilizing randomized subsampling in the template selection, the speed becomes acceptable for practical image coding...

  15. 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.

  16. 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....

  17. A knowledge-based approach to the evaluation of fault trees

    International Nuclear Information System (INIS)

    Hwang, Yann-Jong; Chow, Louis R.; Huang, Henry C.

    1996-01-01

    A list of critical components is useful for determining the potential problems of a complex system. However, to find this list through evaluating the fault trees is expensive and time consuming. This paper intends to propose an integrated software program which consists of a fault tree constructor, a knowledge base, and an efficient algorithm for evaluating minimal cut sets of a large fault tree. The proposed algorithm uses the approaches of top-down heuristic searching and the probability-based truncation. That makes the evaluation of fault trees obviously efficient and provides critical components for solving the potential problems in complex systems. Finally, some practical fault trees are included to illustrate the results

  18. 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.

  19. 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...

  20. 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 ...

  1. Responses of Tree Growths to Tree Size, Competition, and Topographic Conditions in Sierra Nevada Forests Using Bi-temporal Airborne LiDAR Data

    Science.gov (United States)

    Ma, Q.; Su, Y.; Tao, S.; Guo, Q.

    2016-12-01

    Trees in the Sierra Nevada (SN) forests are experiencing rapid changes due to human disturbances and climatic changes. An improved monitoring of tree growth and understanding of how tree growth responses to different impact factors, such as tree competition, forest density, topographic and hydrologic conditions, are urgently needed in tree growth modeling. Traditional tree growth modeling mainly relied on field survey, which was highly time-consuming and labor-intensive. Airborne Light detection and ranging System (ALS) is increasingly used in forest survey, due to its high efficiency and accuracy in three-dimensional tree structure delineation and terrain characterization. This study successfully detected individual tree growth in height (ΔH), crown area (ΔA), and crown volume (ΔV) over a five-year period (2007-2012) using bi-temporal ALS data in two conifer forest areas in SN. We further analyzed their responses to original tree size, competition indices, forest structure indices, and topographic environmental parameters at individual tree and forest stand scales. Our results indicated ΔH was strongly sensitive to topographic wetness index; whereas ΔA and ΔV were highly responsive to forest density and original tree sizes. These ALS based findings in ΔH were consistent with field measurements. Our study demonstrated the promising potential of using bi-temporal ALS data in forest growth measurements and analysis. A more comprehensive study over a longer temporal period and a wider range of forest stands would give better insights into tree growth in the SN, and provide useful guides for forest growth monitoring, modeling, and management.

  2. Resummed tree heptagon

    Science.gov (United States)

    Belitsky, A. V.

    2018-04-01

    The form factor program for the regularized space-time S-matrix in planar maximally supersymmetric gauge theory, known as the pentagon operator product expansion, is formulated in terms of flux-tube excitations propagating on a dual two-dimensional world-sheet, whose dynamics is known exactly as a function of 't Hooft coupling. Both MHV and non-MHV amplitudes are described in a uniform, systematic fashion within this framework, with the difference between the two encoded in coupling-dependent helicity form factors expressed via Zhukowski variables. The nontrivial SU(4) tensor structure of flux-tube transitions is coupling independent and is known for any number of charged excitations from solutions of a system of Watson and Mirror equations. This description allows one to resum the infinite series of form factors and recover the space-time S-matrix exactly in kinematical variables at a given order of perturbation series. Recently, this was done for the hexagon. Presently, we successfully perform resummation for the seven-leg tree NMHV amplitude. To this end, we construct the flux-tube integrands of the fifteen independent Grassmann component of the heptagon with an infinite number of small fermion-antifermion pairs accounted for in NMHV two-channel conformal blocks.

  3. Random ancestor trees

    International Nuclear Information System (INIS)

    Ben-Naim, E; Krapivsky, P L

    2010-01-01

    We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

  4. Trees as metal scavengers

    International Nuclear Information System (INIS)

    Hallman, N.

    2000-01-01

    Full text: Tree roots extract metal ions form wet soils in two different ways. At the soil/root hair interface soluble ions in contact with the cellulose wall move through it and enter the cell through the plasmalemma; the semi permeable membrane that encloses every living cell. Some ions, especially those that are part of cellular metabolic processes eg. Na, K, Fe, Mg, S move into the cytoplasm, are bound into organic complexes and travel from cell to cell within the cytoplasm. This requires energy, and the amount of any of these metabolically active ions taken in tends to be regulated by the plant. The movement of the ions from cell to cell is slow, selective, and regulated by requirements of synthesis of for example Mg in the chlorophyll molecule. This means that more Mg is transported to cells of leaves than of cells of roots. This movement of ions is simplistic, or within the cytoplasm. Other ions are swept along in the transpiration stream and enter the complex plumbing system that brings water to the leaves for metabolism and cooling. Water in this apoplastic pathway travels within the pipes (xylem) of the wood and in the cellulose of the walls. It travels along essentially non-living parts of the plant. Ions such as As, Pb, Ni, Cr accumulate in sites such as leaves and bark. Analysis of plant parts can indicate the presence of heavy metals and can give an indication of ore bodies within the root zone

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

    Science.gov (United States)

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

    2011-01-01

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

  6. 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....

  7. Fremont Tree-Well Filter

    Science.gov (United States)

    Information about the SFBWQP Fremont Tree-Well Filter Spine project, part of an EPA competitive grant program to improve SF Bay water quality focused on restoring impaired waters and enhancing aquatic resources.

  8. 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.

  9. 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.

  10. 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...

  11. Compatibilidade de Dicyma pulvinata com defensivos agrícolas e eficiência do biocontrole do mal-das-folhas da seringueira em campo Compatibility of Dicyma pulvinata with pesticides and biocontrol efficiency of South American leaf blight of rubber tree under field conditions

    Directory of Open Access Journals (Sweden)

    Débora Ferreira Melo

    2008-02-01

    Full Text Available O objetivo deste trabalho foi avaliar quatro isolados do fungo antagonista Dicyma pulvinata quanto à compatibilidade com defensivos agrícolas e adjuvantes, e a eficiência desses isolados no controle do mal-das-folhas (Microcyclus ulei da seringueira (Hevea sp. em campo. A compatibilidade dos isolados com defensivos e adjuvantes foi avaliada com base no crescimento micelial e na esporulação do fungo, em testes conduzidos in vitro. Para avaliação da eficiência do antagonista contra M. ulei, em campo, os quatros isolados do antagonista foram comparados ao controle exercido pelo tratamento com os fungicidas propiconazol + mancozeb. Os ensaios conduzidos em laboratório indicaram a incompatibilidade de D. pulvinata com os fungicidas benomyl, carbendazim, mancozeb, propiconazol e, ainda, com o inseticida acaricida endosulfan. Dois dos adjuvantes testados (Tween 20 e Tween 80 não afetaram o desenvolvimento do fungo. Foi comprovada a ação do antagonista D. pulvinata sobre M. ulei, em campo, com destaque para os isolados CEN 62 e CEN 93, que apresentaram eficiência de controle semelhante ao tratamento fungicida padrão.The objective of this work was to evaluate four isolates of the antagonist fungus Dicyma pulvinata in terms of its compatibility with chemical pesticides and adjuvants products, and the efficiency of these isolates as biocontrol agent against South American leaf blight (Microcyclus ulei of rubber tree (Hevea sp. under field conditions. Isolates compatibility with chemical pesticides and adjuvants was evaluated on mycelial growth and fungus sporulation in vitro. To assess the efficiency of the antagonist against M. ulei under field conditions, the four isolates were compared to the control by the fungicide mixture propiconazol + mancozeb. The assays showed incompatibility of the antagonistic fungus with the fungicides benomyl, carbendazim, mancozeb, propiconazol, besides the insecticide-acaricide endosulfan. Two of the adjuvants

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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...

  18. 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...

  19. New algorithm to detect modules in a fault tree for a PSA

    International Nuclear Information System (INIS)

    Jung, Woo Sik

    2015-01-01

    A module or independent subtree is a part of a fault tree whose child gates or basic events are not repeated in the remaining part of the fault tree. Modules are necessarily employed in order to reduce the computational costs of fault tree quantification. This paper presents a new linear time algorithm to detect modules of large fault trees. The size of cut sets can be substantially reduced by replacing independent subtrees in a fault tree with super-components. Chatterjee and Birnbaum developed properties of modules, and demonstrated their use in the fault tree analysis. Locks expanded the concept of modules to non-coherent fault trees. Independent subtrees were manually identified while coding a fault tree for computer analysis. However, nowadays, the independent subtrees are automatically identified by the fault tree solver. A Dutuit and Rauzy (DR) algorithm to detect modules of a fault tree for coherent or non-coherent fault tree was proposed in 1996. It has been well known that this algorithm quickly detects modules since it is a linear time algorithm. The new algorithm minimizes computational memory and quickly detects modules. Furthermore, it can be easily implemented into industry fault tree solvers that are based on traditional Boolean algebra, binary decision diagrams (BDDs), or Zero-suppressed BDDs. The new algorithm employs only two scalar variables in Eqs. to that are volatile information. After finishing the traversal and module detection of each node, the volatile information is destroyed. Thus, the new algorithm does not employ any other additional computational memory and operations. It is recommended that this method be implemented into fault tree solvers for efficient probabilistic safety assessment (PSA) of nuclear power plants

  20. New algorithm to detect modules in a fault tree for a PSA

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Woo Sik [Sejong University, Seoul (Korea, Republic of)

    2015-05-15

    A module or independent subtree is a part of a fault tree whose child gates or basic events are not repeated in the remaining part of the fault tree. Modules are necessarily employed in order to reduce the computational costs of fault tree quantification. This paper presents a new linear time algorithm to detect modules of large fault trees. The size of cut sets can be substantially reduced by replacing independent subtrees in a fault tree with super-components. Chatterjee and Birnbaum developed properties of modules, and demonstrated their use in the fault tree analysis. Locks expanded the concept of modules to non-coherent fault trees. Independent subtrees were manually identified while coding a fault tree for computer analysis. However, nowadays, the independent subtrees are automatically identified by the fault tree solver. A Dutuit and Rauzy (DR) algorithm to detect modules of a fault tree for coherent or non-coherent fault tree was proposed in 1996. It has been well known that this algorithm quickly detects modules since it is a linear time algorithm. The new algorithm minimizes computational memory and quickly detects modules. Furthermore, it can be easily implemented into industry fault tree solvers that are based on traditional Boolean algebra, binary decision diagrams (BDDs), or Zero-suppressed BDDs. The new algorithm employs only two scalar variables in Eqs. to that are volatile information. After finishing the traversal and module detection of each node, the volatile information is destroyed. Thus, the new algorithm does not employ any other additional computational memory and operations. It is recommended that this method be implemented into fault tree solvers for efficient probabilistic safety assessment (PSA) of nuclear power plants.

  1. 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...

  2. 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.

  3. 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 (≥80 years old) that are structurally complex, but are often...

  4. 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

  5. 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.

  6. 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

  7. Improvement of testing and maintenance based on fault tree analysis

    International Nuclear Information System (INIS)

    Cepin, M.

    2000-01-01

    Testing and maintenance of safety equipment is an important issue, which significantly contributes to safe and efficient operation of a nuclear power plant. In this paper a method, which extends the classical fault tree with time, is presented. Its mathematical model is represented by a set of equations, which include time requirements defined in the house event matrix. House events matrix is a representation of house events switched on and off through the discrete points of time. It includes house events, which timely switch on and off parts of the fault tree in accordance with the status of the plant configuration. Time dependent top event probability is calculated by the fault tree evaluations. Arrangement of components outages is determined on base of minimization of mean system unavailability. The results show that application of the method may improve the time placement of testing and maintenance activities of safety equipment. (author)

  8. Pre-germination treatments on palm tree seeds

    Directory of Open Access Journals (Sweden)

    Maitê dos Santos Ribeiro

    2015-12-01

    Full Text Available Palm tree seeds present slow and uneven germination. Therefore, the objective of this research was to evaluate the efficiency of pre-germination treatments in promoting germination and early seedling growth of palm tree (Euterpe edulis Martius. Treatments were: control, immersion in GA3 solution, exposure to ethylene, water immersion, H2SO4 immersion, mechanical scarification, stratification for 30 days at 10 °C, and scarification followed by stratification. Soaking seeds in gibberellic acid (GA3; 2000 µL L-1 for 24 h or their exposure to ethylene (1000 µL L-1 for 24 h are effective for promoting emergence, which started 30 days after seed treatment, and for early seedling growth of palm tree.

  9. A wind tunnel study on the effect of trees on PM2.5 distribution around buildings.

    Science.gov (United States)

    Ji, Wenjing; Zhao, Bin

    2018-03-15

    Vegetation, especially trees, is effective in reducing the concentration of particulate matter. Trees can efficiently capture particles, improve urban air quality, and may further decrease the introduction of outdoor particles to indoor air. The objective of this study is to investigate the effects of trees on particle distribution and removal around buildings using wind tunnel experiments. The wind tunnel is 18m long, 12m wide, and 3.5m high. Trees were modeled using real cypress branches to mimic trees planted around buildings. At the inlet of the wind tunnel, a "line source" of particles was released, simulating air laden with particulate matter. Experiments with the cypress tree and tree-free models were conducted to compare particle concentrations around the buildings. The results indicate that cypress trees clearly reduce PM 2.5 concentrations compared with the tree-free model. The cypress trees enhanced the PM 2.5 removal rate by about 20%. The effects of trees on PM 2.5 removal and distribution vary at different heights. At the base of the trees, their effect on reducing PM 2.5 concentrations is the most significant. At a great height above the treetops, the effect is almost negligible. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. 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\

  11. Optimizing Use of Girdled Ash Trees for Management of Low-Density Emerald Ash Borer (Coleoptera: Buprestidae) Populations.

    Science.gov (United States)

    Siegert, Nathan W; McCullough, Deborah G; Poland, Therese M; Heyd, Robert L

    2017-06-01

    Effective survey methods to detect and monitor recently established, low-density infestations of emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), remain a high priority because they provide land managers and property owners with time to implement tactics to slow emerald ash borer population growth and the progression of ash mortality. We evaluated options for using girdled ash (Fraxinus spp.) trees for emerald ash borer detection and management in a low-density infestation in a forested area with abundant green ash (F. pennsylvanica). Across replicated 4-ha plots, we compared detection efficiency of 4 versus 16 evenly distributed girdled ash trees and between clusters of 3 versus 12 girdled trees. We also examined within-tree larval distribution in 208 girdled and nongirdled trees and assessed adult emerald ash borer emergence from detection trees felled 11 mo after girdling and left on site. Overall, current-year larvae were present in 85-97% of girdled trees and 57-72% of nongirdled trees, and larval density was 2-5 times greater on girdled than nongirdled trees. Low-density emerald ash borer infestations were readily detected with four girdled trees per 4-ha, and 3-tree clusters were as effective as 12-tree clusters. Larval densities were greatest 0.5 ± 0.4 m below the base of the canopy in girdled trees and 1.3 ± 0.7 m above the canopy base in nongirdled trees. Relatively few adult emerald ash borer emerged from trees felled 11 mo after girdling and left on site through the following summer, suggesting removal or destruction of girdled ash trees may be unnecessary. This could potentially reduce survey costs, particularly in forested areas with poor accessibility. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

  12. A tree-ring perspective on the terrestrial carbon cycle

    International Nuclear Information System (INIS)

    Babst, F.; Alexander, M.R.; Szejner, P.; Trouet, V.; Alexander, M.R.; Moore, D.J.P.; Bouriaud, O.; Klesse, S.; Frank, D.; Roden, J.; Ciais, P.; Poulter, B.

    2014-01-01

    Tree-ring records can provide valuable information to advance our understanding of contemporary terrestrial carbon cycling and to reconstruct key metrics in the decades preceding monitoring data. The growing use of tree rings in carbon-cycle research is being facilitated by increasing recognition of reciprocal benefits among research communities. Yet, basic questions persist regarding what tree rings represent at the ecosystem level, how to optimally integrate them with other data streams, and what related challenges need to be overcome. It is also apparent that considerable unexplored potential exists for tree rings to refine assessments of terrestrial carbon cycling across a range of temporal and spatial domains. Here, we summarize recent advances and highlight promising paths of investigation with respect to (1) growth phenology, (2) forest productivity trends and variability, (3) CO 2 fertilization and water-use efficiency, (4) forest disturbances, and (5) comparisons between observational and computational forest productivity estimates. We encourage the integration of tree-ring data: with eddy-covariance measurements to investigate carbon allocation patterns and water-use efficiency; with remotely sensed observations to distinguish the timing of cambial growth and leaf phenology; and with forest inventories to develop continuous, annually resolved and long-term carbon budgets. In addition, we note the potential of tree-ring records and derivatives thereof to help evaluate the performance of earth system models regarding the simulated magnitude and dynamics of forest carbon uptake, and inform these models about growth responses to (non-)climatic drivers. Such efforts are expected to improve our understanding of forest carbon cycling and place current developments into a long-term perspective. (authors)

  13. 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.

  14. 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...

  15. Energy efficiency

    International Nuclear Information System (INIS)

    2010-01-01

    After a speech of the CEA's (Commissariat a l'Energie Atomique) general administrator about energy efficiency as a first rank challenge for the planet and for France, this publications proposes several contributions: a discussion of the efficiency of nuclear energy, an economic analysis of R and D's value in the field of fourth generation fast reactors, discussions about biofuels and the relationship between energy efficiency and economic competitiveness, and a discussion about solar photovoltaic efficiency

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

    Science.gov (United States)

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

    2015-11-01

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

  17. Developmental light level affects growth, morphology, and leaf physiology of young carambola trees

    International Nuclear Information System (INIS)

    Marler, T.E.; Schaffer, B.; Crane, J.H.

    1994-01-01

    Growth and leaf physiology responses of container-grown 'Arkin' carambola (Averrhoa carambola L.) trees to long-term exposure of approximately 25%, approximately 50%, or 100% sunlight were studied in four experiments in Guam and Florida. Shading increased rachis length and leaflet area, and decreased leaflet thickness. Shaded trees also had a more horizontal branch orientation. Shading reduced dark respiration (Rd) and light compensation and saturation points but increased chlorophyll concentration and N-use efficiency. Light-saturated net CO2 assimilation (A) was not affected by developmental light level. Trees in full sun had smaller total leaf area, canopy diameter, and shoot:root ratio and exhibited leaflet movement to avoid direct solar radiation. Also, trees grown in 100% sunlight had a more vertical branch orientation and greater stomatal density than shaded trees. The ratio of variable to maximum fluorescence (Fv/Fm) declined during midday in 100% sunlight trees. This pattern was accompanied by a midday suppression of A in 100% sunlight-grown trees in Guam. 'Arkin' carambola trees exposed to approximately 25%, approximately 50%, or 100% sunlight for up to 39 weeks exhibited physiological and morphological adaptations that resulted in similar growth. These results indicate that carambola efficiently adapts to different developmental light intensities

  18. A tree-parenchyma coupled model for lung ventilation simulation.

    Science.gov (United States)

    Pozin, Nicolas; Montesantos, Spyridon; Katz, Ira; Pichelin, Marine; Vignon-Clementel, Irene; Grandmont, Céline

    2017-11-01

    In this article, we develop a lung ventilation model. The parenchyma is described as an elastic homogenized media. It is irrigated by a space-filling dyadic resistive pipe network, which represents the tracheobronchial tree. In this model, the tree and the parenchyma are strongly coupled. The tree induces an extra viscous term in the system constitutive relation, which leads, in the finite element framework, to a full matrix. We consider an efficient algorithm that takes advantage of the tree structure to enable a fast matrix-vector product computation. This framework can be used to model both free and mechanically induced respiration, in health and disease. Patient-specific lung geometries acquired from computed tomography scans are considered. Realistic Dirichlet boundary conditions can be deduced from surface registration on computed tomography images. The model is compared to a more classical exit compartment approach. Results illustrate the coupling between the tree and the parenchyma, at global and regional levels, and how conditions for the purely 0D model can be inferred. Different types of boundary conditions are tested, including a nonlinear Robin model of the surrounding lung structures. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Factors influencing bird foraging preferences among conspecific fruit trees

    Science.gov (United States)

    Foster, M.S.

    1990-01-01

    The rates at which birds visit fruiting individuals of Allophylus edulis (Sapindaceae) differ substantially among trees. Such avian feeding preferences are well-known, but usually involve fruits and trees of different species. Factors controlling avian preferences for particular trees in a population of conspecifics are generally undocumented. To address this issue, I attempted to correlate rates at which individual birds and species fed in trees of Allophylus with 27 fruit or plant characteristics. Birds that swallow fruits whole were considered separately from those that feed in other ways. Plant characters were selected on the basis of their potential influence on feeding efficiency or predation risk, assuming that birds would select feeding trees so as to maximize the net rate of energy or nutrient intake and to minimize predation. Correlations were found between feeding visits by some groups of birds and percent water in the pulp, milligrams of mineral ash in the pulp, and crop size. No character was correlated with feeding visits by all groups of birds in both years of the study. The correlations with water and mineral ash are unexplained and may be artifacts. The correlation with crop size may represent a tactic to minimize predation.

  20. The Formation and Extinction of Fear Memory in Tree Shrews

    Directory of Open Access Journals (Sweden)

    Shujiang eShang

    2015-07-01

    Full Text Available Fear is an emotion that is well studied due to its importance for animal survival. Experimental animals, such as rats and mice, have been widely used to model fear. However, higher animals such as nonhuman primates have rarely been used to study fear due to ethical issues and high costs. Tree shrews are small mammals that are closely related to primates; they have been used to model human-related psychosocial conditions such as stress and alcohol tolerance. Here, we describe an experimental paradigm to study the formation and extinction of fear memory in tree shrews. We designed an experimental apparatus of a light/dark box with a voltage foot shock. We found that tree shrews preferred staying in the dark box in the daytime without stimulation and showed avoidance to voltage shocks applied to the footplate in a voltage-dependent manner. Foot shocks applied to the dark box for 5 days (10 minutes per day effectively reversed the light–dark preference of the tree shrews, and this memory lasted for more than 50 days without any sign of memory decay (extinction in the absence of further stimulation. However, this fear memory was reversed with 4 days of reverse training by applying the same stimulus to the light box. When reducing the stimulus intensity during the training period, a memory extinction and subsequently reinstatement effects were observed. Thus, our results describe an efficient method of monitoring fear memory formation and extinction in tree shrews.

  1. Modeling and Testing Landslide Hazard Using Decision Tree

    Directory of Open Access Journals (Sweden)

    Mutasem Sh. Alkhasawneh

    2014-01-01

    Full Text Available This paper proposes a decision tree model for specifying the importance of 21 factors causing the landslides in a wide area of Penang Island, Malaysia. These factors are vegetation cover, distance from the fault line, slope angle, cross curvature, slope aspect, distance from road, geology, diagonal length, longitude curvature, rugosity, plan curvature, elevation, rain perception, soil texture, surface area, distance from drainage, roughness, land cover, general curvature, tangent curvature, and profile curvature. Decision tree models are used for prediction, classification, and factors importance and are usually represented by an easy to interpret tree like structure. Four models were created using Chi-square Automatic Interaction Detector (CHAID, Exhaustive CHAID, Classification and Regression Tree (CRT, and Quick-Unbiased-Efficient Statistical Tree (QUEST. Twenty-one factors were extracted using digital elevation models (DEMs and then used as input variables for the models. A data set of 137570 samples was selected for each variable in the analysis, where 68786 samples represent landslides and 68786 samples represent no landslides. 10-fold cross-validation was employed for testing the models. The highest accuracy was achieved using Exhaustive CHAID (82.0% compared to CHAID (81.9%, CRT (75.6%, and QUEST (74.0% model. Across the four models, five factors were identified as most important factors which are slope angle, distance from drainage, surface area, slope aspect, and cross curvature.

  2. Variation in photosynthesis and stomatal conductance among red maple (Acer rubrum) urban planted cultivars and wildtype trees in the southeastern United States.

    Science.gov (United States)

    Lahr, Eleanor C; Dunn, Robert R; Frank, Steven D

    2018-01-01

    Photosynthesis is a fundamental process that trees perform over fluctuating environmental conditions. This study of red maple (Acer rubrum L.) characterizes photosynthesis, stomatal conductance, and water use efficiency in planted cultivars relative to wildtype trees. Red maple is common in cities, yet there is little understanding of how physiological processes affect the long-term growth, condition, and ecosystem services provided by urban trees. In the first year of our study, we measured leaf-level gas exchange and performed short-term temperature curves on urban planted cultivars and on suburban and rural wildtype trees. In the second year, we compared urban planted cultivars and urban wildtype trees. In the first year, urban planted trees had higher maximum rates of photosynthesis and higher overall rates of photosynthesis and stomatal conductance throughout the summer, relative to suburban or rural wildtype trees. Urban planted trees again had higher maximum rates of photosynthesis in the second year. However, urban wildtype trees had higher water use efficiency as air temperatures increased and similar overall rates of photosynthesis, relative to cultivars, in mid and late summer. Our results show that physiological differences between cultivars and wildtype trees may relate to differences in their genetic background and their responses to local environmental conditions, contingent on the identity of the horticultural variety. Overall, our results suggest that wildtype trees should be considered for some urban locations, and our study is valuable in demonstrating how site type and tree type can inform tree planting strategies and improve long-term urban forest sustainability.

  3. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    Directory of Open Access Journals (Sweden)

    von Reumont Björn M

    2010-03-01

    profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

  4. Taï chimpanzees anticipate revisiting high-valued fruit trees from further distances.

    Science.gov (United States)

    Ban, Simone D; Boesch, Christophe; Janmaat, Karline R L

    2014-11-01

    The use of spatio-temporal memory has been argued to increase food-finding efficiency in rainforest primates. However, the exact content of this memory is poorly known to date. This study investigated what specific information from previous feeding visits chimpanzees (Pan troglodytes verus), in Taï National Park, Côte d'Ivoire, take into account when they revisit the same feeding trees. By following five adult females for many consecutive days, we tested from what distance the females directed their travels towards previously visited feeding trees and how previous feeding experiences and fruit tree properties influenced this distance. To exclude the influence of sensory cues, the females' approach distance was measured from their last significant change in travel direction until the moment they entered the tree's maximum detection field. We found that chimpanzees travelled longer distances to trees at which they had previously made food grunts and had rejected fewer fruits compared to other trees. In addition, the results suggest that the chimpanzees were able to anticipate the amount of fruit that they would find in the trees. Overall, our findings are consistent with the hypothesis that chimpanzees act upon a retrieved memory of their last feeding experiences long before they revisit feeding trees, which would indicate a daily use of long-term prospective memory. Further, the results are consistent with the possibility that positive emotional experiences help to trigger prospective memory retrieval in forest areas that are further away and have fewer cues associated with revisited feeding trees.

  5. DETERMINING GEOMETRIC PARAMETERS OF AGRICULTURAL TREES FROM LASER SCANNING DATA OBTAINED WITH UNMANNED AERIAL VEHICLE

    Directory of Open Access Journals (Sweden)

    E. Hadas

    2018-05-01

    Full Text Available The estimation of dendrometric parameters has become an important issue for agriculture planning and for the efficient management of orchards. Airborne Laser Scanning (ALS data is widely used in forestry and many algorithms for automatic estimation of dendrometric parameters of individual forest trees were developed. Unfortunately, due to significant differences between forest and fruit trees, some contradictions exist against adopting the achievements of forestry science to agricultural studies indiscriminately. In this study we present the methodology to identify individual trees in apple orchard and estimate heights of individual trees, using high-density LiDAR data (3200 points/m2 obtained with Unmanned Aerial Vehicle (UAV equipped with Velodyne HDL32-E sensor. The processing strategy combines the alpha-shape algorithm, principal component analysis (PCA and detection of local minima. The alpha-shape algorithm is used to separate tree rows. In order to separate trees in a single row, we detect local minima on the canopy profile and slice polygons from alpha-shape results. We successfully separated 92 % of trees in the test area. 6 % of trees in orchard were not separated from each other and 2 % were sliced into two polygons. The RMSE of tree heights determined from the point clouds compared to field measurements was equal to 0.09 m, and the correlation coefficient was equal to 0.96. The results confirm the usefulness of LiDAR data from UAV platform in orchard inventory.

  6. Determining Geometric Parameters of Agricultural Trees from Laser Scanning Data Obtained with Unmanned Aerial Vehicle

    Science.gov (United States)

    Hadas, E.; Jozkow, G.; Walicka, A.; Borkowski, A.

    2018-05-01

    The estimation of dendrometric parameters has become an important issue for agriculture planning and for the efficient management of orchards. Airborne Laser Scanning (ALS) data is widely used in forestry and many algorithms for automatic estimation of dendrometric parameters of individual forest trees were developed. Unfortunately, due to significant differences between forest and fruit trees, some contradictions exist against adopting the achievements of forestry science to agricultural studies indiscriminately. In this study we present the methodology to identify individual trees in apple orchard and estimate heights of individual trees, using high-density LiDAR data (3200 points/m2) obtained with Unmanned Aerial Vehicle (UAV) equipped with Velodyne HDL32-E sensor. The processing strategy combines the alpha-shape algorithm, principal component analysis (PCA) and detection of local minima. The alpha-shape algorithm is used to separate tree rows. In order to separate trees in a single row, we detect local minima on the canopy profile and slice polygons from alpha-shape results. We successfully separated 92 % of trees in the test area. 6 % of trees in orchard were not separated from each other and 2 % were sliced into two polygons. The RMSE of tree heights determined from the point clouds compared to field measurements was equal to 0.09 m, and the correlation coefficient was equal to 0.96. The results confirm the usefulness of LiDAR data from UAV platform in orchard inventory.

  7. An Efficient Vital Area Identification Method

    International Nuclear Information System (INIS)

    Jung, Woo Sik

    2017-01-01

    A new Vital Area Identification (VAI) method was developed in this study for minimizing the burden of VAI procedure. It was accomplished by performing simplification of sabotage event trees or Probabilistic Safety Assessment (PSA) event trees at the very first stage of VAI procedure. Target sets and prevention sets are calculated from the sabotage fault tree. The rooms in the shortest (most economical) prevention set are selected and protected as vital areas. All physical protection is emphasized to protect these vital areas. All rooms in the protected area, the sabotage of which could lead to core damage, should be incorporated into sabotage fault tree. So, sabotage fault tree development is a very difficult task that requires high engineering costs. IAEA published INFCIRC/225/Rev.5 in 2011 which includes principal international guidelines for the physical protection of nuclear material and nuclear installations. A new efficient VAI method was developed and demonstrated in this study. Since this method drastically reduces VAI problem size, it provides very quick and economical VAI procedure. A consistent and integrated VAI procedure had been developed by taking advantage of PSA results, and more efficient VAI method was further developed in this study by inserting PSA event tree simplification at the initial stage of VAI procedure.

  8. 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.

  9. 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.

  10. 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...

  11. Biotechnology of temperate fruit trees and grapevines.

    Science.gov (United States)

    Laimer, Margit; Mendonça, Duarte; Maghuly, Fatemeh; Marzban, Gorji; Leopold, Stephan; Khan, Mahmood; Balla, Ildiko; Katinger, Hermann

    2005-01-01

    Challenges concerning fruit trees and grapevines as long lived woody perennial crops require adapted biotechnological approaches, if solutions are to be found within a reasonable time frame. These challenges are represented by the need for correct identification of genetic resources, with the foreseen use either in conservation or in breeding programmes. Molecular markers provide most accurate information and will be the major solution for questions about plant breeders rights. Providing healthy planting material and rapid detection of newly introduced pathogens by reliable methods involving serological and molecular biological tools will be a future challenge of increases importance, given the fact that plant material travels freely in the entire European Union. But also new breeding goals and transgenic solutions are part of the biotechnological benefits, e.g. resistance against biotic and abiotic stress factors, modified growth habits, modified nutritional properties and altered processing and storage qualities. The successful characterization of transgenic grapevines and stone fruit trees carrying genes of viral origin in different vectors constructed under ecological consideration, will be presented. Beyond technical feasibility, efficiency of resistance, environmental safety and Intellectual Property Rights, also public acceptance needs consideration and has been addressed in a specific project. The molecular determination of internal quality parameters of food can also be addressed by the use of biotechnological tools. Patient independent detection tools for apple allergens have been developed and should allow to compare fruits from different production systems, sites, and genotypes for their content of health threatening compounds.

  12. Succinct partial sums and fenwick trees

    DEFF Research Database (Denmark)

    Bille, Philip; Christiansen, Anders Roy; Prezza, Nicola

    2017-01-01

    We consider the well-studied partial sums problem in succint space where one is to maintain an array of n k-bit integers subject to updates such that partial sums queries can be efficiently answered. We present two succint versions of the Fenwick Tree – which is known for its simplicity...... and practicality. Our results hold in the encoding model where one is allowed to reuse the space from the input data. Our main result is the first that only requires nk + o(n) bits of space while still supporting sum/update in O(logbn)/O(blogbn) time where 2 ≤ b ≤ log O(1)n. The second result shows how optimal...... time for sum/update can be achieved while only slightly increasing the space usage to nk + o(nk) bits. Beyond Fenwick Trees, the results are primarily based on bit-packing and sampling – making them very practical – and they also allow for simple optimal parallelization....

  13. 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.

  14. 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.

  15. Integrated fault tree development environment

    International Nuclear Information System (INIS)

    Dixon, B.W.

    1986-01-01

    Probabilistic Risk Assessment (PRA) techniques are utilized in the nuclear industry to perform safety analyses of complex defense-in-depth systems. A major effort in PRA development is fault tree construction. The Integrated Fault Tree Environment (IFTREE) is an interactive, graphics-based tool for fault tree design. IFTREE provides integrated building, editing, and analysis features on a personal workstation. The design philosophy of IFTREE is presented, and the interface is described. IFTREE utilizes a unique rule-based solution algorithm founded in artificial intelligence (AI) techniques. The impact of the AI approach on the program design is stressed. IFTREE has been developed to handle the design and maintenance of full-size living PRAs and is currently in use

  16. The Bregman Variational Dual-Tree Framework

    DEFF Research Database (Denmark)

    Amizadeh, Saeed; Thiesson, Bo; Hauskrecht, Milos

    2013-01-01

    where the Euclidean distance quantifies the similarity. In this paper, we extend the VDT framework beyond the Euclidean distance to more general Bregman divergences that include the Euclidean distance as a special case. By exploiting the properties of the general Bregman divergence, we show how the new....... A significant effort to find more efficient solutions to the problem has been made in the literature. One of the state-of-the-art methods that has been recently introduced is the Variational Dual-Tree (VDT) framework. Despite some of its unique features, VDT is currently restricted only to Euclidean spaces...... framework can maintain all the pivotal features of the VDT framework and yet significantly improve its performance in non-Euclidean domains. We apply the proposed framework to different text categorization problems and demonstrate its benefits over the original VDT....

  17. ADVANCES IN THE PROPAGATION OF RAMBUTAN TREE

    Directory of Open Access Journals (Sweden)

    RENATA APARECIDA DE ANDRADE

    2017-12-01

    Full Text Available ABSTRACT The reality of Brazilian fruit farming is demonstrating increasing demand for sustainable information about native and exotic fruit, which can diversify and elevate the efficiency of fruit exploitation. Research on propagation of fruits tree is very important so that it can provide a protocol for suitable multiplication of this fruitful. Due to the great genetic diversity of rambutan plants, it is recommended the use of vegetative propagated plants. This research aimed to evaluate the propagation of rambutan by cuttings, layering and grafting, as well as seed germination and viability without storage. The results of this research indicate that this species can be successfully propagated by layering, grafting and seeds. We also observed that the germination percentage of seeds kept inside the fruits for six days were not influenced by the different substrates used in this experiment.

  18. Interpreting the universal phylogenetic tree

    Science.gov (United States)

    Woese, C. R.

    2000-01-01

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

  19. Columnar apple tree named 'Moonlight'

    OpenAIRE

    Tupý, J. (Jaroslav); Louda, O. (Otto); Zima, J. (Jan)

    2010-01-01

    A new and distinct Malus domestica (Borkh.) apple tree variety is provided which exhibits a columnar tree type, weakly vigorous compact growth, predominant bearing on spurs and V.sub.f-resistance against scab. The new variety yields late maturing, medium-sized, globose-conical to conical fruits having good storage quality. The fruit color is yellow-green to yellow with a partial red to orange blush. The fruits have a yellow-colored firm flesh that is crisp and juicy with a good sweet/sour bal...

  20. Interpreting CNNs via Decision Trees

    OpenAIRE

    Zhang, Quanshi; Yang, Yu; Wu, Ying Nian; Zhu, Song-Chun

    2018-01-01

    This paper presents a method to learn a decision tree to quantitatively explain the logic of each prediction of a pre-trained convolutional neural networks (CNNs). Our method boosts the following two aspects of network interpretability. 1) In the CNN, each filter in a high conv-layer must represent a specific object part, instead of describing mixed patterns without clear meanings. 2) People can explain each specific prediction made by the CNN at the semantic level using a decision tree, i.e....

  1. Usefulness of problem tree, objective tree and logical framework ...

    African Journals Online (AJOL)

    The discussion has led to the conclusion that higher learning institutions are not adequately preparing graduates to face the increasing labor market demands in terms of skills and competitiveness. Having outlined the roots of the problem through the problem tree, the researchers proposed potential strategies to handle the ...

  2. 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).

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

    Science.gov (United States)

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

    2011-01-01

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

  4. Modeling whole-tree carbon assimilation rate using observed transpiration rates and needle sugar carbon isotope ratios.

    Science.gov (United States)

    Hu, Jia; Moore, David J P; Riveros-Iregui, Diego A; Burns, Sean P; Monson, Russell K

    2010-03-01

    *Understanding controls over plant-atmosphere CO(2) exchange is important for quantifying carbon budgets across a range of spatial and temporal scales. In this study, we used a simple approach to estimate whole-tree CO(2) assimilation rate (A(Tree)) in a subalpine forest ecosystem. *We analysed the carbon isotope ratio (delta(13)C) of extracted needle sugars and combined it with the daytime leaf-to-air vapor pressure deficit to estimate tree water-use efficiency (WUE). The estimated WUE was then combined with observations of tree transpiration rate (E) using sap flow techniques to estimate A(Tree). Estimates of A(Tree) for the three dominant tree species in the forest were combined with species distribution and tree size to estimate and gross primary productivity (GPP) using an ecosystem process model. *A sensitivity analysis showed that estimates of A(Tree) were more sensitive to dynamics in E than delta(13)C. At the ecosystem scale, the abundance of lodgepole pine trees influenced seasonal dynamics in GPP considerably more than Engelmann spruce and subalpine fir because of its greater sensitivity of E to seasonal climate variation. *The results provide the framework for a nondestructive method for estimating whole-tree carbon assimilation rate and ecosystem GPP over daily-to weekly time scales.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Semi-Automatic Anatomical Tree Matching for Landmark-Based Elastic Registration of Liver Volumes

    Directory of Open Access Journals (Sweden)

    Klaus Drechsler

    2010-01-01

    Full Text Available One promising approach to register liver volume acquisitions is based on the branching points of the vessel trees as anatomical landmarks inherently available in the liver. Automated tree matching algorithms were proposed to automatically find pair-wise correspondences between two vessel trees. However, to the best of our knowledge, none of the existing automatic methods are completely error free. After a review of current literature and methodologies on the topic, we propose an efficient interaction method that can be employed to support tree matching algorithms with important pre-selected correspondences or after an automatic matching to manually correct wrongly matched nodes. We used this method in combination with a promising automatic tree matching algorithm also presented in this work. The proposed method was evaluated by 4 participants and a CT dataset that we used to derive multiple artificial datasets.

  11. Use of sonic tomography to detect and quantify wood decay in living trees.

    Science.gov (United States)

    Gilbert, Gregory S; Ballesteros, Javier O; Barrios-Rodriguez, Cesar A; Bonadies, Ernesto F; Cedeño-Sánchez, Marjorie L; Fossatti-Caballero, Nohely J; Trejos-Rodríguez, Mariam M; Pérez-Suñiga, José Moises; Holub-Young, Katharine S; Henn, Laura A W; Thompson, Jennifer B; García-López, Cesar G; Romo, Amanda C; Johnston, Daniel C; Barrick, Pablo P; Jordan, Fulvia A; Hershcovich, Shiran; Russo, Natalie; Sánchez, Juan David; Fábrega, Juan Pablo; Lumpkin, Raleigh; McWilliams, Hunter A; Chester, Kathleen N; Burgos, Alana C; Wong, E Beatriz; Diab, Jonathan H; Renteria, Sonia A; Harrower, Jennifer T; Hooton, Douglas A; Glenn, Travis C; Faircloth, Brant C; Hubbell, Stephen P

    2016-12-01

    Field methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes. Living trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness. Sonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees.

  12. Use of sonic tomography to detect and quantify wood decay in living trees1

    Science.gov (United States)

    Gilbert, Gregory S.; Ballesteros, Javier O.; Barrios-Rodriguez, Cesar A.; Bonadies, Ernesto F.; Cedeño-Sánchez, Marjorie L.; Fossatti-Caballero, Nohely J.; Trejos-Rodríguez, Mariam M.; Pérez-Suñiga, José Moises; Holub-Young, Katharine S.; Henn, Laura A. W.; Thompson, Jennifer B.; García-López, Cesar G.; Romo, Amanda C.; Johnston, Daniel C.; Barrick, Pablo P.; Jordan, Fulvia A.; Hershcovich, Shiran; Russo, Natalie; Sánchez, Juan David; Fábrega, Juan Pablo; Lumpkin, Raleigh; McWilliams, Hunter A.; Chester, Kathleen N.; Burgos, Alana C.; Wong, E. Beatriz; Diab, Jonathan H.; Renteria, Sonia A.; Harrower, Jennifer T.; Hooton, Douglas A.; Glenn, Travis C.; Faircloth, Brant C.; Hubbell, Stephen P.

    2016-01-01

    Premise of the study: Field methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes. Methods and Results: Living trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness. Conclusions: Sonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees. PMID:28101433

  13. Jet Substructure Without Trees

    Energy Technology Data Exchange (ETDEWEB)

    Jankowiak, Martin; Larkoski, Andrew J.; /SLAC /Stanford U., ITP

    2011-08-19

    We present an alternative approach to identifying and characterizing jet substructure. An angular correlation function is introduced that can be used to extract angular and mass scales within a jet without reference to a clustering algorithm. This procedure gives rise to a number of useful jet observables. As an application, we construct a top quark tagging algorithm that is competitive with existing methods. In preparation for the LHC, the past several years have seen extensive work on various aspects of collider searches. With the excellent resolution of the ATLAS and CMS detectors as a catalyst, one area that has undergone significant development is jet substructure physics. The use of jet substructure techniques, which probe the fine-grained details of how energy is distributed in jets, has two broad goals. First, measuring more than just the bulk properties of jets allows for additional probes of QCD. For example, jet substructure measurements can be compared against precision perturbative QCD calculations or used to tune Monte Carlo event generators. Second, jet substructure allows for additional handles in event discrimination. These handles could play an important role at the LHC in discriminating between signal and background events in a wide variety of particle searches. For example, Monte Carlo studies indicate that jet substructure techniques allow for efficient reconstruction of boosted heavy objects such as the W{sup {+-}} and Z{sup 0} gauge bosons, the top quark, and the Higgs boson.

  14. 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.

  15. 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.

  16. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    Science.gov (United States)

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  17. Ecophysiology of the internal cycling of nitrogen in deciduous fruit trees

    International Nuclear Information System (INIS)

    Millard, P.

    2005-01-01

    physiology has led to significant improvements in our understanding of cycling of N in trees. It is clear that nitrogen has a very high mobility in the tree and that its initial partitioning to a target organ does not necessarily represent its final destination. Increasing the effectiveness of the recycling of the N already present in the orchard is a basic step to reduce external N inputs. The better understanding of the role of internal tree cycling of N allows a fine tuning of N supply to improve its uptake efficiency and reduce potential losses [it

  18. 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.

  19. A fast BDD algorithm for large coherent fault trees analysis

    International Nuclear Information System (INIS)

    Jung, Woo Sik; Han, Sang Hoon; Ha, Jaejoo

    2004-01-01

    Although a binary decision diagram (BDD) algorithm has been tried to solve large fault trees until quite recently, they are not efficiently solved in a short time since the size of a BDD structure exponentially increases according to the number of variables. Furthermore, the truncation of If-Then-Else (ITE) connectives by the probability or size limit and the subsuming to delete subsets could not be directly applied to the intermediate BDD structure under construction. This is the motivation for this work. This paper presents an efficient BDD algorithm for large coherent systems (coherent BDD algorithm) by which the truncation and subsuming could be performed in the progress of the construction of the BDD structure. A set of new formulae developed in this study for AND or OR operation between two ITE connectives of a coherent system makes it possible to delete subsets and truncate ITE connectives with a probability or size limit in the intermediate BDD structure under construction. By means of the truncation and subsuming in every step of the calculation, large fault trees for coherent systems (coherent fault trees) are efficiently solved in a short time using less memory. Furthermore, the coherent BDD algorithm from the aspect of the size of a BDD structure is much less sensitive to variable ordering than the conventional BDD algorithm

  20. GumTree: Data reduction

    Energy Technology Data Exchange (ETDEWEB)

    Rayner, Hugh [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)]. E-mail: hrz@ansto.gov.au; Hathaway, Paul [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Hauser, Nick [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Fei, Yang [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Franceschini, Ferdi [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Lam, Tony [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    2006-11-15

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

  1. Tree value conversion standards revisited

    Science.gov (United States)

    Paul S. DeBald; Martin E. Dale; Martin E. Dale

    1991-01-01

    Updated tree value conversion standards (TVCS) are presented for 12 important hardwood species of the oak-hickory forest. These updated standards-developed for each species by butt-log grade, merchantable height, and diameter at breast height-reflect the changes in lumber prices and in conversion costs which have occurred since 1976 when the original TVCS were...

  2. Induction of Ordinal Decision Trees

    NARCIS (Netherlands)

    J.C. Bioch (Cor); V. Popova (Viara)

    2003-01-01

    textabstractThis paper focuses on the problem of monotone decision trees from the point of view of the multicriteria decision aid methodology (MCDA). By taking into account the preferences of the decision maker, an attempt is made to bring closer similar research within machine learning and MCDA.

  3. Are there tides within trees?

    Science.gov (United States)

    Fisahn, Joachim

    2018-01-24

    Tree stem diameters and electrical stem potentials exhibit rhythmic variations with periodicities of 24-25 h. Under free-running conditions of constant light or darkness these rhythms were suggested to be mediated by the lunisolar gravitational force. To further unravel the regulation of tree stem diameter dilatations, many of the published time courses of diameter variations were re-evaluated in conjunction with the contemporaneous time courses of the lunisolar tidal acceleration. This was accomplished by application of the Etide program, which estimates, with high temporal resolution, local gravitational changes as a consequence of the diurnal variations of the lunisolar gravitational force due to the orbits and relative positions of Earth, Moon and Sun. In all instances investigated, it was evident that a synchronism exists between the times of the turning points of both the lunisolar tide and stem diameter variations when the direction of extension changes. This finding of synchrony documents that the lunisolar tide is a regulator of the tree stem diameter dilatations. Under the described experimental conditions, rhythms in tree stem diameter dilations and electrical stem potentials are controlled by the lunisolar gravitational acceleration. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Tree improvement and environmental forestry

    Science.gov (United States)

    Warren T. Doolittle

    1971-01-01

    I was invited to talk to you about some of the things tree improvement can do to help our forest environment. Now I do not claim to have a corner on the market for ideas that geneticists can use in our environment, and I know that a number of scholarly papers have been presented previously on this subject.

  5. Eucalyptus as a landscape tree

    Science.gov (United States)

    W. Douglas Hamilton

    1983-01-01

    Ninety-two species of Eucalyptus were evaluated at the University of California re- search station in San Jose. The purpose: to find acceptable new street and park trees. Growth rates and horticultural characteristics were noted. Forty-three species were studied in locations statewide to evaluate site adaptation and landscape usefulness; flooded, cold, dry, saline....

  6. A Distributed Spanning Tree Algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Sven Hauge

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two-way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well...

  7. Trees of Our National Forests.

    Science.gov (United States)

    Forest Service (USDA), Washington, DC.

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

  8. The Trees that surround us

    Science.gov (United States)

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

    2012-04-01

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

  9. Wellhead and tree standards updated

    International Nuclear Information System (INIS)

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

    1996-01-01

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

  10. The Tree of Life Project

    Science.gov (United States)

    Milbrath, Sherry

    2009-01-01

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

  11. GumTree: Data reduction

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  12. 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

  13. Can Children Read Evolutionary Trees?

    Science.gov (United States)

    Ainsworth, Shaaron; Saffer, Jessica

    2013-01-01

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

  14. Top tips from tree tops

    Science.gov (United States)

    Ornes, Stephen

    2018-04-01

    The ability of trees to cool by transporting water from their roots to the leaves has been known for centuries. But as Stephen Ornes discovers, the principles of transpiration are also inspiring innovative techniques to cool vehicles travelling at hypersonic speeds, where unwanted heat is a problem too

  15. A distributed spanning tree algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Svend Hauge

    1988-01-01

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well as comm...

  16. 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

  17. Recent widespread tree growth decline despite increasing atmospheric CO2.

    Science.gov (United States)

    Silva, Lucas C R; Anand, Madhur; Leithead, Mark D

    2010-07-21

    The synergetic effects of recent rising atmospheric CO(2) and temperature are expected to favor tree growth in boreal and temperate forests. However, recent dendrochronological studies have shown site-specific unprecedented growth enhancements or declines. The question of whether either of these trends is caused by changes in the atmosphere remains unanswered because dendrochronology alone has not been able to clarify the physiological basis of such trends. Here we combined standard dendrochronological methods with carbon isotopic analysis to investigate whether atmospheric changes enhanced water use efficiency (WUE) and growth of two deciduous and two coniferous tree species along a 9 degrees latitudinal gradient across temperate and boreal forests in Ontario, Canada. Our results show that although trees have had around 53% increases in WUE over the past century, growth decline (measured as a decrease in basal area increment--BAI) has been the prevalent response in recent decades irrespective of species identity and latitude. Since the 1950s, tree BAI was predominantly negatively correlated with warmer climates and/or positively correlated with precipitation, suggesting warming induced water stress. However, where growth declines were not explained by climate, WUE and BAI were linearly and positively correlated, showing that declines are not always attributable to warming induced stress and additional stressors may exist. Our results show an unexpected widespread tree growth decline in temperate and boreal forests due to warming induced stress but are also suggestive of additional stressors. Rising atmospheric CO2 levels during the past century resulted in consistent increases in water use efficiency, but this did not prevent growth decline. These findings challenge current predictions of increasing terrestrial carbon stocks under climate change scenarios.

  18. Arquitectura de los árboles Tree architecture

    Directory of Open Access Journals (Sweden)

    Francis Hallé

    2010-12-01

    understand what a tree is: this mechanism turns a tree into a colony; «reiterated trees» (RT grow on top of each other the way parasites do. Reiteration means the birth of an entire tree, with trunk, branches and roots. A young RT grows vertically; then, with the help of wood plasticity and a lever, it inclines and turns horizontal, thus becoming more efficient in light capturing. It has been a relevant discovery to find, within a single tree crown, genetic variations from one RT to another: in several species, a tree is a colony of genomes.

  19. International Tree Ring Data Bank (ITRDB)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives. Data include raw treering measurements (most are...

  20. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sö ren; Jarząbek, Michał; Hadrich, Torsten; Michels, Dominik L.; Palubicki, Wojciech

    2017-01-01

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical