Toxicity of Cephalaria species and their individual constituents against Aedes aegypti

USDA-ARS?s Scientific Manuscript database

Crude acetone and ethanol extracts of the aerial parts of 21 Cephalaria species collected from Turkey were investigated for larvicidal and adult topical activity against Aedes aegypti. The ethanol extracts from C. elazigensis var. purpurea, C. anatolica, and C. elmaliensis possessed the highest mort...

Prototype of a computerized scale for the active search for potential organ donors.

PubMed

Ludwig, Érika Fernanda Dos Santos Bezerra; Pereira, Marta Cristiane Alves; Martinez, Yolanda Dora Évora; Mendes, Karina Dal Sasso; Rossaneis, Mariana Angela

2017-09-12

to develop a prototype of a computerized scale for the active search for potential organ and tissue donors. methodological study, with the analysis of 377 electronic medical records of patients who died due to encephalic death or cardiorespiratory arrest in the intensive care units of a tertiary hospital. Among the deaths due to cardiorespiratory arrest, the study aimed to identify factors indicating underreported encephalic death cases. The Acute Physiology and Chronic Health Evaluation II and Sepsis Related Organ Failure Assessment severity indexes were applied in the protocols. Based on this, a scale was built and sent to five experts for assessment of the scale content, and subsequently, it was computerized by using a prototyping model. 34 underreported encephalic death cases were identified in the medical records of patients with cardiorespiratory arrest. Statistically significant differences were found in the Wilcoxon test between the scores of hospital admissions in the intensive care unit and the opening of the encephalic death protocol for both severity indexes. the prototype was effective for identifying potential organ donors, as well as for the identification of the degree of organ dysfunction in patients with encephalic death. desenvolver protótipo de escala informatizada para busca ativa de potenciais doadores de órgãos e tecidos. pesquisa metodológica, com análise de 377 prontuários eletrônicos de pacientes que evoluíram a óbito, por morte encefálica, ou parada cardiorrespiratória, nas unidades de terapia intensiva de hospital terciário. Nos óbitos por parada cardiorrespiratória, buscou-se identificar fatores que indicassem subnotificação de morte encefálica. Nos protocolos, foram aplicados os índices de gravidade Acute Physiology and Chronic Health Evaluation II e Sepsis Related Organ Failure Assessment. A partir disso, construiu-se a escala que foi encaminhada a cinco especialistas, para avaliação de conteúdo, e, posteriormente, foi informatizada por modelo de prototipação. foram identificadas 34 subnotificações de morte encefálica nos prontuários dos casos de parada cardiorrespiratória. O teste de Wilcoxon demonstrou diferença estatisticamente significativa entre os escores de admissão em unidade de terapia intensiva e abertura do protocolo de morte encefálica, para ambos os índices de gravidade. o protótipo foi efetivo para identificação de potenciais doadores, bem como o grau de disfunção orgânica de pacientes em morte encefálica. desarrollar un prototipo de escala informatizada para la búsqueda activa de potenciales donantes de órganos y tejidos. investigación metodológica, con el análisis de 377 registros médicos electrónicos de pacientes, que fallecieron por muerte encefálica o paro cardiorrespiratorio, en las unidades de cuidados intensivos de un hospital terciario. Entre las muertes por paro cardiorrespiratorio, se buscó identificar los factores que indicasen subnotificación de muerte encefálica. Las puntuaciones de los índices de gravedad Acute Physiology and Chronic Health Evaluation II y Sepsis Related Organ Failure Assessment se aplicaron en los protocolos. A partir de eso, la escala fue construida y enviada a cinco expertos para la evaluación del contenido, y posteriormente, fue informatizada mediante un modelo de prototipación. se identificaron 34 casos de subnotificación de muerte encefálica en los registros médicos de los casos de paro cardiorrespiratorio. Se encontraron diferencias estadísticamente significativas en la prueba de Wilcoxon, entre las puntuaciones de los ingresos hospitalarios en unidad de cuidados intensivos y apertura del protocolo de muerte encefálica para ambos índices de gravedad. el prototipo fue eficaz para la identificación de potenciales donantes, así como para la identificación del grado de disfunción orgánica en pacientes con muerte encefálica.

Application Research of Fault Tree Analysis in Grid Communication System Corrective Maintenance

NASA Astrophysics Data System (ADS)

Wang, Jian; Yang, Zhenwei; Kang, Mei

2018-01-01

This paper attempts to apply the fault tree analysis method to the corrective maintenance field of grid communication system. Through the establishment of the fault tree model of typical system and the engineering experience, the fault tree analysis theory is used to analyze the fault tree model, which contains the field of structural function, probability importance and so on. The results show that the fault tree analysis can realize fast positioning and well repairing of the system. Meanwhile, it finds that the analysis method of fault tree has some guiding significance to the reliability researching and upgrading f the system.

Validation of a real-time PCR assay for pseudorabies virus surveillance purposes

USDA-ARS?s Scientific Manuscript database

Pseudorabies virus (PRV) is of significant economic importance for the swine industry worldwide. PRV is the cause of Aujeszky’s disease, also known as pseudorabies. The main symptoms are related to respiratory and nervous systems, which are the preferred site for PRV. Also, PRV can cause a high mort...

Occurrence and Antimicrobial Resistance of Listeria monocytogenes Recovered from Blue Crab Meat and Blue Crab Processing Plants

USDA-ARS?s Scientific Manuscript database

Listeria monocytogenes is widely distributed in the environment. The ubiquitous nature of this bacterium can result in contamination of foods. Listeriosis is a food-borne disease caused by consumption of L. monocytogenes-contaminated food. It is a public health problem of low incidence but high mort...

Evaluation of chopped switchgrass and chopped bermudagrass as litter materials over multiple heavy broiler flocks

USDA-ARS?s Scientific Manuscript database

Chopped switchgrass (SG) and chopped bermudagrass (BG) were evaluated as alternatives to pine shavings (PS) for broiler litter over 3 flocks. Twenty-four pens were filled with the 3 litter types. Live performance parameters included mortality, BW, BW gain, feed consumption, and feed conversion. Mort...

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

PubMed

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

2013-01-01

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

Integrated Approach To Design And Analysis Of Systems

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Product Support Manager Guidebook

DTIC Science & Technology

2011-04-01

package is being developed using supportability analysis concepts such as Failure Mode, Effects and Criticality Analysis (FMECA), Fault Tree Analysis ( FTA ...Analysis (LORA) Condition Based Maintenance + (CBM+) Fault Tree Analysis ( FTA ) Failure Mode, Effects, and Criticality Analysis (FMECA) Maintenance Task...Reporting and Corrective Action System (FRACAS), Fault Tree Analysis ( FTA ), Level of Repair Analysis (LORA), Maintenance Task Analysis (MTA

Terpenoid Variations within and among Half-Sibling Avocado Trees, Persea americana Mill. (Lauraceae)

PubMed Central

Niogret, Jerome; Epsky, Nancy D.; Schnell, Raymond J.; Boza, Edward J.; Kendra, Paul E.; Heath, Robert R.

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees. PMID:24039994

Terpenoid variations within and among half-sibling avocado trees, Persea americana Mill. (Lauraceae).

PubMed

Niogret, Jerome; Epsky, Nancy D; Schnell, Raymond J; Boza, Edward J; Kendra, Paul E; Heath, Robert R

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees.

Fault Tree in the Trenches, A Success Story

NASA Technical Reports Server (NTRS)

Long, R. Allen; Goodson, Amanda (Technical Monitor)

2000-01-01

Getting caught up in the explanation of Fault Tree Analysis (FTA) minutiae is easy. In fact, most FTA literature tends to address FTA concepts and methodology. Yet there seems to be few articles addressing actual design changes resulting from the successful application of fault tree analysis. This paper demonstrates how fault tree analysis was used to identify and solve a potentially catastrophic mechanical problem at a rocket motor manufacturer. While developing the fault tree given in this example, the analyst was told by several organizations that the piece of equipment in question had been evaluated by several committees and organizations, and that the analyst was wasting his time. The fault tree/cutset analysis resulted in a joint-redesign of the control system by the tool engineering group and the fault tree analyst, as well as bragging rights for the analyst. (That the fault tree found problems where other engineering reviews had failed was not lost on the other engineering groups.) Even more interesting was that this was the analyst's first fault tree which further demonstrates how effective fault tree analysis can be in guiding (i.e., forcing) the analyst to take a methodical approach in evaluating complex systems.

Assessment Update: Progress, Trends, and Practices in Higher Education. Volume 24, Issue 2, March-April 2012

ERIC Educational Resources Information Center

Banta, Trudy W., Ed.

2012-01-01

This issue of "Assessment Update" presents the following articles: (1) Mission Accomplished! The Development of a Competence-based E-portfolio Assessment Model (Shelley Schuurman, Scott Berlin, Jamie Langlois, and Julie Guevara); (2) The Third Rail of Assessment--Dangerous but Powerful (Dale L. Mort); (3) Video Killed the Radio…

Patterns and Policies: The Changing Demographics of Foreign Language Instruction. Issues in Language Program Direction: A Series of Annual Volumes.

ERIC Educational Resources Information Center

Liskin-Gasparro, Judith E., Ed.

This collection of papers is divided into three parts. Part 1, "Changing Patterns: Curricular Implications," includes "Basic Assumptions Revisited: Today's French and Spanish Students at a Large Metropolitan University" (Gail Guntermann, Suzanne Hendrickson, and Carmen de Urioste) and "Le Francais et Mort, Vive le…

Distributed Contour Trees

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

Morozov, Dmitriy; Weber, Gunther H.

2014-03-31

Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di erent problems that rely on contour trees can be solved in parallel with minimal communication.

Try Fault Tree Analysis, a Step-by-Step Way to Improve Organization Development.

ERIC Educational Resources Information Center

Spitzer, Dean

1980-01-01

Fault Tree Analysis, a systems safety engineering technology used to analyze organizational systems, is described. Explains the use of logic gates to represent the relationship between failure events, qualitative analysis, quantitative analysis, and effective use of Fault Tree Analysis. (CT)

Utility of tree crown condition indicators to predict tree survival using remeasured Forest Inventory and Analysis data

Treesearch

Randall S. Morin; Jim Steinman; KaDonna C. Randolph

2012-01-01

The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during surveys of Forest Inventory and Analysis (FIA) Phase 3 (P3) plots since 1999. In this study, remeasured data from 39,357 trees in the northern United States were used to assess the probability of survival among various tree species using the...

Systems Theoretic Process Analysis Applied to an Offshore Supply Vessel Dynamic Positioning System

DTIC Science & Technology

2016-06-01

additional safety issues that were either not identified or inadequately mitigated through the use of Fault Tree Analysis and Failure Modes and...Techniques ...................................................................................................... 15 1.3.1. Fault Tree Analysis...49 3.2. Fault Tree Analysis Comparison

Solar and Climate Variation Relationships Analyzed from Chile Tree Ring Width Time Series (1587 - 1994 A.D.)

NASA Astrophysics Data System (ADS)

Rigozo, Nr; Nordemann, Djr; Faria, Hh; Echer, E.; Vieira, Lea; Prestes, A.

This work presents a study of the relations between solar and climate variations during the last four centuries by spectral analysis of tree ring index and sunspot number time series. Trees used for this study were Pilgerodendron cupressoides from Glaciar Pio XI, in Chile. The spectral analysis of tree ring index shows that 11, 22 and 80 year periodicities of the solar cycle were present in this tree ring data with 0.95 confidence level. This result suggests a solar modulation of climate variations, as recorded by the tree ring growth. Short-term variations, between 2 - 7 years, are also present in tree ring data. Therefore spectral analysis clearly shows that both, solar and climate factors, are recorded in the tree ring data.

Fault Tree Analysis: A Research Tool for Educational Planning. Technical Report No. 1.

ERIC Educational Resources Information Center

Alameda County School Dept., Hayward, CA. PACE Center.

This ESEA Title III report describes fault tree analysis and assesses its applicability to education. Fault tree analysis is an operations research tool which is designed to increase the probability of success in any system by analyzing the most likely modes of failure that could occur. A graphic portrayal, which has the form of a tree, is…

Learning from examples - Generation and evaluation of decision trees for software resource analysis

NASA Technical Reports Server (NTRS)

Selby, Richard W.; Porter, Adam A.

1988-01-01

A general solution method for the automatic generation of decision (or classification) trees is investigated. The approach is to provide insights through in-depth empirical characterization and evaluation of decision trees for software resource data analysis. The trees identify classes of objects (software modules) that had high development effort. Sixteen software systems ranging from 3,000 to 112,000 source lines were selected for analysis from a NASA production environment. The collection and analysis of 74 attributes (or metrics), for over 4,700 objects, captured information about the development effort, faults, changes, design style, and implementation style. A total of 9,600 decision trees were automatically generated and evaluated. The trees correctly identified 79.3 percent of the software modules that had high development effort or faults, and the trees generated from the best parameter combinations correctly identified 88.4 percent of the modules on the average.

Repeated measures from FIA data facilitates analysis across spatial scales of tree growth responses to nitrogen deposition from individual trees to whole ecoregions

Treesearch

Charles H. (Hobie) Perry; Kevin J. Horn; R. Quinn Thomas; Linda H. Pardo; Erica A.H. Smithwick; Doug Baldwin; Gregory B. Lawrence; Scott W. Bailey; Sabine Braun; Christopher M. Clark; Mark Fenn; Annika Nordin; Jennifer N. Phelan; Paul G. Schaberg; Sam St. Clair; Richard Warby; Shaun Watmough; Steven S. Perakis

2015-01-01

The abundance of temporally and spatially consistent Forest Inventory and Analysis data facilitates hierarchical/multilevel analysis to investigate factors affecting tree growth, scaling from plot-level to continental scales. Herein we use FIA tree and soil inventories in conjunction with various spatial climate and soils data to estimate species-specific responses of...

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

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

An overview of the phase-modular fault tree approach to phased mission system analysis

NASA Technical Reports Server (NTRS)

Meshkat, L.; Xing, L.; Donohue, S. K.; Ou, Y.

2003-01-01

We look at how fault tree analysis (FTA), a primary means of performing reliability analysis of PMS, can meet this challenge in this paper by presenting an overview of the modular approach to solving fault trees that represent PMS.

Estimating phylogenetic trees from genome-scale data.

PubMed

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.

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

PubMed

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

2017-12-01

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

Economic analysis of emerald ash borer (Coleoptera: Buprestidae) management options.

PubMed

Vannatta, A R; Hauer, R H; Schuettpelz, N M

2012-02-01

Emerald ash borer, Agrilus planipennis (Fairmaire) (Coleoptera: Buprestidae), plays a significant role in the health and extent of management of native North American ash species in urban forests. An economic analysis of management options was performed to aid decision makers in preparing for likely future infestations. Separate ash tree population valuations were derived from the i-Tree Streets program and the Council of Tree and Landscape Appraisers (CTLA) methodology. A relative economic analysis was used to compare a control option (do-nothing approach, only removing ash trees as they die) to three distinct management options: 1) preemptive removal of all ash trees over a 5 yr period, 2) preemptive removal of all ash trees and replacement with comparable nonash trees, or 3) treating the entire population of ash trees with insecticides to minimize mortality. For each valuation and management option, an annual analysis was performed for both the remaining ash tree population and those lost to emerald ash borer. Retention of ash trees using insecticide treatments typically retained greater urban forest value, followed by doing nothing (control), which was better than preemptive removal and replacement. Preemptive removal without tree replacement, which was the least expensive management option, also provided the lowest net urban forest value over the 20-yr simulation. A "no emerald ash borer" scenario was modeled to further serve as a benchmark for each management option and provide a level of economic justification for regulatory programs aimed at slowing the movement of emerald ash borer.

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

PubMed

Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

2014-02-26

Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

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

PubMed

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

2007-04-01

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

Monte Carlo Simulation of Markov, Semi-Markov, and Generalized Semi- Markov Processes in Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

English, Thomas

2005-01-01

A standard tool of reliability analysis used at NASA-JSC is the event tree. An event tree is simply a probability tree, with the probabilities determining the next step through the tree specified at each node. The nodal probabilities are determined by a reliability study of the physical system at work for a particular node. The reliability study performed at a node is typically referred to as a fault tree analysis, with the potential of a fault tree existing.for each node on the event tree. When examining an event tree it is obvious why the event tree/fault tree approach has been adopted. Typical event trees are quite complex in nature, and the event tree/fault tree approach provides a systematic and organized approach to reliability analysis. The purpose of this study was two fold. Firstly, we wanted to explore the possibility that a semi-Markov process can create dependencies between sojourn times (the times it takes to transition from one state to the next) that can decrease the uncertainty when estimating time to failures. Using a generalized semi-Markov model, we studied a four element reliability model and were able to demonstrate such sojourn time dependencies. Secondly, we wanted to study the use of semi-Markov processes to introduce a time variable into the event tree diagrams that are commonly developed in PRA (Probabilistic Risk Assessment) analyses. Event tree end states which change with time are more representative of failure scenarios than are the usual static probability-derived end states.

[Sectional structure of a tree. Model analysis of the vertical biomass distribution].

PubMed

Galitskiĭ, V V

2010-01-01

A model has been proposed for the architecture of a tree in which virtual trees appear rhythmically on the treetop. Each consecutive virtual tree is a part of the previous tree. The difference between two adjacent virtual trees is a section--an element of the real tree structure. In case of a spruce, the section represents a verticil of a stem with the corresponding internode. Dynamics of a photosynthesizing part of the physiologically active biomass of each section differ from the corresponding dynamics of the virtual trees and the whole real tree. If the tree biomass dynamics has a sigma-shaped form, then the section dynamics have to be bell-shaped. It means that the lower stem should accordingly become bare, which is typically observed in nature. Model analysis reveals the limiting, in the age, form of trees to be an "umbrella". It can be observed in nature and is an outcome of physical limitation of the tree height combined with the sigma-shaped form of the tree biomass dynamics. Variation of model parameters provides for various forms of the tree biomass distribution along the height, which can be associated with certain biological species of trees.

Pragmatic and Idiosyncratic Acts in Human Everyday Routines: The Counterpart of Compulsive Rituals

DTIC Science & Technology

2010-03-25

Mort3, and David Eilam1 1Department of Zoology, Tel-Aviv University, Ramat-Aviv 69978, Israel 2Departments of Psychology and Anthropology, Washington...Introduction Repetitive actions are prevalent in normal and abnormal behavior [7]. In normal behavior, repetitive performance takes the form of...unconscious as repository of chronic goals and motives, in: Gollwitzer PM, Bargh JA, Editors. The psychology of action: Linking cognition and

QUELS FUTURS TRAITEMENTS POUR LA DEPENDANCE AU TABAC ET AU CANNABIS?

PubMed Central

LE FOLL, Bernard; JUSTINOVA, Zuzana; TANDA, Gianlugi; GOLDBERG, Steven R.

2009-01-01

RESUME Plus de trois millions de morts sont attribués au tabagisme dans le monde par an, et l’usage de tabac est en progression dans les pays en voie de développement. L’usage de tabac est donc une des rares causes de mortalité qui augmente, avec une prévision de plus de 10 millions de morts par an dans 30–40 ans. Le cannabis ou marijuana est la drogue illicite la plus consommée dans le monde et il n’y a actuellement pas de traitement disponible. Bien que les systèmes dopaminergiques jouent un rôle central dans les effets renforçants des drogues, d’autres systèmes sont impliqués. Nous présentons ici des résultats récents obtenus avec des antagonistes des récepteurs cannabinoides CB1, des récepteurs D3 de la dopamine et des récepteurs opioïdes. Ces antagonistes qui modulent de façon directe ou indirecte la transmission dopaminergique cérébrale représentent des approches prometteuses pour le traitement du tabagisme ou de la dépendance au cannabis. Ces approches sont à valider dans des essais cliniques. PMID:18663981

The process and utility of classification and regression tree methodology in nursing research

PubMed Central

Kuhn, Lisa; Page, Karen; Ward, John; Worrall-Carter, Linda

2014-01-01

Aim This paper presents a discussion of classification and regression tree analysis and its utility in nursing research. Background Classification and regression tree analysis is an exploratory research method used to illustrate associations between variables not suited to traditional regression analysis. Complex interactions are demonstrated between covariates and variables of interest in inverted tree diagrams. Design Discussion paper. Data sources English language literature was sourced from eBooks, Medline Complete and CINAHL Plus databases, Google and Google Scholar, hard copy research texts and retrieved reference lists for terms including classification and regression tree* and derivatives and recursive partitioning from 1984–2013. Discussion Classification and regression tree analysis is an important method used to identify previously unknown patterns amongst data. Whilst there are several reasons to embrace this method as a means of exploratory quantitative research, issues regarding quality of data as well as the usefulness and validity of the findings should be considered. Implications for Nursing Research Classification and regression tree analysis is a valuable tool to guide nurses to reduce gaps in the application of evidence to practice. With the ever-expanding availability of data, it is important that nurses understand the utility and limitations of the research method. Conclusion Classification and regression tree analysis is an easily interpreted method for modelling interactions between health-related variables that would otherwise remain obscured. Knowledge is presented graphically, providing insightful understanding of complex and hierarchical relationships in an accessible and useful way to nursing and other health professions. PMID:24237048

The process and utility of classification and regression tree methodology in nursing research.

PubMed

Kuhn, Lisa; Page, Karen; Ward, John; Worrall-Carter, Linda

2014-06-01

This paper presents a discussion of classification and regression tree analysis and its utility in nursing research. Classification and regression tree analysis is an exploratory research method used to illustrate associations between variables not suited to traditional regression analysis. Complex interactions are demonstrated between covariates and variables of interest in inverted tree diagrams. Discussion paper. English language literature was sourced from eBooks, Medline Complete and CINAHL Plus databases, Google and Google Scholar, hard copy research texts and retrieved reference lists for terms including classification and regression tree* and derivatives and recursive partitioning from 1984-2013. Classification and regression tree analysis is an important method used to identify previously unknown patterns amongst data. Whilst there are several reasons to embrace this method as a means of exploratory quantitative research, issues regarding quality of data as well as the usefulness and validity of the findings should be considered. Classification and regression tree analysis is a valuable tool to guide nurses to reduce gaps in the application of evidence to practice. With the ever-expanding availability of data, it is important that nurses understand the utility and limitations of the research method. Classification and regression tree analysis is an easily interpreted method for modelling interactions between health-related variables that would otherwise remain obscured. Knowledge is presented graphically, providing insightful understanding of complex and hierarchical relationships in an accessible and useful way to nursing and other health professions. © 2013 The Authors. Journal of Advanced Nursing Published by John Wiley & Sons Ltd.

Fault Tree Analysis: Its Implications for Use in Education.

ERIC Educational Resources Information Center

Barker, Bruce O.

This study introduces the concept of Fault Tree Analysis as a systems tool and examines the implications of Fault Tree Analysis (FTA) as a technique for isolating failure modes in educational systems. A definition of FTA and discussion of its history, as it relates to education, are provided. The step by step process for implementation and use of…

Species Composition of Down Dead and Standing Live Trees: Implications for Forest Inventory Analysis

Treesearch

Christopher W. Woodall; Linda Nagel

2005-01-01

The assessment of species composition in most forest inventory analysis relies solely on standing live tree information characterized by current forest type. With the implementation of the third phase of the U.S. Department of Agriculture Forest Service's Forest Inventory and Analysis program, the species composition of down dead trees, otherwise termed coarse...

Adjustments to forest inventory and analysis estimates of 2001 saw-log volumes for Kentucky

Treesearch

Stanley J. Zarnoch; Jeffery A. Turner

2005-01-01

The 2001 Kentucky Forest Inventory and Analysis survey overestimated hardwood saw-log volume in tree grade 1. This occurred because 2001 field crews classified too many trees as grade 1 trees. Data collected by quality assurance crews were used to generate two types of adjustments, one based on the proportion of trees misclassified and the other on the proportion of...

ETE: a python Environment for Tree Exploration.

PubMed

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

2010-01-13

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

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

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

Evolution and devolution of folkbiological knowledge.

PubMed

Wolff, P; Medin, D L; Pankratz, C

1999-12-07

In this paper we present evidence in support of the hypothesis that the average person's knowledge about trees, and about the natural world in general, has declined during the 20th century. Our investigations are based on examination of a large sample of written material from the 16th through 20th centuries contained in the Oxford English Dictionary. In Analysis 1, we show a precipitous decline in the use of tree terms after, but not before, the 19th century. In Analysis 2, we analyze tree terms at different levels of organization and show that the decline observed in Analysis 1 occurs for all levels of organization. This second analysis also reveals that during the 16th to 19th centuries tree terms became progressively more specific, suggesting that during these periods knowledge about trees increased. In Analysis 3, we show similar rates of decline in other folkbiological categories, indicating that the change in tree terms reflects a general decline in knowledge about living kinds. Also in Analysis 3, we show that several non-biological categories have experienced evolution during the 20th century, indicating that the declines in the 20th century for folkbiological categories are not an inevitable outcome of the corpus. Finally, Analysis 4 also shows declines in the frequency of quotations for which the tree term was not the topic of the sentence, and thus incidental to the purposes of the writer. The results from Analysis 4 reassure us that the results from Analyses 1-3 were not solely due to change in the aims and purposes of writers over the centuries. In sum, the analyses indicate that in the domain of trees, there has been a long and sustained period of conceptual evolution followed by a recent pronounced period of devolution.

Phytoscreening with SPME: Variability Analysis.

PubMed

Limmer, Matt A; Burken, Joel G

2015-01-01

Phytoscreening has been demonstrated at a variety of sites over the past 15 years as a low-impact, sustainable tool in delineation of shallow groundwater contaminated with chlorinated solvents. Collection of tree cores is rapid and straightforward, but low concentrations in tree tissues requires sensitive analytics. Solid-phase microextraction (SPME) is amenable to the complex matrix while allowing for solvent-less extraction. Accurate quantification requires the absence of competitive sorption, examined here both in laboratory experiments and through comprehensive examination of field data. Analysis of approximately 2,000 trees at numerous field sites also allowed testing of the tree genus and diameter effects on measured tree contaminant concentrations. Collectively, while these variables were found to significantly affect site-adjusted perchloroethylene (PCE) concentrations, the explanatory power of these effects was small (adjusted R(2) = 0.031). 90th quantile chemical concentrations in trees were significantly reduced by increasing Henry's constant and increasing hydrophobicity. Analysis of replicate tree core data showed no correlation between replicate relative standard deviation (RSD) and wood type or tree diameter, with an overall median RSD of 30%. Collectively, these findings indicate SPME is an appropriate technique for sampling and analyzing chlorinated solvents in wood and that phytoscreening is robust against changes in tree type and diameter.

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

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

Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws.

PubMed

Altaba, Cristian R

2009-01-01

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

PubMed

Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

2012-01-01

The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed Central

2015-01-01

Abstract Trees contribute to enormous plant oil reserves because many trees contain 50%–80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the “proline knot” motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs. PMID:26258573

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed

Cao, Heping

2015-09-01

Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.

Remnant Pachira quinata pasture trees have greater opportunities to self and suffer reduced reproductive success due to inbreeding depression.

PubMed

Rymer, P D; Sandiford, M; Harris, S A; Billingham, M R; Boshier, D H

2015-08-01

Habitat fragmentation is extensive throughout the world, converting natural ecosystems into fragments of varying size, density and connectivity. The potential value of remnant trees in agricultural landscapes as seed sources and in connecting fragments has formed a fertile area of debate. This study contrasted the mating patterns of bat-pollinated Pachira quinata trees in a continuous forest to those in pasture through microsatellite-based paternity analysis of progeny. The breeding system was determined by analysis of pollen tube growth and seed production from controlled pollinations. Fitness of selfed and outcrossed seed was compared by germination and seedling growth. There was more inbreeding within pasture trees (outcrossing=0.828±0.015) compared with forest trees (0.926±0.005). Pasture trees had fewer sires contributing to mating events, but pollen dispersal distances were greater than those in the forest. Paternity analysis showed variation in outcrossing rates among pasture trees with high proportions of external and self pollen sources detected. A leaky self-incompatibility system was found, with self pollen having reduced germination on stigmas and slower growth rate through the style. Controlled pollinations also showed a varied ability to self among trees, which was reflected in the selfing rates among pasture trees shown by the paternity analysis (0-80% selfing). Self pollination resulted in lower seed set, germination and seedling growth compared with outcrossing. While remnant trees in agricultural landscapes are involved in broader mating patterns, they show increased but varied levels of inbreeding, which result in reduced fitness.

Remnant Pachira quinata pasture trees have greater opportunities to self and suffer reduced reproductive success due to inbreeding depression

PubMed Central

Rymer, P D; Sandiford, M; Harris, S A; Billingham, M R; Boshier, D H

2015-01-01

Habitat fragmentation is extensive throughout the world, converting natural ecosystems into fragments of varying size, density and connectivity. The potential value of remnant trees in agricultural landscapes as seed sources and in connecting fragments has formed a fertile area of debate. This study contrasted the mating patterns of bat-pollinated Pachira quinata trees in a continuous forest to those in pasture through microsatellite-based paternity analysis of progeny. The breeding system was determined by analysis of pollen tube growth and seed production from controlled pollinations. Fitness of selfed and outcrossed seed was compared by germination and seedling growth. There was more inbreeding within pasture trees (outcrossing=0.828±0.015) compared with forest trees (0.926±0.005). Pasture trees had fewer sires contributing to mating events, but pollen dispersal distances were greater than those in the forest. Paternity analysis showed variation in outcrossing rates among pasture trees with high proportions of external and self pollen sources detected. A leaky self-incompatibility system was found, with self pollen having reduced germination on stigmas and slower growth rate through the style. Controlled pollinations also showed a varied ability to self among trees, which was reflected in the selfing rates among pasture trees shown by the paternity analysis (0–80% selfing). Self pollination resulted in lower seed set, germination and seedling growth compared with outcrossing. While remnant trees in agricultural landscapes are involved in broader mating patterns, they show increased but varied levels of inbreeding, which result in reduced fitness. PMID:23963342

User’s guide to the collection and analysis of tree cores to assess the distribution of subsurface volatile organic compounds

USGS Publications Warehouse

Vroblesky, Don A.

2008-01-01

Analysis of the volatile organic compound content of tree cores is an inexpensive, rapid, simple approach to examining the distribution of subsurface volatile organic compound contaminants. The method has been shown to detect several volatile petroleum hydrocarbons and chlorinated aliphatic compounds associated with vapor intrusion and ground-water contamination. Tree cores, which are approximately 3 inches long, are obtained by using an increment borer. The cores are placed in vials and sealed. After a period of equilibration, the cores can be analyzed by headspace analysis gas chromatography. Because the roots are exposed to volatile organic compound contamination in the unsaturated zone or shallow ground water, the volatile organic compound concentrations in the tree cores are an indication of the presence of subsurface volatile organic compound contamination. Thus, tree coring can be used to detect and map subsurface volatile organic compound contamination. For comparison of tree-core data at a particular site, it is important to maintain consistent methods for all aspects of tree-core collection, handling, and analysis. Factors affecting the volatile organic compound concentrations in tree cores include the type of volatile organic compound, the tree species, the rooting depth, ground-water chemistry, the depth to the contaminated horizon, concentration differences around the trunk related to variations in the distribution of subsurface volatile organic compounds, concentration differences with depth of coring related to volatilization loss through the bark and possibly other unknown factors, dilution by rain, seasonal influences, sorption, vapor-exchange rates, and within-tree volatile organic compound degradation.

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

PubMed Central

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

Secure Embedded System Design Methodologies for Military Cryptographic Systems

DTIC Science & Technology

2016-03-31

Fault- Tree Analysis (FTA); Built-In Self-Test (BIST) Introduction Secure access-control systems restrict operations to authorized users via methods...failures in the individual software/processor elements, the question of exactly how unlikely is difficult to answer. Fault- Tree Analysis (FTA) has a...Collins of Sandia National Laboratories for years of sharing his extensive knowledge of Fail-Safe Design Assurance and Fault- Tree Analysis

Automated estimation of individual conifer tree height and crown diameter via Two-dimensional spatial wavelet analysis of lidar data

Treesearch

Michael J. Falkowski; Alistair M.S. Smith; Andrew T. Hudak; Paul E. Gessler; Lee A. Vierling; Nicholas L. Crookston

2006-01-01

We describe and evaluate a new analysis technique, spatial wavelet analysis (SWA), to automatically estimate the location, height, and crown diameter of individual trees within mixed conifer open canopy stands from light detection and ranging (lidar) data. Two-dimensional Mexican hat wavelets, over a range of likely tree crown diameters, were convolved with lidar...

Analysis of biweight site chronologies: relative weights of individual trees over time

Treesearch

Kurt H. Riitters

1990-01-01

The relative weights on individual trees in a biweight site chronology can indicate the consistency of tree growth responses to macroclimate and can be the basis for stratifying trees in climate-growth analyses. This was explored with 45 years of ring-width indices for 200 trees from five even-aged jack pine (Pinus hanksiana Lamb.) stands. Average individual-tree...

Forensic Analysis of Compromised Computers

NASA Technical Reports Server (NTRS)

Wolfe, Thomas

2004-01-01

Directory Tree Analysis File Generator is a Practical Extraction and Reporting Language (PERL) script that simplifies and automates the collection of information for forensic analysis of compromised computer systems. During such an analysis, it is sometimes necessary to collect and analyze information about files on a specific directory tree. Directory Tree Analysis File Generator collects information of this type (except information about directories) and writes it to a text file. In particular, the script asks the user for the root of the directory tree to be processed, the name of the output file, and the number of subtree levels to process. The script then processes the directory tree and puts out the aforementioned text file. The format of the text file is designed to enable the submission of the file as input to a spreadsheet program, wherein the forensic analysis is performed. The analysis usually consists of sorting files and examination of such characteristics of files as ownership, time of creation, and time of most recent access, all of which characteristics are among the data included in the text file.

Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

PubMed

Brienen, Roel J W; Zuidema, Pieter A

2005-11-01

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

A Lidar Point Cloud Based Procedure for Vertical Canopy Structure Analysis And 3D Single Tree Modelling in Forest

PubMed Central

Wang, Yunsheng; Weinacker, Holger; Koch, Barbara

2008-01-01

A procedure for both vertical canopy structure analysis and 3D single tree modelling based on Lidar point cloud is presented in this paper. The whole area of research is segmented into small study cells by a raster net. For each cell, a normalized point cloud whose point heights represent the absolute heights of the ground objects is generated from the original Lidar raw point cloud. The main tree canopy layers and the height ranges of the layers are detected according to a statistical analysis of the height distribution probability of the normalized raw points. For the 3D modelling of individual trees, individual trees are detected and delineated not only from the top canopy layer but also from the sub canopy layer. The normalized points are resampled into a local voxel space. A series of horizontal 2D projection images at the different height levels are then generated respect to the voxel space. Tree crown regions are detected from the projection images. Individual trees are then extracted by means of a pre-order forest traversal process through all the tree crown regions at the different height levels. Finally, 3D tree crown models of the extracted individual trees are reconstructed. With further analyses on the 3D models of individual tree crowns, important parameters such as crown height range, crown volume and crown contours at the different height levels can be derived. PMID:27879916

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.

PubMed

Seidel, Dominik

2018-01-01

The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees' growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure-related properties, like tree growth.

Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

Many commercial software tools exist for fault tree analysis (FTA), an accepted method for mitigating risk in systems. The method embedded in the tools identifies a root as use in system components, but when software is identified as a root cause, it does not build trees into the software component. No commercial software tools have been built specifically for development and analysis of software fault trees. Research indicates that the methods of FTA could be applied to software, but the method is not practical without automated tool support. With appropriate automated tool support, software fault tree analysis (SFTA) may be a practical technique for identifying the underlying cause of software faults that may lead to critical system failures. We strive to demonstrate that existing commercial tools for FTA can be adapted for use with SFTA, and that applied to a safety-critical system, SFTA can be used to identify serious potential problems long before integrator and system testing.

Applied Swarm-based medicine: collecting decision trees for patterns of algorithms analysis.

PubMed

Panje, Cédric M; Glatzer, Markus; von Rappard, Joscha; Rothermundt, Christian; Hundsberger, Thomas; Zumstein, Valentin; Plasswilm, Ludwig; Putora, Paul Martin

2017-08-16

The objective consensus methodology has recently been applied in consensus finding in several studies on medical decision-making among clinical experts or guidelines. The main advantages of this method are an automated analysis and comparison of treatment algorithms of the participating centers which can be performed anonymously. Based on the experience from completed consensus analyses, the main steps for the successful implementation of the objective consensus methodology were identified and discussed among the main investigators. The following steps for the successful collection and conversion of decision trees were identified and defined in detail: problem definition, population selection, draft input collection, tree conversion, criteria adaptation, problem re-evaluation, results distribution and refinement, tree finalisation, and analysis. This manuscript provides information on the main steps for successful collection of decision trees and summarizes important aspects at each point of the analysis.

Multicentury Reconstruction of Precipitations (1300-2014) in Eastern Canada from Tree-Ring Width and Carbon and Oxygen Isotopes

NASA Astrophysics Data System (ADS)

Giguère, Claudie; Boucher, Étienne; Bergeron, Yves

2016-04-01

Tree ring series enabling long hydroclimatic reconstructions are scarce in Northeastern America, mostly because most boreal species are rather thermo-dependant. Here we propose a new multi-proxy analysis (tree-ring, δ13C and δ18O) from one of the oldest Thuja occidentalis population in NE America (lake Duparquet, Quebec). These rare precipitation-sensitive, long-living trees (> 800 years) grow on xeric rocky shores and their potential for paleo-hydroclimatic reconstructions (based on ring widths solely) was previously assessed. The objectives of this study are twofold i) to strengthen the hydroclimatic signal of this long tree-ring chronology by adding analysis of stable isotope ratios (δ13C and δ18O) and ii) to reconstruct summer precipitation back to 1300 AD, which will represent, by far, the longest high-resolution hydroclimatic reconstruction in this region. A tree-ring chronology was constructed from 61 trees sampled in standing position. Eleven trees were also sampled to produce pooled carbon and oxygen isotope chronologies (annually resolved) with a replication of five to six trees per year. Signal analysis (correlation between climatic data and proxy values) confirms that growth is positively influenced by spring precipitations (May-June), while δ13C is negatively correlated to summer precipitation (June to August) and positively to June temperature. Adding δ18O analysis will strengthen the signal even more, since wood cellulose should be enriched in δ18O when high evapotranspiration conditions prevail. Based on a multi-proxy approach, a summer precipitation reconstruction was developed and compared to other temperature reconstructions from this region as well as to southernmost hydroclimatic reconstructions (e.g. Cook et al). A preliminary analysis of external and internal forcing is proposed in conclusion.

The weakest t-norm based intuitionistic fuzzy fault-tree analysis to evaluate system reliability.

PubMed

Kumar, Mohit; Yadav, Shiv Prasad

2012-07-01

In this paper, a new approach of intuitionistic fuzzy fault-tree analysis is proposed to evaluate system reliability and to find the most critical system component that affects the system reliability. Here weakest t-norm based intuitionistic fuzzy fault tree analysis is presented to calculate fault interval of system components from integrating expert's knowledge and experience in terms of providing the possibility of failure of bottom events. It applies fault-tree analysis, α-cut of intuitionistic fuzzy set and T(ω) (the weakest t-norm) based arithmetic operations on triangular intuitionistic fuzzy sets to obtain fault interval and reliability interval of the system. This paper also modifies Tanaka et al.'s fuzzy fault-tree definition. In numerical verification, a malfunction of weapon system "automatic gun" is presented as a numerical example. The result of the proposed method is compared with the listing approaches of reliability analysis methods. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

Factors that influence Christmas tree sales

Treesearch

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...

Tutorial: Advanced fault tree applications using HARP

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Urban trees and forests of the Chicago region

Treesearch

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

2013-01-01

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

[Comparison of Discriminant Analysis and Decision Trees for the Detection of Subclinical Keratoconus].

PubMed

Kleinhans, Sonja; Herrmann, Eva; Kohnen, Thomas; Bühren, Jens

2017-08-15

Background Iatrogenic keratectasia is one of the most dreaded complications of refractive surgery. In most cases, keratectasia develops after refractive surgery of eyes suffering from subclinical stages of keratoconus with few or no signs. Unfortunately, there has been no reliable procedure for the early detection of keratoconus. In this study, we used binary decision trees (recursive partitioning) to assess their suitability for discrimination between normal eyes and eyes with subclinical keratoconus. Patients and Methods The method of decision tree analysis was compared with discriminant analysis which has shown good results in previous studies. Input data were 32 eyes of 32 patients with newly diagnosed keratoconus in the contralateral eye and preoperative data of 10 eyes of 5 patients with keratectasia after laser in-situ keratomileusis (LASIK). The control group was made up of 245 normal eyes after LASIK and 12-month follow-up without any signs of iatrogenic keratectasia. Results Decision trees gave better accuracy and specificity than did discriminant analysis. The sensitivity of decision trees was lower than the sensitivity of discriminant analysis. Conclusion On the basis of the patient population of this study, decision trees did not prove to be superior to linear discriminant analysis for the detection of subclinical keratoconus. Georg Thieme Verlag KG Stuttgart · New York.

EDNA: Expert fault digraph analysis using CLIPS

NASA Technical Reports Server (NTRS)

Dixit, Vishweshwar V.

1990-01-01

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

Obesity as a risk factor for developing functional limitation among older adults: A conditional inference tree analysis

USDA-ARS?s Scientific Manuscript database

Objective: To examine the risk factors of developing functional decline and make probabilistic predictions by using a tree-based method that allows higher order polynomials and interactions of the risk factors. Methods: The conditional inference tree analysis, a data mining approach, was used to con...

Aneurysmal subarachnoid hemorrhage prognostic decision-making algorithm using classification and regression tree analysis.

PubMed

Lo, Benjamin W Y; Fukuda, Hitoshi; Angle, Mark; Teitelbaum, Jeanne; Macdonald, R Loch; Farrokhyar, Forough; Thabane, Lehana; Levine, Mitchell A H

2016-01-01

Classification and regression tree analysis involves the creation of a decision tree by recursive partitioning of a dataset into more homogeneous subgroups. Thus far, there is scarce literature on using this technique to create clinical prediction tools for aneurysmal subarachnoid hemorrhage (SAH). The classification and regression tree analysis technique was applied to the multicenter Tirilazad database (3551 patients) in order to create the decision-making algorithm. In order to elucidate prognostic subgroups in aneurysmal SAH, neurologic, systemic, and demographic factors were taken into account. The dependent variable used for analysis was the dichotomized Glasgow Outcome Score at 3 months. Classification and regression tree analysis revealed seven prognostic subgroups. Neurological grade, occurrence of post-admission stroke, occurrence of post-admission fever, and age represented the explanatory nodes of this decision tree. Split sample validation revealed classification accuracy of 79% for the training dataset and 77% for the testing dataset. In addition, the occurrence of fever at 1-week post-aneurysmal SAH is associated with increased odds of post-admission stroke (odds ratio: 1.83, 95% confidence interval: 1.56-2.45, P < 0.01). A clinically useful classification tree was generated, which serves as a prediction tool to guide bedside prognostication and clinical treatment decision making. This prognostic decision-making algorithm also shed light on the complex interactions between a number of risk factors in determining outcome after aneurysmal SAH.

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

PubMed

Blomberg, S

2000-11-01

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

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

PubMed

Chaudhary, Ruchi; Fernández-Baca, David; Burleigh, John Gordon

2015-02-01

MulRF is a platform-independent software package for phylogenetic analysis using multi-copy gene trees. It seeks the species tree that minimizes the Robinson-Foulds (RF) distance to the input trees using a generalization of the RF distance to multi-labeled trees. The underlying generic tree distance measure and fast running time make MulRF useful for inferring phylogenies from large collections of gene trees, in which multiple evolutionary processes as well as phylogenetic error may contribute to gene tree discord. MulRF implements several features for customizing the species tree search and assessing the results, and it provides a user-friendly graphical user interface (GUI) with tree visualization. The species tree search is implemented in C++ and the GUI in Java Swing. MulRF's executable as well as sample datasets and manual are available at http://genome.cs.iastate.edu/CBL/MulRF/, and the source code is available at https://github.com/ruchiherself/MulRFRepo. ruchic@ufl.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Analysis of Wave Velocity Patterns in Black Cherry Trees and its Effect on Internal Decay Detection

Treesearch

Guanghui Li; Xiping Wang; Jan Wiedenbeck; Robert J. Ross

2013-01-01

In this study, we examined stress wave velocity patterns in the cross sections of black cherry trees, developed analytical models of stress wave velocity in sound healthy trees, and then tested the effectiveness of the models as a tool for tree decay diagnosis. Acoustic tomography data of the tree cross sections were collected from 12 black cherry trees at a production...

Analysis of wave velocity patterns in black cherry trees and its effect on internal decay detection

Treesearch

Guanghui Li; Xiping Wang; Hailin Feng; Jan Wiedenbeck; Robert J. Ross

2014-01-01

In this study, we examined stress wave velocity patterns in the cross sections of black cherry trees, developed analytical models of stress wave velocity in sound healthy trees, and then tested the effectiveness of the models as a tool for tree decay diagnosis. Acoustic tomography data of the tree cross sections were collected from 12 black cherry trees at a production...

Testing microdensitometric ability to determine Monterey pine urban tree stress

Treesearch

David J. Nowak; Joe R. McBride

1993-01-01

Microdensitometric analysis of aerial photographs has been used to quantify urban tree stress of deciduous species. A test of this procedure applied to Monterey pine indicates that variations in ground cover beneath urban trees among cities and variations in crown morphology among tree species can limit the ability of microdensitometry to quantify urban tree stress....

Atmospheric carbon reduction by urban trees

Treesearch

David J. Nowak

1993-01-01

Trees, because they sequester atmospheric carbon through their growth process and conserve energy in urban areas, have been suggested as one means to combat increasing levels of atmospheric carbon. Analysis of the urban forest in Oakland, California (21% tree cover), reveals a tree carbon storage level of 11.0 metric tons/hectare. Trees in the area of the 1991 fire in...

Modifying Taper-Derived Merchantable Height Estimates to Account for Tree Characteristics

Treesearch

James A. Westfall

2006-01-01

The U.S. Department of Agriculture Forest Service Northeastern Forest Inventory and Analysis program (NE-FIA) is developing regionwide tree-taper equations. Unlike most previous work on modeling tree form, this effort necessarily includes a wide array of tree species. For some species, branching patterns can produce undesirable tree form that reduces the merchantable...

An analysis of methods for the selection of trees from wild stands

Treesearch

F. Thomas Ledig

1976-01-01

The commonly applied comparison-tree method of selection is analyzed as a form of within-family selection. If environmental variarion among comparison- and select-tree groups, c2, is a relatively small proportion (17 percent or less with 5 comparison trees) of the total variation, comparison-tree selection will result in less...

Improved FTA methodology and application to subsea pipeline reliability design.

PubMed

Lin, Jing; Yuan, Yongbo; Zhang, Mingyuan

2014-01-01

An innovative logic tree, Failure Expansion Tree (FET), is proposed in this paper, which improves on traditional Fault Tree Analysis (FTA). It describes a different thinking approach for risk factor identification and reliability risk assessment. By providing a more comprehensive and objective methodology, the rather subjective nature of FTA node discovery is significantly reduced and the resulting mathematical calculations for quantitative analysis are greatly simplified. Applied to the Useful Life phase of a subsea pipeline engineering project, the approach provides a more structured analysis by constructing a tree following the laws of physics and geometry. Resulting improvements are summarized in comparison table form.

Improved FTA Methodology and Application to Subsea Pipeline Reliability Design

PubMed Central

Lin, Jing; Yuan, Yongbo; Zhang, Mingyuan

2014-01-01

An innovative logic tree, Failure Expansion Tree (FET), is proposed in this paper, which improves on traditional Fault Tree Analysis (FTA). It describes a different thinking approach for risk factor identification and reliability risk assessment. By providing a more comprehensive and objective methodology, the rather subjective nature of FTA node discovery is significantly reduced and the resulting mathematical calculations for quantitative analysis are greatly simplified. Applied to the Useful Life phase of a subsea pipeline engineering project, the approach provides a more structured analysis by constructing a tree following the laws of physics and geometry. Resulting improvements are summarized in comparison table form. PMID:24667681

Comparative analysis of tree classification models for detecting fusarium oxysporum f. sp cubense (TR4) based on multi soil sensor parameters

NASA Astrophysics Data System (ADS)

Estuar, Maria Regina Justina; Victorino, John Noel; Coronel, Andrei; Co, Jerelyn; Tiausas, Francis; Señires, Chiara Veronica

2017-09-01

Use of wireless sensor networks and smartphone integration design to monitor environmental parameters surrounding plantations is made possible because of readily available and affordable sensors. Providing low cost monitoring devices would be beneficial, especially to small farm owners, in a developing country like the Philippines, where agriculture covers a significant amount of the labor market. This study discusses the integration of wireless soil sensor devices and smartphones to create an application that will use multidimensional analysis to detect the presence or absence of plant disease. Specifically, soil sensors are designed to collect soil quality parameters in a sink node from which the smartphone collects data from via Bluetooth. Given these, there is a need to develop a classification model on the mobile phone that will report infection status of a soil. Though tree classification is the most appropriate approach for continuous parameter-based datasets, there is a need to determine whether tree models will result to coherent results or not. Soil sensor data that resides on the phone is modeled using several variations of decision tree, namely: decision tree (DT), best-fit (BF) decision tree, functional tree (FT), Naive Bayes (NB) decision tree, J48, J48graft and LAD tree, where decision tree approaches the problem by considering all sensor nodes as one. Results show that there are significant differences among soil sensor parameters indicating that there are variances in scores between the infected and uninfected sites. Furthermore, analysis of variance in accuracy, recall, precision and F1 measure scores from tree classification models homogeneity among NBTree, J48graft and J48 tree classification models.

Report of the Working Group on Aerodynamics of Aircraft Afterbody.

DTIC Science & Technology

1986-06-01

14 I 21 2.1.71 Addy A.L. Experimeftal-Theoretical Correlation of Supersonic Jet-on Base Pressure for Cylindrical Afterbodies. J. Aircraft, Vol. 7, No...An Improved Experimental-Theoretical Base Pressure Cor- Addy A.L. relation for Conical and Cylindrical Afterbodies with Agrell J. Centered Propulsive...2.1.92 Carri~re P. Effet d’une Injection de Fluide dans l’Eau-Morte sur les Conditions de Recollement d’un Ecoulement Plan Supersonique. Comptes

International Symposium on Halide Glasses (2nd) (Extended Abstracts).

DTIC Science & Technology

1983-08-05

of these materials. It is hoped that the atmosphere of the 1st Symposium will be maintained at the 2nd Symposium. The meeting will be held in a...purification of HfF4 and ZrFo by sublimation in a hydrogen fluoride atmosphere and purification of individual components and glasses by reactive atmosphere ...Tregoat and G. Fonteneau, U. Rennes, Rennes, France Reactive atmosphere processing developed by Mort Robinson at Hughes Research Labs. for the

Soldier-Based Assessment of a Dual-Row Tactor Display during Simultaneous Navigational and Robot-Monitoring Tasks

DTIC Science & Technology

2015-08-01

Navigational and Robot -Monitoring Tasks by Gina Pomranky-Hartnett, Linda R Elliott, Bruce JP Mortimer, Greg R Mort, Rodger A Pettitt, and Gary A...Tactor Display during Simultaneous Navigational and Robot -Monitoring Tasks by Gina Pomranky-Hartnett, Linda R Elliott, and Rodger A Pettitt...2014–31 March 2015 4. TITLE AND SUBTITLE Soldier-Based Assessment of a Dual-Row Tactor Display during Simultaneous Navigational and Robot -Monitoring

Long-term growth decline in Toona ciliata in a moist tropical forest in Bangladesh: Impact of global warming

NASA Astrophysics Data System (ADS)

Rahman, Mizanur; Islam, Rofiqul; Islam, Mahmuda

2017-04-01

Tropical forests are carbon rich ecosystems and small changes in tropical forest tree growth substantially influence the global carbon cycle. Forest monitoring studies report inconsistent growth changes in tropical forest trees over the past decades. Most of the studies highlighted changes in the forest level carbon gain, neglecting the species-specific growth changes which ultimately determine community-level responses. Tree-ring analysis can provide historical data on species-specific tree growth with annual resolution. Such studies are inadequate in Bangladesh, which is one of the most climate sensitive regions in the tropics. In this study, we investigated long-term growth rates of Toona ciliata in a moist tropical forest of Bangladesh by using tree-ring analysis. We sampled 50 trees of varying size, obtained increment cores from these trees and measured tree-ring width. Analyses of growth patterns revealed size-dependent growth increments. After correcting for the effect of tree size on tree growth (ontogenetic changes) by two different methods we found declining growth rates in T. ciliata from 1960 to 2013. Standardized ring-width index (RWI) was strongly negatively correlated with annual mean and maximum temperatures suggesting that rising temperature might cause the observed growth decline in T. ciliata. Assuming that global temperatures will rise at the current rate, the observed growth decline is assumed to continue. The analysis of stable carbon and oxygen isotopes may reveal more insight on the physiological response of this species to future climatic changes.

Building the Forest Inventory and Analysis Tree-Ring Data set

Treesearch

Robert J. DeRose; John D. Shaw; James N. Long

2017-01-01

The Interior West Forest Inventory and Analysis (IW-FIA) program measures forestland conditions at great extent with relatively high spatial resolution, including the collection of tree-ring data. We describe the development of an unprecedented spatial tree-ring data set for the IW-FIA that enhances the baseline plot data by incorporating ring-width increment measured...

Acoustic tomography for decay detection in red oak trees

Treesearch

Xiping Wang; R. Bruce Allison; Lihai Wang; Robert J. Ross

2007-01-01

The science of tree stability analysis uses both biological and engineering principles in attempting to rate a tree’s structural soundness and make reasonable predictions of potential for failure. In such analysis, arborists are often challenged by internal structural defects hidden from view within the trunks. This paper reports the results of an investigation using...

Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

PubMed

Barazani, Oz; Keren-Keiserman, Alexandra; Westberg, Erik; Hanin, Nir; Dag, Arnon; Ben-Ari, Giora; Fragman-Sapir, Ori; Tugendhaft, Yizhar; Kerem, Zohar; Kadereit, Joachim W

2016-12-13

Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these represent wild var. sylvestris. Leaf samples were collected from a total of 205 trees at six sites of naturally growing olive populations in Israel. The genetic analysis included a multi-locus lineage (MLL) analysis, Rousset's genetic distances, Fst values, private alleles, other diversity values and a Structure analysis. The analyses also included scions and suckers of old cultivated olive trees, for which the dominance of one clone in scions (MLL1) and a second in suckers (MLL7) had been shown earlier. The majority of trees from a Judean Mts. population and from one population from the Galilee showed close genetic similarity to scions of old cultivated trees. Different from that, site-specific and a high number of single occurrence MLLs were found in four olive populations from the Galilee and Carmel which also were genetically more distant from old cultivated trees, had relatively high genetic diversity values and higher numbers of private alleles. Whereas in two of these populations MLL7 (and partly MLL1) were found in low frequency, the two other populations did not contain these MLLs and were very similar in their genetic structure to suckers of old cultivated olive trees that originated from sexual reproduction. The genetic distinctness from old cultivated olive trees, particularly of one population from Galilee and one from Carmel, suggests that trees at these sites might represent wild var. sylvestris. The similarity in genetic structure of these two populations with the suckers of old cultivated trees implies that wild trees were used as rootstocks. Alternatively, trees at these two sites may be remnants of old cultivated trees in which the scion-derived trunk died and was replaced by suckers. However, considering landscape and topographic environment at the two sites this second interpretation is less likely.

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

PubMed

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

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Slower phloem transport in gymnosperm trees can be attributed to higher sieve element resistance.

PubMed

Liesche, Johannes; Windt, Carel; Bohr, Tomas; Schulz, Alexander; Jensen, Kaare H

2015-04-01

In trees, carbohydrates produced in photosynthesizing leaves are transported to roots and other sink organs over distances of up to 100 m inside a specialized transport tissue, the phloem. Angiosperm and gymnosperm trees have a fundamentally different phloem anatomy with respect to cell size, shape and connectivity. Whether these differences have an effect on the physiology of carbohydrate transport, however, is not clear. A meta-analysis of the experimental data on phloem transport speed in trees yielded average speeds of 56 cm h(-1) for angiosperm trees and 22 cm h(-1) for gymnosperm trees. Similar values resulted from theoretical modeling using a simple transport resistance model. Analysis of the model parameters clearly identified sieve element (SE) anatomy as the main factor for the significantly slower carbohydrate transport speed inside the phloem in gymnosperm compared with angiosperm trees. In order to investigate the influence of SE anatomy on the hydraulic resistance, anatomical data on SEs and sieve pores were collected by transmission electron microscopy analysis and from the literature for 18 tree species. Calculations showed that the hydraulic resistance is significantly higher in the gymnosperm than in angiosperm trees. The higher resistance is only partially offset by the considerably longer SEs of gymnosperms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Dissecting the space-time structure of tree-ring datasets using the partial triadic analysis.

PubMed

Rossi, Jean-Pierre; Nardin, Maxime; Godefroid, Martin; Ruiz-Diaz, Manuela; Sergent, Anne-Sophie; Martinez-Meier, Alejandro; Pâques, Luc; Rozenberg, Philippe

2014-01-01

Tree-ring datasets are used in a variety of circumstances, including archeology, climatology, forest ecology, and wood technology. These data are based on microdensity profiles and consist of a set of tree-ring descriptors, such as ring width or early/latewood density, measured for a set of individual trees. Because successive rings correspond to successive years, the resulting dataset is a ring variables × trees × time datacube. Multivariate statistical analyses, such as principal component analysis, have been widely used for extracting worthwhile information from ring datasets, but they typically address two-way matrices, such as ring variables × trees or ring variables × time. Here, we explore the potential of the partial triadic analysis (PTA), a multivariate method dedicated to the analysis of three-way datasets, to apprehend the space-time structure of tree-ring datasets. We analyzed a set of 11 tree-ring descriptors measured in 149 georeferenced individuals of European larch (Larix decidua Miller) during the period of 1967-2007. The processing of densitometry profiles led to a set of ring descriptors for each tree and for each year from 1967-2007. The resulting three-way data table was subjected to two distinct analyses in order to explore i) the temporal evolution of spatial structures and ii) the spatial structure of temporal dynamics. We report the presence of a spatial structure common to the different years, highlighting the inter-individual variability of the ring descriptors at the stand scale. We found a temporal trajectory common to the trees that could be separated into a high and low frequency signal, corresponding to inter-annual variations possibly related to defoliation events and a long-term trend possibly related to climate change. We conclude that PTA is a powerful tool to unravel and hierarchize the different sources of variation within tree-ring datasets.

Analysis of growth trend changes for 51 temperate tree species using Korea national forest inventory data

NASA Astrophysics Data System (ADS)

Park, M.; Moon, M.; Park, J.; Cho, S.; Kim, H. S.

2016-12-01

Individual tree growth rates can be affected by various factors such as species, soil fertility, stand development stage, disturbance, and climate etc. To estimate the effect of changes in tree growth rate on the structure and functionality of forest ecosystem in the future, we analyzed the change of species-specific growth trends using the fifth Korea national forest inventory data, which was collected from 2006 to 2010. The ring samples of average tree were collected from nationwide inventory plots and the total number of individual tree ring series was 69,128 covering 185 tree species. Among those, fifty one species with more than 100 tree ring series were used for our analysis. For growth-trend analysis, standardized regional curves of individual species growth were generated from three forest zone in South Korea; subarctic, cool temperate, warm temperate forest zone. Then individual tree ring series was indexed by dividing the growth of the tree by expected growth from standardized regional curves. Then the ratio of all tree ring series were aligned by year and the Spearman's correlation coefficient of each species was calculated. The results show that most of species had increasing growth rates as forests developed after Korean war. For the last thirty years, 67.3% of species including Quercus spp. and Zelkova serrata had positive growth trends, on the other hand, 11.5% of species including Pinus spp. showed negative growth trends probably due to the changes in successional stages in Korean forests and climate change. These trends also vary with climate zone and species. For examples, Pinus densiflora, which showed negative growth trend overall, had steep negative growth trends in boreal and temperate zone, whereas it showed no specific trend in sub-tropical climate zone. Our trend analysis on 51 temperate tree species growth will be essential to predict the temperate forests species change for the this century.

Northern Mountain and Prairie Community Tree Guide

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.E. Maco; Q. Xiao; P.J. Hoefer

2003-01-01

This tree guide quantifies benefits and costs for typical large-, medium-, small-stature, deciduous trees, as well as a conifer. The analysis assumed that trees were planted in a residential yard site or a public (street/park) site, under a 40-year time frame, and having a 60% survival rate. Tree care costs were based on findings from a survey of municipal and...

Using specific volume increment (SVI) for quantifying growth responses in trees - theoretical and practical considerations

Treesearch

Eddie Bevilacqua

2002-01-01

Comparative analysis of growth responses among trees following natural or anthropogenic disturbances is often confounded when comparing trees of different size because of the high correlation between growth and initial tree size: large trees tend to have higher absolute grow rates. Relative growth rate (RGR) may not be the most suitable size-dependent measure of growth...

Analysis of Market Factors Associatedwith Sales of Cut Natural Christmas Trees

Treesearch

Lawrence D. Garrett

1977-01-01

A study of the market performance of natural Christmas tree retailers in Winston-Salem, North Carolins, revealed that success was strongly related to location in active retail shopping areas. Christmas tree retailers in shopping centers or areas high in retail sales sold more trees, received a higher average price, and had fewer trees left unsold than retailers in...

Fault Tree Analysis: A Bibliography

NASA Technical Reports Server (NTRS)

2000-01-01

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

A New Approach to Strategy Formulation: Opening the Black Box.

ERIC Educational Resources Information Center

Boyd, Lynn; Gupta, Mahesh; Sussman, Lyle

2001-01-01

An approach to teaching business strategy formulation uses the thinking process tools of the theory of constraints: current reality tree for situational analysis, evaporating cloud and future reality tree to identify change outcomes, and prerequisite tree and transition tree to identify implementation strategies. (SK)

Real-Time and Delayed Analysis of Tree and Shrub Cores as Indicators of Subsurface Volatile Organic Compound Contamination, Durham Meadows Superfund Site, Durham, Connecticut, August 29, 2006

USGS Publications Warehouse

Vroblesky, Don A.; Willey, Richard E.; Clifford, Scott; Murphy, James J.

2008-01-01

This study examined volatile organic compound concentrations in cores from trees and shrubs for use as indicators of vadose-zone contamination or potential vapor intrusion by volatile organic compounds into buildings at the Durham Meadows Superfund Site, Durham, Connecticut. The study used both (1) real-time tree- and shrub-core analysis, which involved field heating the core samples for 5 to 10 minutes prior to field analysis, and (2) delayed analysis, which involved allowing the gases in the cores to equilibrate with the headspace gas in the sample vials unheated for 1 to 2 days prior to analysis. General correspondence was found between the two approaches, indicating that preheating and field analysis of vegetation cores is a viable approach to real-time monitoring of subsurface volatile organic compounds. In most cases, volatile organic compounds in cores from trees and shrubs at the Merriam Manufacturing Company property showed a general correspondence to the distribution of volatile organic compounds detected in a soil-gas survey, despite the fact that most of the soil-gas survey data in close proximity to the relevant trees were collected about 3 years prior to the tree-core collection. Most of the trees cored at the Durham Meadows Superfund Site, outside of the Merriam Manufacturing Company property, contained no volatile organic compounds and were in areas where indoor air sampling and soil-gas sampling showed little or no volatile organic compound concentrations. An exception was tree DM11, which contained barely detectable concentrations of trichloroethene near a house where previous investigations found low concentrations of trichloroethene (0.13 to 1.2 parts per billion by volume) in indoor air and 7.7 micrograms per liter of trichloroethene in the ground water. The barely detectable concentration of trichloroethene in tree DM11 and the lack of volatile organic compound detection in nearby tree DM10 (adjacent to the well having 7.7 micrograms of trichloroethene) may be attributable to the relatively large depth to water (17.6 feet), the relatively low soil-vapor trichloroethene concentration, and the large amount of rainfall during and preceding the tree-coring event. The data indicate that real-time and delayed analyses of tree cores are viable approaches to examining subsurface volatile organic compound soil-gas or vadose-zone contamination at the Durham Meadows Superfund Site and other similar sites. Thus, the methods may have application for determining the potential for vapor intrusion into buildings.

Probabilistic fault tree analysis of a radiation treatment system.

PubMed

Ekaette, Edidiong; Lee, Robert C; Cooke, David L; Iftody, Sandra; Craighead, Peter

2007-12-01

Inappropriate administration of radiation for cancer treatment can result in severe consequences such as premature death or appreciably impaired quality of life. There has been little study of vulnerable treatment process components and their contribution to the risk of radiation treatment (RT). In this article, we describe the application of probabilistic fault tree methods to assess the probability of radiation misadministration to patients at a large cancer treatment center. We conducted a systematic analysis of the RT process that identified four process domains: Assessment, Preparation, Treatment, and Follow-up. For the Preparation domain, we analyzed possible incident scenarios via fault trees. For each task, we also identified existing quality control measures. To populate the fault trees we used subjective probabilities from experts and compared results with incident report data. Both the fault tree and the incident report analysis revealed simulation tasks to be most prone to incidents, and the treatment prescription task to be least prone to incidents. The probability of a Preparation domain incident was estimated to be in the range of 0.1-0.7% based on incident reports, which is comparable to the mean value of 0.4% from the fault tree analysis using probabilities from the expert elicitation exercise. In conclusion, an analysis of part of the RT system using a fault tree populated with subjective probabilities from experts was useful in identifying vulnerable components of the system, and provided quantitative data for risk management.

A framework for sensitivity analysis of decision trees.

PubMed

Kamiński, Bogumił; Jakubczyk, Michał; Szufel, Przemysław

2018-01-01

In the paper, we consider sequential decision problems with uncertainty, represented as decision trees. Sensitivity analysis is always a crucial element of decision making and in decision trees it often focuses on probabilities. In the stochastic model considered, the user often has only limited information about the true values of probabilities. We develop a framework for performing sensitivity analysis of optimal strategies accounting for this distributional uncertainty. We design this robust optimization approach in an intuitive and not overly technical way, to make it simple to apply in daily managerial practice. The proposed framework allows for (1) analysis of the stability of the expected-value-maximizing strategy and (2) identification of strategies which are robust with respect to pessimistic/optimistic/mode-favoring perturbations of probabilities. We verify the properties of our approach in two cases: (a) probabilities in a tree are the primitives of the model and can be modified independently; (b) probabilities in a tree reflect some underlying, structural probabilities, and are interrelated. We provide a free software tool implementing the methods described.

Descriptive statistics of tree crown condition in the Southern United States and impacts on data analysis and interpretation

Treesearch

KaDonna C. Randolph

2006-01-01

The U.S. Department of Agriculture Forest Service, Forest Inventory and Analysis Program (FIA) utilizes visual assessments of tree crown condition to monitor changes and trends in forest health. This report describes and discusses distributions of three FIA crown condition indicators (crown density, crown dieback, and foliage transparency) for trees in the Southern...

New Tree-Classification System Used by the Southern Forest Inventory and Analysis Unit

Treesearch

Dennis M. May; John S. Vissage; D. Vince Few

1990-01-01

Trees at USDA Forest Service, Southern Forest Inventory and Analysis, sample locations are classified as growing stock or cull based on their ability to produce sawlogs. The old and new classification systems are compared, and the impacts of the new system on the reporting of tree volumes are illustrated with inventory data from north Alabama.

Fault Tree Analysis: An Operations Research Tool for Identifying and Reducing Undesired Events in Training.

ERIC Educational Resources Information Center

Barker, Bruce O.; Petersen, Paul D.

This paper explores the fault-tree analysis approach to isolating failure modes within a system. Fault tree investigates potentially undesirable events and then looks for failures in sequence that would lead to their occurring. Relationships among these events are symbolized by AND or OR logic gates, AND used when single events must coexist to…

Urban forest assessment in northern Delaware

Treesearch

David J. Nowak; Robert E. Hoehn; Jun Wang; Andy Lee; Vikram Krishnamurthy; Gary Schwetz

2009-01-01

Presents results of an analysis of the urban forest of the Wilmington, Delaware, the metropolitan corridor in New Castle County (NCC), and Rattlesnake Run sewershed in the city of Wilmington using the Urban Forest Effects (UFORE) model. This analysis reveals that there are about 882,700 trees (19.3 percent tree cover) in the NCC metro corridor and about 136,000 trees (...

Evidential Networks for Fault Tree Analysis with Imprecise Knowledge

NASA Astrophysics Data System (ADS)

Yang, Jianping; Huang, Hong-Zhong; Liu, Yu; Li, Yan-Feng

2012-06-01

Fault tree analysis (FTA), as one of the powerful tools in reliability engineering, has been widely used to enhance system quality attributes. In most fault tree analyses, precise values are adopted to represent the probabilities of occurrence of those events. Due to the lack of sufficient data or imprecision of existing data at the early stage of product design, it is often difficult to accurately estimate the failure rates of individual events or the probabilities of occurrence of the events. Therefore, such imprecision and uncertainty need to be taken into account in reliability analysis. In this paper, the evidential networks (EN) are employed to quantify and propagate the aforementioned uncertainty and imprecision in fault tree analysis. The detailed conversion processes of some logic gates to EN are described in fault tree (FT). The figures of the logic gates and the converted equivalent EN, together with the associated truth tables and the conditional belief mass tables, are also presented in this work. The new epistemic importance is proposed to describe the effect of ignorance degree of event. The fault tree of an aircraft engine damaged by oil filter plugs is presented to demonstrate the proposed method.

DIF Trees: Using Classification Trees to Detect Differential Item Functioning

ERIC Educational Resources Information Center

Vaughn, Brandon K.; Wang, Qiu

2010-01-01

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

City of Minneapolis, Minnesota Municipal Tree Resource Analysis

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.E. Maco; S.L. Gardner; K.E. Vargas; S. Cozad; Q. Xiao

2005-01-01

Minneapolis, a vibrant city, renowned for its lakes, its livability, and its cultural wealth, maintains trees as an integral component of the urban infrastructure. Research indicates that healthy trees can mitigate impacts associated with the built environment by reducing stormwater runoff, energy consumption, and air pollutants. Trees improve urban life, making...

Stereotaxic 18F-FDG PET and MRI templates with three-dimensional digital atlas for statistical parametric mapping analysis of tree shrew brain.

PubMed

Huang, Qi; Nie, Binbin; Ma, Chen; Wang, Jing; Zhang, Tianhao; Duan, Shaofeng; Wu, Shang; Liang, Shengxiang; Li, Panlong; Liu, Hua; Sun, Hua; Zhou, Jiangning; Xu, Lin; Shan, Baoci

2018-01-01

Tree shrews are proposed as an alternative animal model to nonhuman primates due to their close affinity to primates. Neuroimaging techniques are widely used to study brain functions and structures of humans and animals. However, tree shrews are rarely applied in neuroimaging field partly due to the lack of available species specific analysis methods. In this study, 10 PET/CT and 10 MRI images of tree shrew brain were used to construct PET and MRI templates; based on histological atlas we reconstructed a three-dimensional digital atlas with 628 structures delineated; then the digital atlas and templates were aligned into a stereotaxic space. Finally, we integrated the digital atlas and templates into a toolbox for tree shrew brain spatial normalization, statistical analysis and results localization. We validated the feasibility of the toolbox by simulated data with lesions in laterodorsal thalamic nucleus (LD). The lesion volumes of simulated PET and MRI images were (12.97±3.91)mm 3 and (7.04±0.84)mm 3 . Statistical results at p<0.005 showed the lesion volumes of PET and MRI were 13.18mm 3 and 8.06mm 3 in LD. To our knowledge, we report the first PET template and digital atlas of tree shrew brain. Compared to the existing MRI templates, our MRI template was aligned into stereotaxic space. And the toolbox is the first software dedicated for tree shrew brain analysis. The templates and digital atlas of tree shrew brain, as well as the toolbox, facilitate the use of tree shrews in neuroimaging field. Copyright © 2017 Elsevier B.V. All rights reserved.

The value of decision tree analysis in planning anaesthetic care in obstetrics.

PubMed

Bamber, J H; Evans, S A

2016-08-01

The use of decision tree analysis is discussed in the context of the anaesthetic and obstetric management of a young pregnant woman with joint hypermobility syndrome with a history of insensitivity to local anaesthesia and a previous difficult intubation due to a tongue tumour. The multidisciplinary clinical decision process resulted in the woman being delivered without complication by elective caesarean section under general anaesthesia after an awake fibreoptic intubation. The decision process used is reviewed and compared retrospectively to a decision tree analytical approach. The benefits and limitations of using decision tree analysis are reviewed and its application in obstetric anaesthesia is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE

PubMed Central

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

2013-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a ‘species tree’. PMID:22399455

Looking for trees in the forest: summary tree from posterior samples

PubMed Central

2013-01-01

Background Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. Results We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the “truth”, i.e to the tree used to generate the sequences. Conclusions Our simulations indicate that no single method is “best”. Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree. PMID:24093883

Looking for trees in the forest: summary tree from posterior samples.

PubMed

Heled, Joseph; Bouckaert, Remco R

2013-10-04

Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the "truth", i.e to the tree used to generate the sequences. Our simulations indicate that no single method is "best". Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree.

The Dynamics of Germinal Centre Selection as Measured by Graph-Theoretical Analysis of Mutational Lineage Trees

PubMed Central

Dunn-Walters, Deborah K.; Belelovsky, Alex; Edelman, Hanna; Banerjee, Monica; Mehr, Ramit

2002-01-01

We have developed a rigorous graph-theoretical algorithm for quantifying the shape properties of mutational lineage trees. We show that information about the dynamics of hypermutation and antigen-driven clonal selection during the humoral immune response is contained in the shape of mutational lineage trees deduced from the responding clones. Age and tissue related differences in the selection process can be studied using this method. Thus, tree shape analysis can be used as a means of elucidating humoral immune response dynamics in various situations. PMID:15144020

Evidence of solar activity and El Niño signals in tree rings of Araucaria araucana and A. angustifolia in South America

NASA Astrophysics Data System (ADS)

Perone, A.; Lombardi, F.; Marchetti, M.; Tognetti, R.; Lasserre, B.

2016-10-01

Tree rings reveal climatic variations through years, but also the effect of solar activity in influencing the climate on a large scale. In order to investigate the role of solar cycles on climatic variability and to analyse their influences on tree growth, we focused on tree-ring chronologies of Araucaria angustifolia and Araucaria araucana in four study areas: Irati and Curitiba in Brazil, Caviahue in Chile, and Tolhuaca in Argentina. We obtained an average tree-ring chronology of 218, 117, 439, and 849 years for these areas, respectively. Particularly, the older chronologies also included the period of the Maunder and Dalton minima. To identify periodicities and trends observable in tree growth, the time series were analysed using spectral, wavelet and cross-wavelet techniques. Analysis based on the Multitaper method of annual growth rates identified 2 cycles with periodicities of 11 (Schwebe cycle) and 5.5 years (second harmonic of Schwebe cycle). In the Chilean and Argentinian sites, significant agreement between the time series of tree rings and the 11-year solar cycle was found during the periods of maximum solar activity. Results also showed oscillation with periods of 2-7 years, probably induced by local environmental variations, and possibly also related to the El-Niño events. Moreover, the Morlet complex wavelet analysis was applied to study the most relevant variability factors affecting tree-ring time series. Finally, we applied the cross-wavelet spectral analysis to evaluate the time lags between tree-ring and sunspot-number time series, as well as for the interaction between tree rings, the Southern Oscillation Index (SOI) and temperature and precipitation. Trees sampled in Chile and Argentina showed more evident responses of fluctuations in tree-ring time series to the variations of short and long periodicities in comparison with the Brazilian ones. These results provided new evidence on the solar activity-climate pattern-tree ring connections over centuries.

Fault-Tree Compiler

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Boerschlein, David P.

1993-01-01

Fault-Tree Compiler (FTC) program, is software tool used to calculate probability of top event in fault tree. Gates of five different types allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language easy to understand and use. In addition, program supports hierarchical fault-tree definition feature, which simplifies tree-description process and reduces execution time. Set of programs created forming basis for reliability-analysis workstation: SURE, ASSIST, PAWS/STEM, and FTC fault-tree tool (LAR-14586). Written in PASCAL, ANSI-compliant C language, and FORTRAN 77. Other versions available upon request.

Houston’s Urban Forest, 2015

Treesearch

David J. Nowak; Allison R. Bodine; Robert E. Hoehn; Christopher B. Edgar; Gretchen Riley; Dudley R. Hartel; Kerry J. Dooley; Sharon M. Stanton; Mark A. Hatfield; Thomas J. Brandeis; Tonya W. Lister

2017-01-01

An analysis of the urban forest in Houston, Texas, reveals that this area has an estimated 33.3 million live trees with tree canopy that covers 18.4 percent of the city. Roughly 19.2 million of the city’s trees are located on private lands. The most common tree species are yaupon, Chinese tallowtree, Chinese privet, Japanese privet, and sugarberry. Trees in Houston...

Assessing urban forest effects and values: Douglas County, Kansas

Treesearch

David J. Nowak; Allison R. Bodine; Robert E. Hoehn; Alexis Ellis; Kim Bomberger; Daniel E. Crane; Theodore A. Endreny; Thomas Taggert; Emily. Stephan

2014-01-01

An analysis of trees in Douglas County, Kansas, reveals that this area has about 14,164,000 trees with tree and shrub canopy that covers 25.2 percent of the county. The most common tree species are American elm, northern hackberry, eastern redcedar, Osage-orange, and honeylocust. Trees in Douglas County currently store about 1.7 million tons of carbon (6.4 million tons...

Mortality rates associated with crown health for eastern forest tree species

Treesearch

Randall S. Morin; KaDonna C. Randolph; Jim Steinman

2015-01-01

The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during inventories of the US Forest Service Forest Inventory and Analysis (FIA) program since 1999. In this study, remeasured data from 55,013 trees on 2616 FIA plots in the eastern USA were used to assess the probability of survival among various tree...

A broad scale analysis of tree risk, mitigation and potential habitat for cavity-nesting birds

Treesearch

Brian Kane; Paige S. Warren; Susannah B. Lerman

2015-01-01

Trees in towns and cities provide habitat for wildlife. In particular, cavity-nesting birds nest in the deadand decayed stems and branches of these trees. The same dead and decayed stems and branches alsohave a greater likelihood of failure, which, in some circumstances, increases risk. We examined 1760trees in Baltimore, MD, USA and western MA, USA, assessing tree...

Assessing urban forest effects and values: the greater Kansas City region

Treesearch

David J. Nowak; Allison R. Bodine; Robert E. III Hoehn; Daniel E. Crane; Alexis Ellis; Theodore A. Endreny; Yang Yang; Tom Jacobs; Kassie Shelton

2013-01-01

An analysis of trees in the greater Kansas City region of Missouri and Kansas reveals that this area has about 249,450,000 trees with tree and shrub canopy that covers 28.3 percent of the region. The most common tree species are American elm, northern hackberry, Osage-orange, honeylocust, and eastern redcedar. Trees in the greater Kansas City region currently store...

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context.

PubMed

Herrero-Huerta, Mónica; Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees.

Automatic tree parameter extraction by a Mobile LiDAR System in an urban context

PubMed Central

Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

In an urban context, tree data are used in city planning, in locating hazardous trees and in environmental monitoring. This study focuses on developing an innovative methodology to automatically estimate the most relevant individual structural parameters of urban trees sampled by a Mobile LiDAR System at city level. These parameters include the Diameter at Breast Height (DBH), which was estimated by circle fitting of the points belonging to different height bins using RANSAC. In the case of non-circular trees, DBH is calculated by the maximum distance between extreme points. Tree sizes were extracted through a connectivity analysis. Crown Base Height, defined as the length until the bottom of the live crown, was calculated by voxelization techniques. For estimating Canopy Volume, procedures of mesh generation and α-shape methods were implemented. Also, tree location coordinates were obtained by means of Principal Component Analysis. The workflow has been validated on 29 trees of different species sampling a stretch of road 750 m long in Delft (The Netherlands) and tested on a larger dataset containing 58 individual trees. The validation was done against field measurements. DBH parameter had a correlation R2 value of 0.92 for the height bin of 20 cm which provided the best results. Moreover, the influence of the number of points used for DBH estimation, considering different height bins, was investigated. The assessment of the other inventory parameters yield correlation coefficients higher than 0.91. The quality of the results confirms the feasibility of the proposed methodology, providing scalability to a comprehensive analysis of urban trees. PMID:29689076

Sur les processus linéaires de naissance et de mort sous-critiques dans un environnement aléatoire.

PubMed

Bacaër, Nicolas

2017-07-01

An explicit formula is found for the rate of extinction of subcritical linear birth-and-death processes in a random environment. The formula is illustrated by numerical computations of the eigenvalue with largest real part of the truncated matrix for the master equation. The generating function of the corresponding eigenvector satisfies a Fuchsian system of singular differential equations. A particular attention is set on the case of two environments, which leads to Riemann's differential equation.

Towards lidar-based mapping of tree age at the Arctic forest tundra ecotone.

NASA Astrophysics Data System (ADS)

Jensen, J.; Maguire, A.; Oelkers, R.; Andreu-Hayles, L.; Boelman, N.; D'Arrigo, R.; Griffin, K. L.; Jennewein, J. S.; Hiers, E.; Meddens, A. J.; Russell, M.; Vierling, L. A.; Eitel, J.

2017-12-01

Climate change may cause spatial shifts in the forest-tundra ecotone (FTE). To improve our ability to study these spatial shifts, information on tree demography along the FTE is needed. The objective of this study was to assess the suitability of lidar derived tree heights as a surrogate for tree age. We calculated individual tree age from 48 tree cores collected at basal height from white spruce (Picea glauca) within the FTE in northern Alaska. Tree height was obtained from terrestrial lidar scans (<1cm spatial resolution). The relationship between age and height was examined using a linear regression model forced through the origin. We found a very strong predictive relationship between tree height and age (R2 = 0.90, RMSE = 19.34 years) for trees that ranged between 14 to 230 years. Separate regression models were also developed for small (height < 3 m) and large trees (height >= 3 m), yielding strong predictive relationships between height and age (R2 = 0.86, RMSE 12.21 years, and R2 = 0.93, RMSE = 25.16 years, respectively). The slope coefficient for small and large tree models (16.83 and 12.98 years/m, respectively) indicate that small trees grow 1.3 times faster than large trees at these FTE study sites. Although a strong, predictive relationship between age and height is uncommon in light-limited forest environments, our findings suggest that the sparseness of trees within the FTE may explain the strong tree height-age relationships found herein. Further analysis of 36 additional tree cores recently collected within the FTE near Inuvik, Canada will be performed. Our preliminary analysis suggests that lidar derived tree height could be a reliable proxy for tree age at the FTE, thereby establishing a new technique for scaling tree structure and demographics across larger portions of this sensitive ecotone.

Fault-Tree Compiler Program

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1992-01-01

FTC, Fault-Tree Compiler program, is reliability-analysis software tool used to calculate probability of top event of fault tree. Five different types of gates allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language of FTC easy to understand and use. Program supports hierarchical fault-tree-definition feature simplifying process of description of tree and reduces execution time. Solution technique implemented in FORTRAN, and user interface in Pascal. Written to run on DEC VAX computer operating under VMS operating system.

A nonparametric analysis of plot basal area growth using tree based models

Treesearch

G. L. Gadbury; H. K. lyer; H. T. Schreuder; C. Y. Ueng

1997-01-01

Tree based statistical models can be used to investigate data structure and predict future observations. We used nonparametric and nonlinear models to reexamine the data sets on tree growth used by Bechtold et al. (1991) and Ruark et al. (1991). The growth data were collected by Forest Inventory and Analysis (FIA) teams from 1962 to 1972 (4th cycle) and 1972 to 1982 (...

Mapping and characterizing selected canopy tree species at the Angkor World Heritage site in Cambodia using aerial data.

PubMed

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia's tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman's rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables.

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data

PubMed Central

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia’s tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman’s rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables. PMID:25902148

Tree-regeneration and mortality patterns and hydrologic change in a forested karst wetland--Sinking Pond, Arnold Air Force Base, Tennessee

USGS Publications Warehouse

Wolfe, William J.; Evans, Jonathan P.; McCarthy, Sarah; Gain, W. Scott; Bryan, Bradley A.

2004-01-01

Multiple lines of evidence point to climate change as the driving factor suppressing tree regeneration since 1970 in Sinking Pond, a 35-hectare seasonally flooded karst depression located on Arnold Air Force Base near Manchester, Tennessee. Annual censuses of 162-193 seedling plots from 1997 through 2001 demonstrate that the critical stage for tree survival is the transition from seedling to sapling and that this transition is limited to shallow (less than 0.5 meters) ponding depths. Recruitment of saplings to the small adult class also was restricted to shallow areas. Analysis of the spatial and elevation distribution of tree-size classes in a representative 2.3-hectare area of Sinking Pond showed a general absence of overcup oak saplings and young adults in deep (ponding depth greater than 1 meter) and intermediate (ponding depth 0.5-1 meter) areas, even though overcup oak seedlings and mature trees are concentrated in these areas. Analysis of tree rings from 45 trees sampled in a 2.3-hectare spatial-analysis plot showed an even distribution of tree ages across ponding-depth classes from the 1800s through 1970, followed by complete suppression of recruitment in deep and intermediate areas after 1970. Trees younger than 30 years were spatially and vertically concentrated in a small area with shallow ponding depth, about 0.5 meter below the spillway elevation. Results of hydrologic modeling, based on rainfall and temperature records covering the period January 1854 through September 2002, show ponding durations after 1970 considerably longer than historical norms, across ponding-depth classes. This increase in ponding duration corresponds closely with similar increases documented in published analyses of streamflow and precipitation in the eastern United States and with the suppression of tree regeneration at ponding depths greater than 0.5 meter indicated by tree-ring analysis. Comparison of the simulated stage record for Sinking Pond with the ages and elevations of sampled trees shows that prolonged (200 days or more per year) inundation in more than 2 of the first 5 years after germination is inversely related to successful tree recruitment and that such inundation was rare before 1970 and common afterwards.

Analysis of vegetation changes in Rock Creek Park, 1991-2007

USGS Publications Warehouse

Hatfield, Jeff S.; Krafft, Cairn

2009-01-01

Vegetation data collected at Rock Creek Park every 4 years during 1991-2007 were analyzed for differences among 3 regions within the park and among years. The variables measured and analyzed were percentage of twigs browsed, percentage of canopy cover, species richness of herbaceous plants, number of tree seedlings in each of 7 height classes, tree seedling stocking rate for low deer density and high deer density areas, percentage of tree and shrub cover < 2 m in height, mean diameter at breast height (DBH) of trees > 1 cm DBH, number of tree stems > 1 cm DBH, species richness of trees and shrubs, and mean height of the 5 tallest trees in each plot quadrant. Repeated measures analysis of variance (ANOVA) was used to test for differences and, except for some differences in tree species composition among the 3 regions, no differences (P > 0.01) were found among the 3 regions in the variables discussed above. Many of the variables showed very significant differences (P < 0.01) among years, and causative factors should be investigated further. In addition, importance values were calculated for the 10 most important tree species in each region and changes over time were reported. Future sampling recommendations are also discussed.

TreeGenes and CartograTree: Enabling visualization and analysis in forest tree genomics

Treesearch

E.S. Grau; S.A. Demurjian; H.A. Vasquez-Gross; D.G. Gessler; D.B. Neale; J.L. Wegrzyn

2017-01-01

Association studies integrating environmental, phenotypic, and genetic data are key in understanding forest tree resilience to climate change and disease. As genomic resources increase, both in terms of complete reference sequences and magnitude of individuals genotyped, researchers are better equipped to identify correlations between genetic variation and adaptive or...

Guam's forest resources, 2002.

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Walter Grabowiecki; Bruce A. Hiserote; David. Limtiaco

2004-01-01

The Forest Inventory and Analysis Program collected, analyzed, and summarized field data on 46 forested plots on the island of Guam. Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this statistical sample. Detailed tables and graphical highlights provide a summary of Guam...

Assessing urban forest effects and values, Chicago's urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Jack C. Stevens; Cherie Leblanc Fisher

2010-01-01

An analysis of trees in Chicago, IL, reveals that this city has about 3,585,000 trees with canopies that cover 17.2 percent of the area. The most common tree species are white ash, mulberry species, green ash, and tree-of-heaven. Chicago's urban forest currently stores about 716,000 tons of carbon...

Palau's forest resources, 2003.

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Brent J. Stroud; Bruce A. Hiserote; Kashgar. Rengulbai

2007-01-01

The Forest Inventory and Analysis Program collected, analyzed, and summarized field data on 54 forested plots on the islands in the Republic of Palau. Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this statistical sample. Detailed tables and graphical highlights provide...

City of Berkeley, California Municipal Tree Resource Analysis

Treesearch

S.E. Maco; E.G. McPherson; J.R. Simpson; P.J. Peper; Q. Xiao

2005-01-01

Vibrant, renowned for its livability and cultural wealth, the city of Berkeley maintains trees as an integral component of the urban infrastructure. Research indicates that healthy trees can mitigate impacts associated with the built environment by reducing stormwater runoff, energy consumption, and air pollutants. Put simply, trees improve urban life, making Berkeley...

Mathematical form models of tree trunks

Treesearch

Rudolfs Ozolins

2000-01-01

Assortment structure analysis of tree trunks is a characteristic and proper problem that can be solved by using mathematical modeling and standard computer programs. Mathematical form model of tree trunks consists of tapering curve equations and their parameters. Parameters for nine species were obtained by processing measurements of 2,794 model trees and studying the...

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

PubMed Central

2014-01-01

Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates. PMID:24678701

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines.

PubMed

DeGiorgio, Michael; Syring, John; Eckert, Andrew J; Liston, Aaron; Cronn, Richard; Neale, David B; Rosenberg, Noah A

2014-03-29

As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each "strategy" for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.

Olive tree-ring problematic dating: a comparative analysis on Santorini (Greece).

PubMed

Cherubini, Paolo; Humbel, Turi; Beeckman, Hans; Gärtner, Holger; Mannes, David; Pearson, Charlotte; Schoch, Werner; Tognetti, Roberto; Lev-Yadun, Simcha

2013-01-01

Olive trees are a classic component of Mediterranean environments and some of them are known historically to be very old. In order to evaluate the possibility to use olive tree-rings for dendrochronology, we examined by various methods the reliability of olive tree-rings identification. Dendrochronological analyses of olive trees growing on the Aegean island Santorini (Greece) show that the determination of the number of tree-rings is impossible because of intra-annual wood density fluctuations, variability in tree-ring boundary structure, and restriction of its cambial activity to shifting sectors of the circumference, causing the tree-ring sequences along radii of the same cross section to differ.

Assessing urban forest effects and values, Los Angeles' urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Lorraine Weller; Antonio Davila

2011-01-01

An analysis of trees in Los Angeles, CA, reveals that this area has about 6 million trees with tree and shrub canopies that cover 24.9 percent of the city. The most common tree species are Italian cypress, scrub oak, laurel sumac, Mexican fan palm, and Indian laurel, Trees in Los Angeles currently store about 1.3 million tons of carbon (4.7 million tons CO2...

Methods and equations for estimating aboveground volume, biomass, and carbon for trees in the U.S. forest inventory, 2010

Treesearch

Christopher W. Woodall; Linda S. Heath; Grant M. Domke; Michael C. Nichols

2011-01-01

The U.S. Forest Service, Forest Inventory and Analysis (FIA) program uses numerous models and associated coefficients to estimate aboveground volume, biomass, and carbon for live and standing dead trees for most tree species in forests of the United States. The tree attribute models are coupled with FIA's national inventory of sampled trees to produce estimates of...

Assessing urban forest effects and values, Philladelphia's urban forest

Treesearch

David J. Nowak; Robert E., III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2007-01-01

An analysis of trees in Philadelphia reveals that this city has about 2.1 million trees with canopies that cover 15.7 percent of the area. The most common tree species are black cherry, crabapple, and tree of heaven. The urban forest currently stores about 530,000 tons of carbon valued at $9.8 million. In addition, these trees remove about 16,100 tons of carbon per...

Fast Image Texture Classification Using Decision Trees

NASA Technical Reports Server (NTRS)

Thompson, David R.

2011-01-01

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

Observation of eight ancient olive trees (Olea europaea L.) growing in the Garden of Gethsemane.

PubMed

Petruccelli, Raffaella; Giordano, Cristiana; Salvatici, Maria Cristina; Capozzoli, Laura; Ciaccheri, Leonardo; Pazzini, Massimo; Lain, Orietta; Testolin, Raffaele; Cimato, Antonio

2014-05-01

For thousands of years, olive trees (Olea europaea L.) have been a significant presence and a symbol in the Garden of Gethsemane, a place located at the foot of the Mount of Olives, Jerusalem, remembered for the agony of Jesus Christ before his arrest. This investigation comprises the first morphological and genetic characterization of eight olive trees in the Garden of Gethsemane. Pomological traits, morphometric, and ultrastructural observations as well as SSR (Simple Sequence Repeat) analysis were performed to identify the olive trees. Statistical analyses were conducted to evaluate their morphological variability. The study revealed a low morphological variability and minimal dissimilarity among the olive trees. According to molecular analysis, these trees showed the same allelic profile at all microsatellite loci analyzed. Combining the results of the different analyses carried out in the frame of the present work, we could conclude that the eight olive trees of the Gethsemane Garden have been propagated from a single genotype. Copyright © 2014. Published by Elsevier SAS.

Nonlinear behaviors of FRP-wrapped tall trees subjected to high wind loads

NASA Astrophysics Data System (ADS)

Kang, J.; Yi, Z. Z.; Choi, S. G.

2017-12-01

This study investigated the mechanical stability of historical tall trees wrapped with fiber-reinforced polymer (FRP) laminates using finite element (FE) analysis. High wind loads are considered as external loading conditions as they are one of the major threats on the structural stability of tall old trees. There have been several traditional practices to enhance the stability of tall trees exposed to high windstorms such as tree supporters and anchorages. They, however, have been sometimes causing negative effects with their misuses as the application guidelines for those methods were not adequately studied or documented. Furthermore, the oldest known trees in the country should be protected from the damage of external surface as well as ruin of the landscape. The objective of this study was to evaluate the structural effects of FRP wraps applied to tall trees subjected to high wind loads. The anisotropic material properties of wood and FRP laminates were considered in the analysis in addition to geometrically nonlinear behaviors. This study revealed that FRP wrapping for tall trees could effectively reduce the deflections and maximum stresses of trees, which results in the enhanced stability of tall trees. The optimum geometry and thicknesses of FRP wraps proposed in this study would provide fundemental guidelines for designing and constructing the application of innovative FRP wraps on tall trees, which are structurally unstable or should be preserved nationally and historically.

Dendroscope: An interactive viewer for large phylogenetic trees

PubMed Central

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

2007-01-01

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

Strategic conservation of orchard germplasm based on indigenous knowledge and genetic diversity: a case study of sour orange populations in China.

PubMed

Ming, Feng; Liu, Qi-Kun; Shi, Jin-Lei; Wang, Wei; Lu, Bao-Rong

2009-01-01

To effectively conserve sour orange (Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified polymorphic DNA (RAPD). Results based on RAPD analyses showed considerable genetic diversity in the parental populations (H(e)=0.202). The overall populations including the parental and young trees showed slightly higher genetic diversity (H(e)=0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers' knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.

Smoking and Mortality in Eastern Europe: Results From the PrivMort Retrospective Cohort Study of 177 376 Individuals.

PubMed

Stefler, Denes; Murphy, Michael; Irdam, Darja; Horvat, Pia; Jarvis, Martin; King, Lawrence; McKee, Martin; Bobak, Martin

2018-05-03

The estimated prevalence of smoking and proportion of deaths due to tobacco in Eastern European countries are among the highest in the world. Existing estimates of mortality attributable to smoking in the region are mostly indirect. The aim of this analysis was to calculate the proportion of tobacco-attributed deaths in three Eastern European countries using individual level cohort data. The PrivMort project established a cohort of relatives of participants in population sample surveys in Russia, Belarus and Hungary. Survey participants provided data on smoking habits and vital statistics of their close relatives between 1982 and 2013. Population attributable risk fractions (PARF) in men (n = 99528) and women (n = 77848) aged 40-79 years were calculated from the prevalence rates of smoking and hazard ratios of mortality for smokers versus non-smokers. Trends in PARF over four 8-year time periods (1982-1989, 1990-1997, 1998-2005, and 2006-2013) were examined. In men in the most recent period (2006-2013), the proportions of deaths attributable to tobacco were 23% in Russia, 22% in Belarus, and 22% in Hungary. The respective estimates in women were lower (2%, 2%, and 13%), possibly due to underestimation of smoking prevalence. PARF estimates have declined slightly since the early 1990s in men but increased in women. Consistently with existing indirect estimates, our results based on individual level cohort data suggest that over one fifth of all deaths in men aged 40-79 years are attributable to tobacco. While these proportions are lower in women, the increasing trend is a major concern. This is the first large scale, individual-level cohort study that estimated the mortality attributable to tobacco smoking directly in Eastern European population samples. The results confirm previous indirect estimates and show that more than 20% of all deaths in Eastern European men can be attributed to tobacco. The study also confirms the increasing trend in smoking-related deaths among women. These findings emphasize the importance of targeted policy interventions in Eastern European countries.

Fault Tree Analysis: An Emerging Methodology for Instructional Science.

ERIC Educational Resources Information Center

Wood, R. Kent; And Others

1979-01-01

Describes Fault Tree Analysis, a tool for systems analysis which attempts to identify possible modes of failure in systems to increase the probability of success. The article defines the technique and presents the steps of FTA construction, focusing on its application to education. (RAO)

Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states.

PubMed

Staver, A Carla; Archibald, Sally; Levin, Simon

2011-05-01

Savannas are known as ecosystems with tree cover below climate-defined equilibrium values. However, a predictive framework for understanding constraints on tree cover is lacking. We present (a) a spatially extensive analysis of tree cover and fire distribution in sub-Saharan Africa, and (b) a model, based on empirical results, demonstrating that savanna and forest may be alternative stable states in parts of Africa, with implications for understanding savanna distributions. Tree cover does not increase continuously with rainfall, but rather is constrained to low (<50%, "savanna") or high tree cover (>75%, "forest"). Intermediate tree cover rarely occurs. Fire, which prevents trees from establishing, differentiates high and low tree cover, especially in areas with rainfall between 1000 mm and 2000 mm. Fire is less important at low rainfall (<1000 mm), where rainfall limits tree cover, and at high rainfall (>2000 mm), where fire is rare. This pattern suggests that complex interactions between climate and disturbance produce emergent alternative states in tree cover. The relationship between tree cover and fire was incorporated into a dynamic model including grass, savanna tree saplings, and savanna trees. Only recruitment from sapling to adult tree varied depending on the amount of grass in the system. Based on our empirical analysis and previous work, fires spread only at tree cover of 40% or less, producing a sigmoidal fire probability distribution as a function of grass cover and therefore a sigmoidal sapling to tree recruitment function. This model demonstrates that, given relatively conservative and empirically supported assumptions about the establishment of trees in savannas, alternative stable states for the same set of environmental conditions (i.e., model parameters) are possible via a fire feedback mechanism. Integrating alternative stable state dynamics into models of biome distributions could improve our ability to predict changes in biome distributions and in carbon storage under climate and global change scenarios.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

PubMed

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

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .

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

NASA Astrophysics Data System (ADS)

Poliaková, Adela

2015-06-01

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

Feasibility of high-density climate reconstruction based on Forest Inventory and Analysis (FIA) collected tree-ring data

Treesearch

R. Justin DeRose; Shih-Yu Wang; John D. Shaw

2013-01-01

This study introduces a novel tree-ring dataset, with unparalleled spatial density, for use as a climate proxy. Ancillary Douglas fir and pinyon pine tree-ring data collected by the U.S. Forest Service Forest Inventory and Analysis Program (FIA data) were subjected to a series of tests to determine their feasibility as climate proxies. First, temporal coherence between...

Differences in Risk Factors for Rotator Cuff Tears between Elderly Patients and Young Patients.

PubMed

Watanabe, Akihisa; Ono, Qana; Nishigami, Tomohiko; Hirooka, Takahiko; Machida, Hirohisa

2018-02-01

It has been unclear whether the risk factors for rotator cuff tears are the same at all ages or differ between young and older populations. In this study, we examined the risk factors for rotator cuff tears using classification and regression tree analysis as methods of nonlinear regression analysis. There were 65 patients in the rotator cuff tears group and 45 patients in the intact rotator cuff group. Classification and regression tree analysis was performed to predict rotator cuff tears. The target factor was rotator cuff tears; explanatory variables were age, sex, trauma, and critical shoulder angle≥35°. In the results of classification and regression tree analysis, the tree was divided at age 64. For patients aged≥64, the tree was divided at trauma. For patients aged<64, the tree was divided at critical shoulder angle≥35°. The odds ratio for critical shoulder angle≥35° was significant for all ages (5.89), and for patients aged<64 (10.3) while trauma was only a significant factor for patients aged≥64 (5.13). Age, trauma, and critical shoulder angle≥35° were related to rotator cuff tears in this study. However, these risk factors showed different trends according to age group, not a linear relationship.

Estimating root collar diameter growth for multi-stem western woodland tree species on remeasured forest inventory and analysis plots

Treesearch

Michael T. Thompson; Maggie. Toone

2012-01-01

Tree diameter growth models are widely used in many forestry applications, often to predict tree size at a future point in time. Also, there are instances where projections of past diameters are needed. An individual tree model has been developed to estimate diameter growth of multi-stem woodland tree species where the diameter is measured at root collar. The model was...

Assessing urban forest effects and values, New York City's urban forest

Treesearch

David J. Nowak; Robert E., III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2007-01-01

An analysis of trees in New York City reveals that this city has about 5.2 million trees with canopies that cover 20.9 percent of the area. The most common tree species are tree of heaven, black cherry, and sweetgum. The urban forest currently stores about 1.35 million tons of carbon valued at $24.9 million. In addition, these trees remove about 42,300 tons of carbon...

DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

Distribution of cavity trees in midwestern old-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Distribution of cavity trees in midwesternold-growth and second-growth forests

Treesearch

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R., III Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Federated States of Micronesia's forest resources, 2006

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Bruce A. Hiserote

2011-01-01

The Forest Inventory and Analysis program collected, analyzed, and summarized field data on 73 forested field plots on the islands of Kosrae, Chuuk, Pohnpei, and Yap in the Federated States of Micronesia (FSM). Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this...

Standing dead tree resources in forests of the United States

Treesearch

Christopher W. Woodall; Karen L. Waddell; Christopher M. Oswalt; James E. Smith

2013-01-01

Given the importance of standing dead trees to numerous forest ecosystem attributes/ processes such as fuel loadings and wildlife habitat, the Forest Inventory and Analysis (FIA) Program of the Forest Service, U.S. Department of Agriculture, initiated a consistent nationwide inventory of standing dead trees in 1999. As the first cycle of annual standing dead tree...

Differences in Computed Individual-Tree Volumes Caused by Differences in Field Measurements

Treesearch

James A. Westfall

2008-01-01

Individual-tree volumes are primarily predicted using volume equations that rely on measured tree attributes. In the northeastern United States, the Forest Inventory and Analysis program determines tree volume using dbh, bole height, proportion of cull, and species information. These measurements are subject to variability due to a host of factors. The sensitivity of...

Alabama, 2012 - forest inventory and analysis factsheet

Treesearch

Andrew J. Hartsell

2013-01-01

These early surveys were not concerned with the forests, species, and tree sizes that were not considered commercially viable. Early surveys reported only on growing-stock trees on timberlands, i.e. commercially important tree species and tree sizes on forests that could sustain harvest operations. Currently, FIA reports on all of the forest lands regardless of site...

Commonwealth of the Northern Mariana Islands' forest resources, 2004

Treesearch

Joseph A. Donnegan; Sarah L. Butler; Olaf Kuegler; Bruce A. Hiserote

2011-01-01

The Forest Inventory and Analysis program collected, analyzed, and summarized field data on 37 field plots on the islands of Rota, Tinian, and Saipan in the Commonwealth of the Northern Mariana Islands (CNMI). Estimates of forest area, tree stem volume and biomass, the numbers of trees, tree damages, and the distribution of tree sizes were summarized for this...

Olive Tree-Ring Problematic Dating: A Comparative Analysis on Santorini (Greece)

PubMed Central

Cherubini, Paolo; Humbel, Turi; Beeckman, Hans; Gärtner, Holger; Mannes, David; Pearson, Charlotte; Schoch, Werner; Tognetti, Roberto; Lev-Yadun, Simcha

2013-01-01

Olive trees are a classic component of Mediterranean environments and some of them are known historically to be very old. In order to evaluate the possibility to use olive tree-rings for dendrochronology, we examined by various methods the reliability of olive tree-rings identification. Dendrochronological analyses of olive trees growing on the Aegean island Santorini (Greece) show that the determination of the number of tree-rings is impossible because of intra-annual wood density fluctuations, variability in tree-ring boundary structure, and restriction of its cambial activity to shifting sectors of the circumference, causing the tree-ring sequences along radii of the same cross section to differ. PMID:23382949

Seismic azimuthal anisotropy in crevasse fields

NASA Astrophysics Data System (ADS)

Lindner, F.; Laske, G.; Walter, F.

2017-12-01

Crevasses and englacial fracture networks route meltwater from a glacier's surface to the subglacial drainage system and thus strongly influence glacial hydraulics. However, rapid fracture growth may also lead to sudden (and potentially hazardous) structural failure of unstable glaciers and ice dams, rifting of ice shelves, or iceberg calving.Here, we use passive seismic recordings from Glacier de la Plaine Morte, Switzerland, to investigate the englacial fracture network. Glacier de la Plaine Morte is the largest plateau glacier in the European Alps and extremely vulnerable to climate change. The annual drainage of an ice-marginal lake gives rise to numerous icequakes, thereby demonstrating the interplay between hydraulics and fracturing. The majority of these naturally occurring events exhibits dispersed, high-frequency Rayleigh waves at about 10 Hz and higher. A wide distribution of events allows us to study azimuthal anisotropy of englacial seismic velocities in regions of preferentially oriented fractures.Results from beamforming applied to a 100m-aperture array show strong (up to 9%) azimuthal anisotropy of Rayleigh wave velocities. We find that the fast direction coincides with the observed surface strike of the fractures and that anisotropy is strongest for high-frequency (around 30 Hz) Rayleigh waves that are sensitive only to the uppermost (few tens of meters) part of the glacier. In addition to these results, we propose to study temporal variations in the anisotropy pattern that can potentially be related to growth, shrinkage, and changing water content of the fractures during the course of the lake drainage or other hydrological events.

Comparative analysis of techniques for evaluating the effectiveness of aircraft computing systems

NASA Technical Reports Server (NTRS)

Hitt, E. F.; Bridgman, M. S.; Robinson, A. C.

1981-01-01

Performability analysis is a technique developed for evaluating the effectiveness of fault-tolerant computing systems in multiphase missions. Performability was evaluated for its accuracy, practical usefulness, and relative cost. The evaluation was performed by applying performability and the fault tree method to a set of sample problems ranging from simple to moderately complex. The problems involved as many as five outcomes, two to five mission phases, permanent faults, and some functional dependencies. Transient faults and software errors were not considered. A different analyst was responsible for each technique. Significantly more time and effort were required to learn performability analysis than the fault tree method. Performability is inherently as accurate as fault tree analysis. For the sample problems, fault trees were more practical and less time consuming to apply, while performability required less ingenuity and was more checkable. Performability offers some advantages for evaluating very complex problems.

[Analysis of the molecular characteristics and cloning of full-length coding sequence of interleukin-2 in tree shrews].

PubMed

Huang, Xiao-Yan; Li, Ming-Li; Xu, Juan; Gao, Yue-Dong; Wang, Wen-Guang; Yin, An-Guo; Li, Xiao-Fei; Sun, Xiao-Mei; Xia, Xue-Shan; Dai, Jie-Jie

2013-04-01

While the tree shrew (Tupaia belangeri chinensis) is an excellent animal model for studying the mechanisms of human diseases, but few studies examine interleukin-2 (IL-2), an important immune factor in disease model evaluation. In this study, a 465 bp of the full-length IL-2 cDNA encoding sequence was cloned from the RNA of tree shrew spleen lymphocytes, which were then cultivated and stimulated with ConA (concanavalin). Clustal W 2.0 was used to compare and analyze the sequence and molecular characteristics, and establish the similarity of the overall structure of IL-2 between tree shrews and other mammals. The homology of the IL-2 nucleotide sequence between tree shrews and humans was 93%, and the amino acid homology was 80%. The phylogenetic tree results, derived through the Neighbour-Joining method using MEGA5.0, indicated a close genetic relationship between tree shrews, Homo sapiens, and Macaca mulatta. The three-dimensional structure analysis showed that the surface charges in most regions of tree shrew IL-2 were similar to between tree shrews and humans; however, the N-glycosylation sites and local structures were different, which may affect antibody binding. These results provide a fundamental basis for the future study of IL-2 monoclonal antibody in tree shrews, thereby improving their utility as a model.

Tree crown mapping in managed woodlands (parklands) of semi-arid West Africa using WorldView-2 imagery and geographic object based image analysis.

PubMed

Karlson, Martin; Reese, Heather; Ostwald, Madelene

2014-11-28

Detailed information on tree cover structure is critical for research and monitoring programs targeting African woodlands, including agroforestry parklands. High spatial resolution satellite imagery represents a potentially effective alternative to field-based surveys, but requires the development of accurate methods to automate information extraction. This study presents a method for tree crown mapping based on Geographic Object Based Image Analysis (GEOBIA) that use spectral and geometric information to detect and delineate individual tree crowns and crown clusters. The method was implemented on a WorldView-2 image acquired over the parklands of Saponé, Burkina Faso, and rigorously evaluated against field reference data. The overall detection rate was 85.4% for individual tree crowns and crown clusters, with lower accuracies in areas with high tree density and dense understory vegetation. The overall delineation error (expressed as the difference between area of delineated object and crown area measured in the field) was 45.6% for individual tree crowns and 61.5% for crown clusters. Delineation accuracies were higher for medium (35-100 m(2)) and large (≥100 m(2)) trees compared to small (<35 m(2)) trees. The results indicate potential of GEOBIA and WorldView-2 imagery for tree crown mapping in parkland landscapes and similar woodland areas.

Tree Crown Mapping in Managed Woodlands (Parklands) of Semi-Arid West Africa Using WorldView-2 Imagery and Geographic Object Based Image Analysis

PubMed Central

Karlson, Martin; Reese, Heather; Ostwald, Madelene

2014-01-01

Detailed information on tree cover structure is critical for research and monitoring programs targeting African woodlands, including agroforestry parklands. High spatial resolution satellite imagery represents a potentially effective alternative to field-based surveys, but requires the development of accurate methods to automate information extraction. This study presents a method for tree crown mapping based on Geographic Object Based Image Analysis (GEOBIA) that use spectral and geometric information to detect and delineate individual tree crowns and crown clusters. The method was implemented on a WorldView-2 image acquired over the parklands of Saponé, Burkina Faso, and rigorously evaluated against field reference data. The overall detection rate was 85.4% for individual tree crowns and crown clusters, with lower accuracies in areas with high tree density and dense understory vegetation. The overall delineation error (expressed as the difference between area of delineated object and crown area measured in the field) was 45.6% for individual tree crowns and 61.5% for crown clusters. Delineation accuracies were higher for medium (35–100 m2) and large (≥100 m2) trees compared to small (<35 m2) trees. The results indicate potential of GEOBIA and WorldView-2 imagery for tree crown mapping in parkland landscapes and similar woodland areas. PMID:25460815

Fault Tree Analysis for an Inspection Robot in a Nuclear Power Plant

NASA Astrophysics Data System (ADS)

Ferguson, Thomas A.; Lu, Lixuan

2017-09-01

The life extension of current nuclear reactors has led to an increasing demand on inspection and maintenance of critical reactor components that are too expensive to replace. To reduce the exposure dosage to workers, robotics have become an attractive alternative as a preventative safety tool in nuclear power plants. It is crucial to understand the reliability of these robots in order to increase the veracity and confidence of their results. This study presents the Fault Tree (FT) analysis to a coolant outlet piper snake-arm inspection robot in a nuclear power plant. Fault trees were constructed for a qualitative analysis to determine the reliability of the robot. Insight on the applicability of fault tree methods for inspection robotics in the nuclear industry is gained through this investigation.

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

PubMed

Stevens, John R; Jones, Todd R; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C

2017-01-01

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree , a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

Boreal Tree Light- and Water-Use: Asynchronous, Diverging, yet Complementary

NASA Astrophysics Data System (ADS)

Pappas, C.; Baltzer, J. L.; Barr, A.; Black, T. A.; Bohrer, G.; Detto, M.; Maillet, J.; Matheny, A. M.; Roy, A.; Sonnentag, O.; Stephens, J.

2017-12-01

Water stress has been suggested as a key mechanism behind the contemporary increase in tree mortality rates in northwestern North America. However, a detailed analysis of boreal tree light- and water-use strategies as well as their interspecific differences are still lacking. Here, we examine the tree hydraulic behaviour of co-occurring larch (Larix laricina) and black spruce (Picea mariana), two characteristic boreal tree species, near the southern limit of the boreal ecozone in central Canada. Sap flux density (Js) and concurrently recorded stem radius fluctuations and meteorological conditions are used to quantify tree hydraulic functioning and to scrutinize tree light- and water-use strategies. Our analysis reveals an asynchrony in the diel hydrodynamics of the two species with the initial rise in Js occurring two hours earlier in larch than in black spruce. Structural differences in the crown architecture of larch and black spruce lead to interspecific differences in light harvesting that can explain the observed asynchrony in their hydraulic function. Furthermore, the two species exhibit diverging stomatal regulation strategies with larch employing relatively isohydric whereas black spruce anisohydric behaviour. Such asynchronous and diverging tree-level light- and water-use strategies provide new insights into the ecosystem-level complementarity of tree form and function, with implications for understanding boreal forests' water and carbon dynamics and resilience to environmental stress.

Tracing footprints of environmental events in tree ring chemistry using neutron activation analysis

NASA Astrophysics Data System (ADS)

Sahin, Dagistan

The aim of this study is to identify environmental effects on tree-ring chemistry. It is known that industrial pollution, volcanic eruptions, dust storms, acid rain and similar events can cause substantial changes in soil chemistry. Establishing whether a particular group of trees is sensitive to these changes in soil environment and registers them in the elemental chemistry of contemporary growth rings is the over-riding goal of any Dendrochemistry research. In this study, elemental concentrations were measured in tree-ring samples of absolutely dated eleven modern forest trees, grown in the Mediterranean region, Turkey, collected and dated by the Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology laboratory at Cornell University. Correlations between measured elemental concentrations in the tree-ring samples were analyzed using statistical tests to answer two questions. Does the current concentration of a particular element depend on any other element within the tree? And, are there any elements showing correlated abnormal concentration changes across the majority of the trees? Based on the detailed analysis results, the low mobility of sodium and bromine, positive correlations between calcium, zinc and manganese, positive correlations between trace elements lanthanum, samarium, antimony, and gold within tree-rings were recognized. Moreover, zinc, lanthanum, samarium and bromine showed strong, positive correlations among the trees and were identified as possible environmental signature elements. New Dendrochemistry information found in this study would be also useful in explaining tree physiology and elemental chemistry in Pinus nigra species grown in Turkey. Elemental concentrations in tree-ring samples were measured using Neutron Activation Analysis (NAA) at the Pennsylvania State University Radiation Science and Engineering Center (RSEC). Through this study, advanced methodologies for methodological, computational and experimental NAA were developed to ensure an acceptable accuracy and certainty in the elemental concentration measurements in tree-ring samples. Two independent analysis methods of NAA were used; the well known k-zero method and a novel method developed in this study, called the Multi-isotope Iterative Westcott (MIW) method. The MIW method uses reaction rate probabilities for a group of isotopes, which can be calculated by a neutronic simulation or measured by experimentation, and determines the representative values for the neutron flux and neutron flux characterization parameters based on Westcott convention. Elemental concentration calculations for standard reference material and tree-ring samples were then performed using the MIW and k-zero analysis methods of the NAA and the results were cross verified. In the computational part of this study, a detailed burnup coupled neutronic simulation was developed to analyze real-time neutronic changes in a TRIGA Mark III reactor core, in this study, the Penn State Breazeale Reactor (PSBR) core. To the best of the author`s knowledge, this is the first burnup coupled neutronic simulation with realistic time steps and full fuel temperature profile for a TRIGA reactor using Monte Carlo Utility for Reactor Evolutions (MURE) code and Monte Carlo Neutral-Particle Code (MCNP) coupling. High fidelity and flexibility in the simulation was aimed to replicate the real core operation through the day. This approach resulted in an enhanced accuracy in neutronic representation of the PSBR core with respect to previous neutronic simulation models for the PSBR core. An important contribution was made in the NAA experimentation practices employed in Dendrochemistry studies at the RSEC. Automated laboratory control and analysis software for NAA measurements in the RSEC Radionuclide Applications Laboratory was developed. Detailed laboratory procedures were written in this study comprising preparation, handling and measurements of tree-ring samples in the Radionuclide Applications Laboratory.

Analysis of polycyclic aromatic hydrocarbons in tree-rings of Masson pine (Pinus massoniana L.) from two industrial sites in the Pearl River Delta, south China.

PubMed

Kuang, Yuan-wen; Zhou, Guo-yi; Wen, Da-zhi; Li, Jiong; Sun, Fang-fang

2011-09-01

Concentrations of polycyclic aromatic hydrocarbons (PAHs) were examined and potential sources of PAHs were identified from the dated tree-rings of Masson pine (Pinus massoniana L.) near two industrial sites (Danshuikeng, DSK and Xiqiaoshan, XQS) in the Pearl River Delta of south China. Total concentrations of PAHs (∑PAHs) were revealed with similar patterns of temporal trends in the tree-rings at both sites, suggesting tree-rings recorded the historical variation in atmospheric PAHs. The differences of individual PAHs and of ∑PAHs detected in the tree-rings between the two sites reflected the historical differences of airborne PAHs. Regional changes in industrial activities might contribute to the site-specific and period-specific patterns of the tree-ring PAHs. The diagnostic PAH ratios of Ant/(Ant + PA), FL/(FL + Pyr), and BaA/(BaA + Chr)) revealed that PAHs in the tree-rings at both sites mainly stemmed from the combustion process (pyrogenic sources). Principal component analysis further confirmed that wood burning, coal combustion, diesel, and gasoline-powered vehicular emissions were the dominant contributors of PAHs sources at DSK, while diesel combustion, gasoline and natural gas combustion, and incomplete coal combustion were responsible for the main origins of PAHs at XQS. Tree-ring analysis of PAHs was indicative of PAHs from a mixture of sources of combustion, thus minimizing the bias of short-term active air sampling.

Risk Analysis of Return Support Material on Gas Compressor Platform Project

NASA Astrophysics Data System (ADS)

Silvianita; Aulia, B. U.; Khakim, M. L. N.; Rosyid, Daniel M.

2017-07-01

On a fixed platforms project are not only carried out by a contractor, but two or more contractors. Cooperation in the construction of fixed platforms is often not according to plan, it is caused by several factors. It takes a good synergy between the contractor to avoid miss communication may cause problems on the project. For the example is about support material (sea fastening, skid shoe and shipping support) used in the process of sending a jacket structure to operation place often does not return to the contractor. It needs a systematic method to overcome the problem of support material. This paper analyses the causes and effects of GAS Compressor Platform that support material is not return, using Fault Tree Analysis (FTA) and Event Tree Analysis (ETA). From fault tree analysis, the probability of top event is 0.7783. From event tree analysis diagram, the contractors lose Rp.350.000.000, - to Rp.10.000.000.000, -.

Correlation analysis of tree growth, climate, and acid deposition in the Lake States.

Treesearch

Margaret R. Holdaway

1990-01-01

Describes research designed to detect subtle regional tree growth trends related to sulfate (SO4) deposition in the Lake States. Correlation methods were used to analyze climatic and SO4 deposition. Effects of SO4 deposition are greater on climatically stressed trees, especially pine species on dry sites, than on unstressed trees. Jack pine growth shows the...

Estimating cavity tree abundance using nearest neighbor imputation methods for western Oregon and Washington forests

Treesearch

Hailemariam Temesgen; Tara M. Barrett; Greg Latta

2008-01-01

Cavity trees contribute to diverse forest structure and wildlife habitat. For a given stand, the size and density of cavity trees indicate its diversity, complexity, and suitability for wildlife habitat. Size and density of cavity trees vary with stand age, density, and structure. Using Forest Inventory and Analysis (FIA) data collected in western Oregon and western...

The effect of acid precipitation on tree growth in eastern North America

Treesearch

Charles V. Cogbill

1976-01-01

Detailed study of the history of forest tree growth by tree-ring analysis is used to assess the effect of acid precipitation. The pattern and historical trends of acid precipitation deposition are compared with growth trends from mature forest stands in New Hampshire and Tennessee. No clear indication of a regional, synchronized decrease in tree growth was found. The...

Short-term dynamics of second-growth mixed mesophytic forest strata in West Virginia

Treesearch

Cynthia C. Huebner; Steven L. Stephenson; Harold S. Adams; Gary W. Miller

2007-01-01

The short-term dynamics of mixed mesophytic forest strata in West Virginia were examined using similarity analysis and linear correlation of shared ordination space. The overstory tree, understory tree, shrub/vine, and herb strata were stable over a six year interval, whereas the tree seedling and sapling strata were unstable. All strata but the shrub/vine and tree...

The zero inflation of standing dead tree carbon stocks

Treesearch

Christopher W. Woodall; David W. MacFarlane

2012-01-01

Given the importance of standing dead trees in numerous forest ecosystem attributes/processes such as carbon (C) stocks, the USDA Forest Service’s Forest Inventory and Analysis (FIA) program began consistent nationwide sampling of standing dead trees in 1999. Modeled estimates of standing dead tree C stocks are currently used as the official C stock estimates for the...

Predicting Potential Changes in Suitable Habitat and Distribution by 2100 for Tree Species of the Eastern United States

Treesearch

Louis R Iverson; Anantha M. Prasad; Mark W. Schwartz; Mark W. Schwartz

2005-01-01

We predict current distribution and abundance for tree species present in eastern North America, and subsequently estimate potential suitable habitat for those species under a changed climate with 2 x CO2. We used a series of statistical models (i.e., Regression Tree Analysis (RTA), Multivariate Adaptive Regression Splines (MARS), Bagging Trees (...

The urban forests of Philadelphia

Treesearch

David J. Nowak; Allison R. Bodine; Robert Hoehn; Alexis Ellis; Sarah C. Low; Lara A. Roman; Jason G. Henning; Emily Stephan; Tom Taggert; Ted Endreny

2016-01-01

An analysis of the urban forest in Philadelphia, Pennsylvania, reveals that this city has an estimated 2.9 million trees (encompassing all woody plants greater than 1 inch diameter at breast height [d.b.h]) with tree canopy that covers 20 percent of the city. The most common tree species are spicebush, black cherry, ash, tree-of-heaven, and boxelder, but the most...

Tree canopy change and neighborhood stability: A comparative analysis of Washington, D.C. and Baltimore, MD

Treesearch

Wen-Ching Chuang; Christopher G. Boone; Dexter H. Locke; J. Morgan Grove; Ali Whitmer; Geoffrey Buckley; Sainan Zhang

2017-01-01

Trees provide important health, ecosystem, and aesthetic services in urban areas, but they are unevenly distributed. Some neighborhoods have abundant tree canopy and others nearly none. We analyzed how neighborhood characteristics and changes in income over time related to the distribution of urban tree canopy in Washington, D.C. and Baltimore, MD. We used stepwise...

Austin's Urban Forest, 2014

Treesearch

David J. Nowak; Allison R. Bodine; Robert E. Hoehn; Christopher B. Edgar; Dudley R. Hartel; Tonya W. Lister; Thomas J. Brandeis

2016-01-01

An analysis of the urban forest in Austin, Texas, reveals that this area has an estimated 33.8 million trees with tree canopy that covers 30.8 percent of the city. The most common tree species are Ashe juniper, cedar elm, live oak, sugarberry, and Texas persimmon. Trees in Austin currently store about 1.9 million tons of carbon (7.0 million tons of carbon dioxide [CO...

Modeling Tree Mortality Following Wildfire in Pinus ponderosa Forests in the Central Sierra Nevada of California

Treesearch

Jon C. Regelbrugge

1993-01-01

Abstract. We modeled tree mortality occurring two years following wildfire in Pinus ponderosa forests using data from 1275 trees in 25 stands burned during the 1987 Stanislaus Complex fires. We used logistic regression analysis to develop models relating the probability of wildfire-induced mortality with tree size and fire severity for Pinus ponderosa, Calocedrus...

Thinning cherry-maple stands in West Virginia: 5-year results

Treesearch

Neil I. Lamson; H. Clay. Smith; H. Clay. Smith

1988-01-01

In northern West Virginia, 60-year-old cherry-maple stands were thinned to 75,60, and 45 percent relative stand density. Analysis of 5-year growth data showed that basal-area growth was not reduced by thinning. Cubic-foot and board-foot volume growth decreased slightly. Individual-tree growth of all trees, dominant/codominant trees, and the 50 largest diameter trees...

Boreal tree hydrodynamics: asynchronous, diverging, yet complementary.

PubMed

Pappas, Christoforos; Matheny, Ashley M; Baltzer, Jennifer L; Barr, Alan G; Black, T Andrew; Bohrer, Gil; Detto, Matteo; Maillet, Jason; Roy, Alexandre; Sonnentag, Oliver; Stephens, Jilmarie

2018-05-08

Water stress has been identified as a key mechanism of the contemporary increase in tree mortality rates in northwestern North America. However, a detailed analysis of boreal tree hydrodynamics and their interspecific differences is still lacking. Here we examine the hydraulic behaviour of co-occurring larch (Larix laricina) and black spruce (Picea mariana), two characteristic boreal tree species, near the southern limit of the boreal ecozone in central Canada. Sap flux density (Js), concurrently recorded stem radius fluctuations and meteorological conditions are used to quantify tree hydraulic functioning and to scrutinize tree water-use strategies. Our analysis revealed asynchrony in the diel hydrodynamics of the two species with the initial rise in Js occurring 2 h earlier in larch than in black spruce. Interspecific differences in larch and black spruce crown architecture explained the observed asynchrony in their hydraulic functioning. Furthermore, the two species exhibited diverging stomatal regulation strategies with larch and black spruce employing relatively isohydric and anisohydric behaviour, respectively. Such asynchronous and diverging tree-level hydrodynamics provide new insights into the ecosystem-level complementarity in tree form and function, with implications for understanding boreal forests' water and carbon dynamics and their resilience to environmental stress.

The decision tree classifier - Design and potential. [for Landsat-1 data

NASA Technical Reports Server (NTRS)

Hauska, H.; Swain, P. H.

1975-01-01

A new classifier has been developed for the computerized analysis of remote sensor data. The decision tree classifier is essentially a maximum likelihood classifier using multistage decision logic. It is characterized by the fact that an unknown sample can be classified into a class using one or several decision functions in a successive manner. The classifier is applied to the analysis of data sensed by Landsat-1 over Kenosha Pass, Colorado. The classifier is illustrated by a tree diagram which for processing purposes is encoded as a string of symbols such that there is a unique one-to-one relationship between string and decision tree.

Solar and climate signal records in tree ring width from Chile (AD 1587 1994)

NASA Astrophysics Data System (ADS)

Rodolfo Rigozo, Nivaor; Roger Nordemann, Daniel Jean; Evangelista da Silva, Heitor; Pereira de Souza Echer, Mariza; Echer, Ezequiel

2007-01-01

Tree growth rings represent an important natural record of past climate variations and solar activity effects registered on them. We performed in this study a wavelet analysis of tree ring samples of Pilgerodendron cupressoides species, from Glaciar Pio XI (Lat: 49°12'S; 74°55'W; Alt: 25 m), Chile. We obtained an average chronology of about 400 years from these trees. The 11-yr solar cycle was present during the whole period in tree ring data, being more intense during Maunder minimum (1645-1715). The short-term periods, around 2-7 yr, that were found are more likely associated with ENSO effects. Further, we found significant periods around 52 and 80-100 yr. These periodicities are coincident with the fourth harmonic (52 yr) of the Suess cycle (208 yr) and Gleissberg (˜80-100 yr) solar cycles. Therefore, the present analysis shows evidence of solar activity effect/modulation on climatic conditions that affect tree ring growth. Although we cannot say with the present analysis if this effect is on local, regional or global climate, these results add evidence to an important role of solar activity over terrestrial climate over the past ˜400 yr.

Predictability of the future development of aggressive behavior of cranial dural arteriovenous fistulas based on decision tree analysis.

PubMed

Satomi, Junichiro; Ghaibeh, A Ammar; Moriguchi, Hiroki; Nagahiro, Shinji

2015-07-01

The severity of clinical signs and symptoms of cranial dural arteriovenous fistulas (DAVFs) are well correlated with their pattern of venous drainage. Although the presence of cortical venous drainage can be considered a potential predictor of aggressive DAVF behaviors, such as intracranial hemorrhage or progressive neurological deficits due to venous congestion, accurate statistical analyses are currently not available. Using a decision tree data mining method, the authors aimed at clarifying the predictability of the future development of aggressive behaviors of DAVF and at identifying the main causative factors. Of 266 DAVF patients, 89 were eligible for analysis. Under observational management, 51 patients presented with intracranial hemorrhage/infarction during the follow-up period. The authors created a decision tree able to assess the risk for the development of aggressive DAVF behavior. Evaluated by 10-fold cross-validation, the decision tree's accuracy, sensitivity, and specificity were 85.28%, 88.33%, and 80.83%, respectively. The tree shows that the main factor in symptomatic patients was the presence of cortical venous drainage. In its absence, the lesion location determined the risk of a DAVF developing aggressive behavior. Decision tree analysis accurately predicts the future development of aggressive DAVF behavior.

[Analysis of the characteristics of the older adults with depression using data mining decision tree analysis].

PubMed

Park, Myonghwa; Choi, Sora; Shin, A Mi; Koo, Chul Hoi

2013-02-01

The purpose of this study was to develop a prediction model for the characteristics of older adults with depression using the decision tree method. A large dataset from the 2008 Korean Elderly Survey was used and data of 14,970 elderly people were analyzed. Target variable was depression and 53 input variables were general characteristics, family & social relationship, economic status, health status, health behavior, functional status, leisure & social activity, quality of life, and living environment. Data were analyzed by decision tree analysis, a data mining technique using SPSS Window 19.0 and Clementine 12.0 programs. The decision trees were classified into five different rules to define the characteristics of older adults with depression. Classification & Regression Tree (C&RT) showed the best prediction with an accuracy of 80.81% among data mining models. Factors in the rules were life satisfaction, nutritional status, daily activity difficulty due to pain, functional limitation for basic or instrumental daily activities, number of chronic diseases and daily activity difficulty due to disease. The different rules classified by the decision tree model in this study should contribute as baseline data for discovering informative knowledge and developing interventions tailored to these individual characteristics.

A field-to-desktop toolchain for X-ray CT densitometry enables tree ring analysis

PubMed Central

De Mil, Tom; Vannoppen, Astrid; Beeckman, Hans; Van Acker, Joris; Van den Bulcke, Jan

2016-01-01

Background and Aims Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. Methods Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. Key Results Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. Conclusions A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species. PMID:27107414

Chlorinated ethenes from groundwater in tree trunks

USGS Publications Warehouse

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

1999-01-01

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

A Laser Photoacoustic Analysis of Residual CO2 and H2O in Larch Stems

PubMed Central

Ageev, Boris; Ponomarev, Yurii; Sapozhnikova, Valeria; Savchuk, Dmitry

2014-01-01

Every so often, the results obtained from investigations into the effects of varying environmental conditions on the tree growth rate at the same sites and on the change in the carbon balance in plants, using traditional methods, are found to differ widely. We believe that the reason for the ambiguity of the data has to do with failure to account for the role of the residual CO2 (and H2O) in the tree wood exhibiting a climate response. In our earlier work, the results of a laser photoacoustic gas analysis of CO2 and H2O vacuum-desorbed from disc tree rings of evergreen conifer trees were presented. In this paper, laser photoacoustic measurements of tree ring gases in deciduous conifer trees and CO2 carbon isotope composition determined by means of a mass spectrometer are given. Conclusions are made regarding the response of annual larch CO2 disc tree ring distributions to climatic parameters (temperatures and precipitation). The data about the CO2 disc content for different sites are compared. PMID:25808838

Looking/Learning Drawing: Trees.

ERIC Educational Resources Information Center

Hurwitz, Al; Blume, Sharon

1985-01-01

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

Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach.

PubMed

Petruzziello, Filomena; Fouillen, Laetitia; Wadensten, Henrik; Kretz, Robert; Andren, Per E; Rainer, Gregor; Zhang, Xiaozhe

2012-02-03

Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.

Gap-free segmentation of vascular networks with automatic image processing pipeline.

PubMed

Hsu, Chih-Yang; Ghaffari, Mahsa; Alaraj, Ali; Flannery, Michael; Zhou, Xiaohong Joe; Linninger, Andreas

2017-03-01

Current image processing techniques capture large vessels reliably but often fail to preserve connectivity in bifurcations and small vessels. Imaging artifacts and noise can create gaps and discontinuity of intensity that hinders segmentation of vascular trees. However, topological analysis of vascular trees require proper connectivity without gaps, loops or dangling segments. Proper tree connectivity is also important for high quality rendering of surface meshes for scientific visualization or 3D printing. We present a fully automated vessel enhancement pipeline with automated parameter settings for vessel enhancement of tree-like structures from customary imaging sources, including 3D rotational angiography, magnetic resonance angiography, magnetic resonance venography, and computed tomography angiography. The output of the filter pipeline is a vessel-enhanced image which is ideal for generating anatomical consistent network representations of the cerebral angioarchitecture for further topological or statistical analysis. The filter pipeline combined with computational modeling can potentially improve computer-aided diagnosis of cerebrovascular diseases by delivering biometrics and anatomy of the vasculature. It may serve as the first step in fully automatic epidemiological analysis of large clinical datasets. The automatic analysis would enable rigorous statistical comparison of biometrics in subject-specific vascular trees. The robust and accurate image segmentation using a validated filter pipeline would also eliminate operator dependency that has been observed in manual segmentation. Moreover, manual segmentation is time prohibitive given that vascular trees have more than thousands of segments and bifurcations so that interactive segmentation consumes excessive human resources. Subject-specific trees are a first step toward patient-specific hemodynamic simulations for assessing treatment outcomes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Record of the Solar Activity and of Other Geophysical Phenomenons in Tree Ring

NASA Astrophysics Data System (ADS)

Rigozo, Nivaor Rodolfo

1999-01-01

Tree ring studies are usually used to determine or verify climatic factors which prevail in a given place or region and may cause tree ring width variations. Few studies are dedicated to the geophysical phenomena which may underlie these tree ring width variations. In order to look for periodicities which may be associated to the solar activity and/or to other geophysical phenomena which may influence tree ring growth, a new interactive image analysis method to measure tree ring width was developed and is presented here. This method makes use of a computer and a high resolution flatbed scanner; a program was also developed in Interactive Data Language (IDL 5.0) to study ring digitized images and transform them into time series. The main advantage of this method is the tree ring image interactive analysis without needing complex and high cost instrumentation. Thirty-nine samples were collected: 12 from Concordia - S. C., 9 from Canela - R. S., 14 from Sao Francisco de Paula - R. S., one from Nova Petropolis - R. S., 2 from Sao Martinho da Serra - R. S. e one from Chile. Fit functions are applied to ring width time series to obtain the best long time range trend (growth rate of every tree) curves and are eliminated through a standardization process that gives the tree ring index time series from which is performed spectral analysis by maximum entropy method and iterative regression. The results obtained show periodicities close to 11 yr, 22 yr Hale solar cycles and 5.5 yr for all sampling locations 52 yr and Gleissberg cycles for Concordia - S. C. and Chile samples. El Nino events were also observed with periods around 4 e 7 yr.

Automatic Inference of Cryptographic Key Length Based on Analysis of Proof Tightness

DTIC Science & Technology

2016-06-01

within an attack tree structure, then expand attack tree methodology to include cryptographic reductions. We then provide the algorithms for...maintaining and automatically reasoning about these expanded attack trees . We provide a software tool that utilizes machine-readable proof and attack metadata...and the attack tree methodology to provide rapid and precise answers regarding security parameters and effective security. This eliminates the need

Analysis of the 'A72' peach tree growth habit and its inheritance in progeny obtained from crosses of 'A72' with columnar peach trees

USDA-ARS?s Scientific Manuscript database

Since the first report of the 'A72' semi-dwarf peach tree (Nn) by Monet and Salesses (1975), little information has become available on this genotype. We evaluated the growth habit and verified the inheritance of 'A72' in a population of 220 progeny derived from self-pollination. Detailed tree and ...

Sap-Sugar Content of Grafted Sugar Maple Trees

Treesearch

Maurice E. Jr. Demeritt; Maurice E. Jr. Demeritt

1985-01-01

In March and April 1983, 289 and 196 young grafted sugar maple trees were tapped and evaluated for sap-sugar content. In April, sap was collected from taps both above and below the graft union. Diameter of all tapped trees at 18 inches above the ground was measured. Analysis of the data revealed that: (1) trees selected for high sugar yield cannot be reproduced by...

Predicting height increment of young-growth red fir in California and southern Oregon

Treesearch

K. Leroy Dolph

1992-01-01

An equation is given to estimate 10-year height increment for young-growth red fir trees in California and southern Oregon. The independent variables are the individual tree, stand, and site characteristics significantly related to a tree's height growth. Data used to develop the equation came from stem analysis of 492 trees sampled from 56 stands in the study...

A diameter growth model for the SRS FIA

Treesearch

David Gartner

2015-01-01

Changes in the national Forest Inventory and Analysis (FIA) processing system required the Southern Research Station’s FIA unit to create a diameter growth model to estimate the growth of trees that could not be measured at both ends of a measurement interval. Examples of such trees are trees that have died or been harvested, and trees that grow over the minimum...

An analysis of phenotypic selection in natural stands of northern red oak (Quercus rubra L.)

Treesearch

Jeffery W. Stringer; David B. Wagner; Scott E. Schlarbaum; Daniel B. Houston

1995-01-01

Comparison of growth and stem quality parameters of 19-year-old progeny from superior and comparison trees indicates that rigorous phenotypic selection of trees in natural stands may not be an efficient method of parent tree selection for Quercus rubra L. Total tree height, dbh, number of branches in the butt log, fork height, and number of mainstem...

Pilot Inventory of FIA plots traditionally called `nonforest'

Treesearch

Rachel Riemann

2003-01-01

Forest-inventory data were collected on plots defined as ?nonforest? by the USDA Forest Service?s Forest Inventory and Analysis (FIA) unit. Nonforest plots may have trees on them, but they do not fit FIA?s definition of forest because the area covered by trees is too small, too sparsely populated by trees, too narrow (e.g., trees between fields or in the middle of a...

Parallel peak pruning for scalable SMP contour tree computation

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

Carr, Hamish A.; Weber, Gunther H.; Sewell, Christopher M.

As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this formmore » of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.« less

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

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

Newer classification and regression tree techniques: Bagging and Random Forests for ecological prediction

Treesearch

Anantha M. Prasad; Louis R. Iverson; Andy Liaw; Andy Liaw

2006-01-01

We evaluated four statistical models - Regression Tree Analysis (RTA), Bagging Trees (BT), Random Forests (RF), and Multivariate Adaptive Regression Splines (MARS) - for predictive vegetation mapping under current and future climate scenarios according to the Canadian Climate Centre global circulation model.

Amount and distribution of isozyme variation in various conifer species

Treesearch

M. Thompson Conkle

1980-01-01

Estimation of the relative amount and the geographic distribution of genetically controlled variation is a central topic of tree resource management. Biochemical data from the analysis of forest tree enzyme variants provides a direct and precise measure of allele frequencies of tree genes.

Trees as bioindicators of industrial air pollution during implementation of pro-environmental policy in Silesia region (Poland).

NASA Astrophysics Data System (ADS)

Sensuła, Barbara; Wilczyński, Slawomir; Opała, Magdalena; Pawełczyk, Sławomira; Piotrowska, Natalia

2015-04-01

The aim of research conducted within the project entitled "Trees as bioindicators of industrial air pollutants during the implementation of pro-environmental policies in the area of Silesia" (acronym BIOPOL) is the reconstruction of climate changes and anthropogenic effects and monitoring of the influence of human activities related to industrial development and the introduction of pro-environmental policy. The analysis will concern the climatic and anthropogenic signals recorded in annual tree rings width of Scots pine and in the isotopic composition of wood and its compenents (such as alpha-cellulose and glucose). Only a few studies made a complex multiproxies analysis of the influence of industrial air pollutants on changes in the tree rings width and their isotopic composition in any selected region. In addition, research is usually for a period of industrial development, is a lack of analysis for the period of implementation of EU law and standards on air quality to Polish law. The research area are the forests close to 3 different industrial plants (chemical- nitrogen plants, steel mills, power plants), in Silesia, where operating companies have strategic importance for the region and country. By analyzing the structure of land in Silesia noted a significant advantage of forest land and agricultural land. A large percentage of forest land providing protection for residents in case of failure in any of the plants. A cloud of noxious fumes is possible in large part retained in the trees. Waste generated by the chemical industry, metallurgy and energy represent the largest proportion of waste generated in the region. Already in the beginning of 21stcentury, the Waste Management Plans for various cities in Silesia are set out various strategic objectives to 2015, including in the economic sector: the implementation of non-waste technology and less and the best available techniques (BAT), the introduction of the principles of "cleaner production". The BIOPOL innovation is: a) multiproxy spatio-temporal analysis of the effects of climate changes and emission of air industrial pollution on trees during the development of industry and the implementation of pro-environmental policies in Silesia: - Analysis of the width of annual tree rings (since 1975) - Analysis of underestimation of the 14C concentration during the implementation of European standards (since 2000) - Analysis of the recorded signals of environmental changes in the composition of stable isotopes in annual tree rings - wood and its components b) modeling of the influence of pollutants emitted into the atmosphere on the width of annual growth of trees and C,O,N stable isotopes and radiocarbon - Spatio-temporal model of environmental change in the tree rings width and their isotopic composition close to each of the selected plants - comparison to the impact of climate change and industrial pollution for 3 different industries (steel mills, power plants, nitrogen plants) in the period from 1975 to present - Space model of environmental changes in the isotopic composition of trees near each of the selected plants (at varying distances from the chosen site) based on analysis of isotopic composition of annual shoots of pine trees in three consecutive years: from 2012 to 2014) - Estimation of emission components originating from industrial pollution for individual plants This project was funded by the National Science Centre allocated on the basis of the decision number DEC-2011/03/D/ST10/05251

Tree Height and DBH Growth Model Establishment of Main Tree Species in Wuling Mountain Small Watershed

NASA Astrophysics Data System (ADS)

Luo, Jia; Zhang, Min; Zhou, Xiaoling; Chen, Jianhua; Tian, Yuxin

2018-01-01

Taken 4 main tree species in the Wuling mountain small watershed as research objects, 57 typical sample plots were set up according to the stand type, site conditions and community structure. 311 goal diameter-class sample trees were selected according to diameter-class groups of different tree-height grades, and the optimal fitting models of tree height and DBH growth of main tree species were obtained by stem analysis using Richard, Logistic, Korf, Mitscherlich, Schumacher, Weibull theoretical growth equations, and the correlation coefficient of all optimal fitting models reached above 0.9. Through the evaluation and test, the optimal fitting models possessed rather good fitting precision and forecast dependability.

Bit Synchronization with Cross Spectrum Synchronization Loop. Attachment III.

DTIC Science & Technology

1981-10-01

AO-AII 1 ICMCR AAE~C BIT SYNCHRONIZATION WITH CROSS SPECTRUM SYNCHRONIZATION LOOP .A_ ETC(U) O’ASFE CT A1 R A MA A 6. A C LINDSEY, C M CHIE NOOOI𔃾...BUR[AU OF STANOARDS 196.- A I~I -I I I Yinwoa on. IAoalt [ S0Box0 2793D, Pasadena Calif 91105 82 03 09098 I7- ATTACHMENT III BIT SYNCHRONIZATION WITH...CROSS SPECTRUM SYNCHRONIZATION LOOP I ’I PREPARED FOR NAVAL RESEARCH LABORATORY WASHINGTON, D.C. 20375 .Jr TECHNICAL MONITOR: MR. MORT FRANK I CONTRACT

Surface Wave Effects on High-Frequency Currents Over a Shelf Edge Bank

DTIC Science & Technology

2013-08-01

as part of projects sponsored by the Naval Research Laboratory (NRL) [Mixing Over Rough Topography (MORT)] and by the Bureau of Ocean Energy Management ...random wave fieldUS(z) is calculated as an ensemble average of wave components (Kenyon 1969), where US(z)5 4p ðf c f min ð2p 0 fkE(f , u)G(f , z) du df...Energy Management (BOEM; formerly Min- erals Management Service) in the project referred to as ‘‘Currents Over Banks (COB)’’ through the Interagency

Improving Cluster Analysis with Automatic Variable Selection Based on Trees

DTIC Science & Technology

2014-12-01

regression trees Daisy DISsimilAritY PAM partitioning around medoids PMA penalized multivariate analysis SPC sparse principal components UPGMA unweighted...unweighted pair-group average method ( UPGMA ). This method measures dissimilarities between all objects in two clusters and takes the average value

Fault Tree Analysis as a Planning and Management Tool: A Case Study

ERIC Educational Resources Information Center

Witkin, Belle Ruth

1977-01-01

Fault Tree Analysis is an operations research technique used to analyse the most probable modes of failure in a system, in order to redesign or monitor the system more closely in order to increase its likelihood of success. (Author)

Tree Line Structure and Dynamics at the Northern Limit of the Larch Forest: Anabar Plateau, Siberia, Russia

NASA Technical Reports Server (NTRS)

Kharuk, Viacheslav I.; Ranson, Kenneth J.; Im, Sergey T.; Oskorbin, Pavel A.; Dvinskaya, Maria L.; Ovchinnikov, Dmitriy V.

2013-01-01

The goal of the study was to provide an analysis of climate impact before, during, and after the Little Ice Age (LIA) on the larch (Larix gmelinii) tree line at the northern extreme of Siberian forests. Recent decadal climate change impacts on the tree line, regeneration abundance, and age structure were analyzed. The location of the study area was within the forest-tundra ecotone (elevation range 170-450 m) in the Anabar Plateau, northern Siberia. Field studies were conducted along elevational transects. Tree natality/mortality and radial increment were determined based on dendrochronology analyses. Tree morphology, number of living and subfossil trees, regeneration abundance, and age structure were studied. Locations of pre-LIA, LIA, and post-LIA tree lines and refugia boundaries were established. Long-term climate variables and drought index were included in the analysis. It was found that tree mortality from the 16th century through the beginning of the 19th century caused a downward tree line recession. Sparse larch stands experienced deforestation, transforming into tundra with isolated relict trees. The maximum tree mortality and radial growth decrease were observed to have occurred at the beginning of 18th century. Now larch, at its northern boundary in Siberia, is migrating into tundra areas. Upward tree migration was induced by warming in the middle of the 19th century. Refugia played an important role in repopulation of the forest-tundra ecotone by providing a seed source and shelter for recruitment of larch regeneration. Currently this ecotone is being repopulated mainly by tree cohorts that were established after the 1930s. The last two decades of warming did not result in an acceleration of regeneration recruitment because of increased drought conditions. The regeneration line reached (but did not exceed) the pre-LIA tree line location, although contemporary tree heights and stand densities are comparatively lower than in the pre-LIA period. The mean rate of tree line upward migration has been about 0.35 m/yr (with a range of 0.21-0.58), which translates to a tree line response to temperature of about 55 m/deg C.

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae).

PubMed

Knowles, Lacey L; Klimov, Pavel B

2011-11-01

With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

Pan-Tropical Analysis of Climate Effects on Seasonal Tree Growth

PubMed Central

Wagner, Fabien; Rossi, Vivien; Aubry-Kientz, Mélaine; Bonal, Damien; Dalitz, Helmut; Gliniars, Robert; Stahl, Clément; Trabucco, Antonio; Hérault, Bruno

2014-01-01

Climate models predict a range of changes in tropical forest regions, including increased average temperatures, decreased total precipitation, reduced soil moisture and alterations in seasonal climate variations. These changes are directly related to the increase in anthropogenic greenhouse gas concentrations, primarily CO2. Assessing seasonal forest growth responses to climate is of utmost importance because woody tissues, produced by photosynthesis from atmospheric CO2, water and light, constitute the main component of carbon sequestration in the forest ecosystem. In this paper, we combine intra-annual tree growth measurements from published tree growth data and the corresponding monthly climate data for 25 pan-tropical forest sites. This meta-analysis is designed to find the shared climate drivers of tree growth and their relative importance across pan-tropical forests in order to improve carbon uptake models in a global change context. Tree growth reveals significant intra-annual seasonality at seasonally dry sites or in wet tropical forests. Of the overall variation in tree growth, 28.7% was explained by the site effect, i.e. the tree growth average per site. The best predictive model included four climate variables: precipitation, solar radiation (estimated with extrasolar radiation reaching the atmosphere), temperature amplitude and relative soil water content. This model explained more than 50% of the tree growth variations across tropical forests. Precipitation and solar radiation are the main seasonal drivers of tree growth, causing 19.8% and 16.3% of the tree growth variations. Both have a significant positive association with tree growth. These findings suggest that forest productivity due to tropical tree growth will be reduced in the future if climate extremes, such as droughts, become more frequent. PMID:24670981

Pan-tropical analysis of climate effects on seasonal tree growth.

PubMed

Wagner, Fabien; Rossi, Vivien; Aubry-Kientz, Mélaine; Bonal, Damien; Dalitz, Helmut; Gliniars, Robert; Stahl, Clément; Trabucco, Antonio; Hérault, Bruno

2014-01-01

Climate models predict a range of changes in tropical forest regions, including increased average temperatures, decreased total precipitation, reduced soil moisture and alterations in seasonal climate variations. These changes are directly related to the increase in anthropogenic greenhouse gas concentrations, primarily CO2. Assessing seasonal forest growth responses to climate is of utmost importance because woody tissues, produced by photosynthesis from atmospheric CO2, water and light, constitute the main component of carbon sequestration in the forest ecosystem. In this paper, we combine intra-annual tree growth measurements from published tree growth data and the corresponding monthly climate data for 25 pan-tropical forest sites. This meta-analysis is designed to find the shared climate drivers of tree growth and their relative importance across pan-tropical forests in order to improve carbon uptake models in a global change context. Tree growth reveals significant intra-annual seasonality at seasonally dry sites or in wet tropical forests. Of the overall variation in tree growth, 28.7% was explained by the site effect, i.e. the tree growth average per site. The best predictive model included four climate variables: precipitation, solar radiation (estimated with extrasolar radiation reaching the atmosphere), temperature amplitude and relative soil water content. This model explained more than 50% of the tree growth variations across tropical forests. Precipitation and solar radiation are the main seasonal drivers of tree growth, causing 19.8% and 16.3% of the tree growth variations. Both have a significant positive association with tree growth. These findings suggest that forest productivity due to tropical tree growth will be reduced in the future if climate extremes, such as droughts, become more frequent.

Multivariate analysis of flow cytometric data using decision trees.

PubMed

Simon, Svenja; Guthke, Reinhard; Kamradt, Thomas; Frey, Oliver

2012-01-01

Characterization of the response of the host immune system is important in understanding the bidirectional interactions between the host and microbial pathogens. For research on the host site, flow cytometry has become one of the major tools in immunology. Advances in technology and reagents allow now the simultaneous assessment of multiple markers on a single cell level generating multidimensional data sets that require multivariate statistical analysis. We explored the explanatory power of the supervised machine learning method called "induction of decision trees" in flow cytometric data. In order to examine whether the production of a certain cytokine is depended on other cytokines, datasets from intracellular staining for six cytokines with complex patterns of co-expression were analyzed by induction of decision trees. After weighting the data according to their class probabilities, we created a total of 13,392 different decision trees for each given cytokine with different parameter settings. For a more realistic estimation of the decision trees' quality, we used stratified fivefold cross validation and chose the "best" tree according to a combination of different quality criteria. While some of the decision trees reflected previously known co-expression patterns, we found that the expression of some cytokines was not only dependent on the co-expression of others per se, but was also dependent on the intensity of expression. Thus, for the first time we successfully used induction of decision trees for the analysis of high dimensional flow cytometric data and demonstrated the feasibility of this method to reveal structural patterns in such data sets.

Estimating the number of tree species in forest populations using current vegetation survey and forest inventory and analysis approximation plots and grid intensities

Treesearch

Hans T. Schreuder; Jin-Mann S. Lin; John Teply

2000-01-01

We estimate number of tree species in National Forest populations using the nonparametric estimator. Data from the Current Vegetation Survey (CVS) of Region 6 of the USDA Forest Service were used to estimate the number of tree species with a plot close in size to the Forest Inventory and Analysis (FIA) plot and the actual CVS plot for the 5.5 km FIA grid and the 2.7 km...

Structural system reliability calculation using a probabilistic fault tree analysis method

NASA Technical Reports Server (NTRS)

Torng, T. Y.; Wu, Y.-T.; Millwater, H. R.

1992-01-01

The development of a new probabilistic fault tree analysis (PFTA) method for calculating structural system reliability is summarized. The proposed PFTA procedure includes: developing a fault tree to represent the complex structural system, constructing an approximation function for each bottom event, determining a dominant sampling sequence for all bottom events, and calculating the system reliability using an adaptive importance sampling method. PFTA is suitable for complicated structural problems that require computer-intensive computer calculations. A computer program has been developed to implement the PFTA.

Tests with VHR images for the identification of olive trees and other fruit trees in the European Union

NASA Astrophysics Data System (ADS)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

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

MrEnt: an editor for publication-quality phylogenetic tree illustrations.

PubMed

Zuccon, Alessandro; Zuccon, Dario

2014-09-01

We developed MrEnt, a Windows-based, user-friendly software that allows the production of complex, high-resolution, publication-quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication. © 2014 John Wiley & Sons Ltd.

Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3

USDA-ARS?s Scientific Manuscript database

We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Usin...

GLOBAL WARMING MITIGATION POTENTIAL OF THREE TREE PLANTATION SCENARIIOS

EPA Science Inventory

The report gives results of an analysis of three alternative uses of forests in the U.S. to reduce atmospheric carbon dioxide (CO2)concentrations: (1) planting trees with no harvesting, (2) traditional forestry, and (3) short-rotation intensive culture of trees for biomass. ncrea...

Tree biology and dendrochemistry

Treesearch

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...

Quality of Life Score as a Predictor of Death in Dogs with Degenerative Mitral Valve Disease.

PubMed

Strunz, Célia M C; Marcondes-Santos, Mário; Takada, Julio Yoshio; Fragata, Fernanda S; Mansur, Antônio de Pádua

2017-04-01

The knowledge of the variables predicting mortality is important in clinical practice and for therapeutic monitoring in mitral valve disease. To determine whether a quality of life score evaluated with the Functional Evaluation of Cardiac Health questionnaire would predict mortality in dogs with degenerative mitral valve disease (DMVD). Thirty-six client-owned dogs with mitral valve disease underwent clinical, laboratory, and echocardiographic evaluations at baseline and were monitored for 6 months. Cardiovascular death was the primary outcome. The 36 dogs were classified as survivors or nonsurvivors. Higher values of the following variables were obtained at baseline in the nonsurviving group (12 dogs): amino-terminal pro-B-type natriuretic peptide (NT-proBNP) levels, plasma norepinephrine, heart rate, quality of life score, diastolic left ventricular internal dimension to aortic root ratio, systolic left ventricular internal dimension to aortic root ratio, and left atrium to aortic root ratio. NT-proBNP levels and quality life score were independently associated with death in the multivariable analysis. The quality life score was an independent variable for cardiac death in dogs with DMVD. This result is encouraging, as this score is easy to apply and does not require any technology, only a veterinarian and an observant owner. O conhecimento das variáveis preditoras de mortalidade é importante para a prática clínica e para o acompanhamento terapêutico na doença da valva mitral. Determinar se um escore de qualidade de vida avaliado com o Functional Evaluation of Cardiac Health poderia auxiliar na predição de mortalidade em cães com doença degenerativa da valva mitral (DDVM). Trinta e seis cães de estimação com doença valvar mitral foram submetidos a avaliação clínica, laboratorial e ecocardiográfica no início do estudo e monitorizados durante 6 meses. A morte cardiovascular foi o desfecho primário. Os 36 cães foram classificados como sobreviventes ou não sobreviventes. Os valores mais elevados das seguintes variáveis foram obtidos no início do estudo no grupo de não sobreviventes (12 cães): fragmento N-terminal do peptídeo natriurético tipo B (NT-proBNP), norepinefrina plasmática, frequência cardíaca, escore de qualidade de vida, razão da dimensão interna diastólica do ventrículo esquerdo e raiz aórtica, razão da dimensão interna sistólica do ventrículo esquerdo e raiz aórtica e a relação da dimensão do átrio esquerdo e a raiz aórtica. Concentrações de NT-proBNP e o escore de qualidade de vida foram independentemente associados com morte na análise multivariada. O escore de qualidade de vida foi uma variável independente para a morte por doença cardíaca em cães com DDVM. Este resultado é encorajador, pois este escore é de fácil aplicação e não requer o emprego de tecnologia, necessitando apenas de um veterinário e um dono observador.

Decision tree analysis to stratify risk of de novo non-melanoma skin cancer following liver transplantation.

PubMed

Tanaka, Tomohiro; Voigt, Michael D

2018-03-01

Non-melanoma skin cancer (NMSC) is the most common de novo malignancy in liver transplant (LT) recipients; it behaves more aggressively and it increases mortality. We used decision tree analysis to develop a tool to stratify and quantify risk of NMSC in LT recipients. We performed Cox regression analysis to identify which predictive variables to enter into the decision tree analysis. Data were from the Organ Procurement Transplant Network (OPTN) STAR files of September 2016 (n = 102984). NMSC developed in 4556 of the 105984 recipients, a mean of 5.6 years after transplant. The 5/10/20-year rates of NMSC were 2.9/6.3/13.5%, respectively. Cox regression identified male gender, Caucasian race, age, body mass index (BMI) at LT, and sirolimus use as key predictive or protective factors for NMSC. These factors were entered into a decision tree analysis. The final tree stratified non-Caucasians as low risk (0.8%), and Caucasian males > 47 years, BMI < 40 who did not receive sirolimus, as high risk (7.3% cumulative incidence of NMSC). The predictions in the derivation set were almost identical to those in the validation set (r 2  = 0.971, p < 0.0001). Cumulative incidence of NMSC in low, moderate and high risk groups at 5/10/20 year was 0.5/1.2/3.3, 2.1/4.8/11.7 and 5.6/11.6/23.1% (p < 0.0001). The decision tree model accurately stratifies the risk of developing NMSC in the long-term after LT.

Sampling strategy and climatic implication of tree-ring cellulose oxygen isotopes of Hippophae tibetana and Abies georgei on the southeastern Tibetan Plateau

NASA Astrophysics Data System (ADS)

Xu, Chenxi; Zhu, Haifeng; Nakatsuka, Takeshi; Sano, Masaki; Li, Zhen; Shi, Feng; Liang, Eryuan; Guo, Zhengtang

2017-05-01

The tree-ring cellulose oxygen isotopes (δ18O) for four trees of Hippophae tibetana and four trees of Abies georgei growing in different locations around the terminal moraine in Xincuo from 1951 to 2010 were measured to explore its potential for reconstructing climatic variations in the southeastern Tibetan Plateau. The mean and standard deviation of tree-ring δ18O at different heights do not have significant differences, and there are no significant differences in the mean and standard deviation of tree-ring δ18O between trees near the brook and trees at the top of moraine, indicating that we can collect samples for tree-ring δ18O analysis regardless of sampling heights and that the micro-environment does not affect tree-ring δ18O significantly. The mean inter-series correlations of cellulose δ18O for A. georgei/H. tibetana are 0.84/0.93, and the correlation between δ18O for A. georgei and H. tibetana is 0.92. The good coherence between inter-tree and inter-species cellulose δ18O demonstrates the possibility of using different species to develop a long chronology. Correlation analysis between tree-ring δ18O and climate parameters revealed that δ18O for A. georgei/H. tibetana had negative correlations (r = -0.62/r = -0.69) with relative humidity in July-August, and spatial correlation revealed that δ18O for A. georgei/H. tibetana reflected the regional Standardized Precipitation Evapotranspiration Index (29°-32° N, 88°-98° E). In addition, tree-ring δ18O in Xincuo has a significant correlation with tree-ring δ18O in Bhutan. The results indicate that cellulose δ18O for A. georgei and H. tibetana in Xincuo is a good proxy for the regional hydroclimate.

Assessing urban forest effects and values, Minneapolis' urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2006-01-01

An analysis of trees in Minneapolis, MN, reveals that the city has about 979,000 trees with canopies that cover 26.4 percent of the area. The most common tree species are green ash, American elm, and boxelder. The urban forest currently stores about 250,000 tons of carbon valued at $4.6 million. In addition, these trees remove about 8,900 tons of carbon per year ($164,...

Assessing urban forest effects and values, Casper's urban forest

Treesearch

David J. Nowak; Robert E., III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2006-01-01

An analysis of trees in Casper, WY reveals that this city has about 123,000 trees with canopies that cover 8.9 percent of the area. The most common tree species are plains cottonwood, blue spruce, and American elm. The urban forest currently store about 37,000 tons of carbon valued at $689,000. In addition, these trees remove about 1,200 tons of carbon per year ($22,...

The improvement of precision for estimating the abundance of standing dead trees using auxiliary information under the FIA pot design

Treesearch

Hong Su An; David W. MacFarlane; Christopher W. Woodall

2012-01-01

Standing dead trees are an important component of forest ecosystems. However, reliable estimates of standing dead tree population parameters can be difficult to obtain due to their low abundance and spatial and temporal variation. After 1999, the Forest Inventory and Analysis (FIA) Program began collecting data for standing dead trees at the Phase 2 stage of sampling....

Recent changes in the estimation of standing dead tree biomass and carbon stocks in the U.S. forest inventory

Treesearch

Grant M. Domke; Christopher W. Woodall; James E. Smith

2012-01-01

Until recently, standing dead tree biomass and carbon (C) has been estimated as a function of live tree growing stock volume in the U.S. Forest Service, Forest Inventory and Analysis (FIA) Program. Traditional estimates of standing dead tree biomass/C attributes were based on merchantability standards that did not reflect density reductions or structural loss due to...

Assessing urban forest effects and values: Toronto's urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Allison R. Bodine; Eric J. Greenfield; Alexis Ellis; Theodore A. Endreny; Yang Yang; Tian Zhou; Ruthanne Henry

2013-01-01

An analysis of trees in Toronto, Ontario, reveals that this city has about 10.2 million trees with a tree and shrub canopy that covers approximately 26.6 percent of the city. The most common tree species are eastern white-cedar, sugar maple, and Norway maple. The urban forest currently stores an estimated 1.1 million metric tons of carbon valued at CAD$25.0 million. In...

Assessing urban forest effects and values, San Francisco's urban forest

Treesearch

David J. Nowak; Robert E., III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2007-01-01

An analysis of trees in San Francisco, CA reveals that this city has about 669,000 trees with canopies that cover 11.9 percent of the area. The most common tree species are blue gum eucalyptus, Monterey pine, and Monterey cypress. The urban forest currently stores about 196,000 tons of carbon valued at $3.6 million. In addition, these trees remove about 5,200 tons of...

Binary tree eigen solver in finite element analysis

NASA Technical Reports Server (NTRS)

Akl, F. A.; Janetzke, D. C.; Kiraly, L. J.

1993-01-01

This paper presents a transputer-based binary tree eigensolver for the solution of the generalized eigenproblem in linear elastic finite element analysis. The algorithm is based on the method of recursive doubling, which parallel implementation of a number of associative operations on an arbitrary set having N elements is of the order of o(log2N), compared to (N-1) steps if implemented sequentially. The hardware used in the implementation of the binary tree consists of 32 transputers. The algorithm is written in OCCAM which is a high-level language developed with the transputers to address parallel programming constructs and to provide the communications between processors. The algorithm can be replicated to match the size of the binary tree transputer network. Parallel and sequential finite element analysis programs have been developed to solve for the set of the least-order eigenpairs using the modified subspace method. The speed-up obtained for a typical analysis problem indicates close agreement with the theoretical prediction given by the method of recursive doubling.

ESTimating plant phylogeny: lessons from partitioning

PubMed Central

de la Torre, Jose EB; Egan, Mary G; Katari, Manpreet S; Brenner, Eric D; Stevenson, Dennis W; Coruzzi, Gloria M; DeSalle, Rob

2006-01-01

Background While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. Results A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. Conclusion Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products. PMID:16776834

A Deliberate Practice Approach to Teaching Phylogenetic Analysis

PubMed Central

Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

2013-01-01

One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or “one-shot,” in-class activities. Using a deliberate practice instructional approach, we designed a set of five assignments for a 300-level plant systematics course that incrementally introduces the concepts and skills used in phylogenetic analysis. In our assignments, students learned the process of constructing phylogenetic trees through a series of increasingly difficult tasks; thus, skill development served as a framework for building content knowledge. We present results from 5 yr of final exam scores, pre- and postconcept assessments, and student surveys to assess the impact of our new pedagogical materials on student performance related to constructing and interpreting phylogenetic trees. Students improved in their ability to interpret relationships within trees and improved in several aspects related to between-tree comparisons and tree construction skills. Student feedback indicated that most students believed our approach prepared them to engage in tree construction and gave them confidence in their abilities. Overall, our data confirm that instructional approaches implementing deliberate practice address student misconceptions, improve student experiences, and foster deeper understanding of difficult scientific concepts. PMID:24297294

A field-to-desktop toolchain for X-ray CT densitometry enables tree ring analysis.

PubMed

De Mil, Tom; Vannoppen, Astrid; Beeckman, Hans; Van Acker, Joris; Van den Bulcke, Jan

2016-06-01

Disentangling tree growth requires more than ring width data only. Densitometry is considered a valuable proxy, yet laborious wood sample preparation and lack of dedicated software limit the widespread use of density profiling for tree ring analysis. An X-ray computed tomography-based toolchain of tree increment cores is presented, which results in profile data sets suitable for visual exploration as well as density-based pattern matching. Two temperate (Quercus petraea, Fagus sylvatica) and one tropical species (Terminalia superba) were used for density profiling using an X-ray computed tomography facility with custom-made sample holders and dedicated processing software. Density-based pattern matching is developed and able to detect anomalies in ring series that can be corrected via interactive software. A digital workflow allows generation of structure-corrected profiles of large sets of cores in a short time span that provide sufficient intra-annual density information for tree ring analysis. Furthermore, visual exploration of such data sets is of high value. The dated profiles can be used for high-resolution chronologies and also offer opportunities for fast screening of lesser studied tropical tree species. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Tree-Structured Infinite Sparse Factor Model

PubMed Central

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

2013-01-01

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

Automatic translation of digraph to fault-tree models

NASA Technical Reports Server (NTRS)

Iverson, David L.

1992-01-01

The author presents a technique for converting digraph models, including those models containing cycles, to a fault-tree format. A computer program which automatically performs this translation using an object-oriented representation of the models has been developed. The fault-trees resulting from translations can be used for fault-tree analysis and diagnosis. Programs to calculate fault-tree and digraph cut sets and perform diagnosis with fault-tree models have also been developed. The digraph to fault-tree translation system has been successfully tested on several digraphs of varying size and complexity. Details of some representative translation problems are presented. Most of the computation performed by the program is dedicated to finding minimal cut sets for digraph nodes in order to break cycles in the digraph. Fault-trees produced by the translator have been successfully used with NASA's Fault-Tree Diagnosis System (FTDS) to produce automated diagnostic systems.

Tree Classification Software

NASA Technical Reports Server (NTRS)

Buntine, Wray

1993-01-01

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

Structural Equation Model Trees

ERIC Educational Resources Information Center

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

2013-01-01

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

75 FR 28055 - General Management Plan; Joshua Tree National Park; San Bernardino and Riverside Counties, CA...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-19

... DEPARTMENT OF THE INTERIOR National Park Service General Management Plan; Joshua Tree National... National Park Service is updating the General Management Plan (GMP) for Joshua Tree National Park... park management and resource analysis, other designations such as establishment of 594,502 acres by...

Chapter 7 - Crown condition

Treesearch

KaDonna C. Randolph

2018-01-01

Tree crown conditions are visually assessed by the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program as an indicator of forest health. These assessments are useful because individual tree photosynthetic capacity is dependent upon the size and condition of the crown. In general, trees with full, vigorous crowns are associated...

American Samoa's forest resources, 2001.

Treesearch

Joseph A. Donnegan; Sheri S. Mann; Sarah L. Butler; Bruce A. Hiserote

2004-01-01

The Forest Inventory and Analysis Program of the Pacific Northwest Research Station collected, analyzed, and summarized data from field plots, and mapped land cover on four islands in American Samoa. This statistical sample provides estimates of forest area, stem volume, biomass, numbers of trees, damages to trees, and tree size distribution. The summary provides...

Age Distribution of Oak Forests in North-Central Arkansas

Treesearch

Rick Soucy; Eric Heitzman; Martin A. Spetich

2004-01-01

We used tree ring analysis to reconstruct the tree establishment patterns in four mature white oak (Quercus alba L.)-northern red oak (Quercus rubra L.)-hickory (Carya spp.) forests in the Ozark Mountains of north-central Arkasas. Cross sections were removed from the stumps of 321 recently harvested trees and...

Tree mortality risk of oak due to gypsy moth

Treesearch

K.W. Gottschalk; J.J. Colbert; D.L. Feicht

1998-01-01

We present prediction models for estimating tree mortality resulting from gypsy moth, Lymantria dispar, defoliation in mixed oak, Quercus sp., forests. These models differ from previous work by including defoliation as a factor in the analysis. Defoliation intensity, initial tree crown condition (crown vigour), crown position, and...

Transcriptomic Analysis of Leaf in Tree Peony Reveals Differentially Expressed Pigments Genes.

PubMed

Luo, Jianrang; Shi, Qianqian; Niu, Lixin; Zhang, Yanlong

2017-02-20

Tree peony (Paeonia suffruticosa Andrews) is an important traditional flower in China. Besides its beautiful flower, the leaf of tree peony has also good ornamental value owing to its leaf color change in spring. So far, the molecular mechanism of leaf color change in tree peony is unclear. In this study, the pigment level and transcriptome of three different color stages of tree peony leaf were analyzed. The purplish red leaf was rich in anthocyanin, while yellowish green leaf was rich in chlorophyll and carotenoid. Transcriptome analysis revealed that 4302 differentially expressed genes (DEGs) were upregulated, and 4225 were downregulated in the purplish red leaf vs. yellowish green leaf. Among these DEGs, eight genes were predicted to participate in anthocyanin biosynthesis, eight genes were predicted involved in porphyrin and chlorophyll metabolism, and 10 genes were predicted to participate in carotenoid metabolism. In addition, 27 MYBs, 20 bHLHs, 36 WD40 genes were also identified from DEGs. Anthocyanidin synthase (ANS) is the key gene that controls the anthocyanin level in tree peony leaf. Protochlorophyllide oxido-reductase (POR) is the key gene which regulated the chlorophyll content in tree peony leaf.

Faults Discovery By Using Mined Data

NASA Technical Reports Server (NTRS)

Lee, Charles

2005-01-01

Fault discovery in the complex systems consist of model based reasoning, fault tree analysis, rule based inference methods, and other approaches. Model based reasoning builds models for the systems either by mathematic formulations or by experiment model. Fault Tree Analysis shows the possible causes of a system malfunction by enumerating the suspect components and their respective failure modes that may have induced the problem. The rule based inference build the model based on the expert knowledge. Those models and methods have one thing in common; they have presumed some prior-conditions. Complex systems often use fault trees to analyze the faults. Fault diagnosis, when error occurs, is performed by engineers and analysts performing extensive examination of all data gathered during the mission. International Space Station (ISS) control center operates on the data feedback from the system and decisions are made based on threshold values by using fault trees. Since those decision-making tasks are safety critical and must be done promptly, the engineers who manually analyze the data are facing time challenge. To automate this process, this paper present an approach that uses decision trees to discover fault from data in real-time and capture the contents of fault trees as the initial state of the trees.

An introduction to tree-structured modeling with application to quality of life data.

PubMed

Su, Xiaogang; Azuero, Andres; Cho, June; Kvale, Elizabeth; Meneses, Karen M; McNees, M Patrick

2011-01-01

Investigators addressing nursing research are faced increasingly with the need to analyze data that involve variables of mixed types and are characterized by complex nonlinearity and interactions. Tree-based methods, also called recursive partitioning, are gaining popularity in various fields. In addition to efficiency and flexibility in handling multifaceted data, tree-based methods offer ease of interpretation. The aims of this study were to introduce tree-based methods, discuss their advantages and pitfalls in application, and describe their potential use in nursing research. In this article, (a) an introduction to tree-structured methods is presented, (b) the technique is illustrated via quality of life (QOL) data collected in the Breast Cancer Education Intervention study, and (c) implications for their potential use in nursing research are discussed. As illustrated by the QOL analysis example, tree methods generate interesting and easily understood findings that cannot be uncovered via traditional linear regression analysis. The expanding breadth and complexity of nursing research may entail the use of new tools to improve efficiency and gain new insights. In certain situations, tree-based methods offer an attractive approach that help address such needs.

Chlorinated ethenes from groundwater in tree trunks

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

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

1999-02-01

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

A reference guide for tree analysis and visualization

PubMed Central

2010-01-01

The quantities of data obtained by the new high-throughput technologies, such as microarrays or ChIP-Chip arrays, and the large-scale OMICS-approaches, such as genomics, proteomics and transcriptomics, are becoming vast. Sequencing technologies become cheaper and easier to use and, thus, large-scale evolutionary studies towards the origins of life for all species and their evolution becomes more and more challenging. Databases holding information about how data are related and how they are hierarchically organized expand rapidly. Clustering analysis is becoming more and more difficult to be applied on very large amounts of data since the results of these algorithms cannot be efficiently visualized. Most of the available visualization tools that are able to represent such hierarchies, project data in 2D and are lacking often the necessary user friendliness and interactivity. For example, the current phylogenetic tree visualization tools are not able to display easy to understand large scale trees with more than a few thousand nodes. In this study, we review tools that are currently available for the visualization of biological trees and analysis, mainly developed during the last decade. We describe the uniform and standard computer readable formats to represent tree hierarchies and we comment on the functionality and the limitations of these tools. We also discuss on how these tools can be developed further and should become integrated with various data sources. Here we focus on freely available software that offers to the users various tree-representation methodologies for biological data analysis. PMID:20175922

Program listing for fault tree analysis of JPL technical report 32-1542

NASA Technical Reports Server (NTRS)

Chelson, P. O.

1971-01-01

The computer program listing for the MAIN program and those subroutines unique to the fault tree analysis are described. Some subroutines are used for analyzing the reliability block diagram. The program is written in FORTRAN 5 and is running on a UNIVAC 1108.

A retrospective analysis to identify the factors affecting infection in patients undergoing chemotherapy.

PubMed

Park, Ji Hyun; Kim, Hyeon-Young; Lee, Hanna; Yun, Eun Kyoung

2015-12-01

This study compares the performance of the logistic regression and decision tree analysis methods for assessing the risk factors for infection in cancer patients undergoing chemotherapy. The subjects were 732 cancer patients who were receiving chemotherapy at K university hospital in Seoul, Korea. The data were collected between March 2011 and February 2013 and were processed for descriptive analysis, logistic regression and decision tree analysis using the IBM SPSS Statistics 19 and Modeler 15.1 programs. The most common risk factors for infection in cancer patients receiving chemotherapy were identified as alkylating agents, vinca alkaloid and underlying diabetes mellitus. The logistic regression explained 66.7% of the variation in the data in terms of sensitivity and 88.9% in terms of specificity. The decision tree analysis accounted for 55.0% of the variation in the data in terms of sensitivity and 89.0% in terms of specificity. As for the overall classification accuracy, the logistic regression explained 88.0% and the decision tree analysis explained 87.2%. The logistic regression analysis showed a higher degree of sensitivity and classification accuracy. Therefore, logistic regression analysis is concluded to be the more effective and useful method for establishing an infection prediction model for patients undergoing chemotherapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.

PubMed

Gatesy, John; Springer, Mark S

2014-11-01

Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree of Life. Currently, two divergent systematic methods are commonly applied to such datasets: the traditional supermatrix approach (= concatenation) and "shortcut" coalescence (= coalescence methods wherein gene trees and the species tree are not co-estimated). When applied to ancient clades, these contrasting frameworks often produce congruent results, but in recent phylogenetic analyses of Placentalia (placental mammals), this is not the case. A recent series of papers has alternatively disputed and defended the utility of shortcut coalescence methods at deep phylogenetic scales. Here, we examine this exchange in the context of published phylogenomic data from Mammalia; in particular we explore two critical issues - the delimitation of data partitions ("genes") in coalescence analysis and hidden support that emerges with the combination of such partitions in phylogenetic studies. Hidden support - increased support for a clade in combined analysis of all data partitions relative to the support evident in separate analyses of the various data partitions, is a hallmark of the supermatrix approach and a primary rationale for concatenating all characters into a single matrix. In the most extreme cases of hidden support, relationships that are contradicted by all gene trees are supported when all of the genes are analyzed together. A valid fear is that shortcut coalescence methods might bypass or distort character support that is hidden in individual loci because small gene fragments are analyzed in isolation. Given the extensive systematic database for Mammalia, the assumptions and applicability of shortcut coalescence methods can be assessed with rigor to complement a small but growing body of simulation work that has directly compared these methods to concatenation. We document several remarkable cases of hidden support in both supermatrix and coalescence paradigms and argue that in most instances, the emergent support in the shortcut coalescence analyses is an artifact. By referencing rigorous molecular clock studies of Mammalia, we suggest that inaccurate gene trees that imply unrealistically deep coalescences debilitate shortcut coalescence analyses of the placental dataset. We document contradictory coalescence results for Placentalia, and outline a critical conundrum that challenges the general utility of shortcut coalescence methods at deep phylogenetic scales. In particular, the basic unit of analysis in coalescence analysis, the coalescence-gene, is expected to shrink in size as more taxa are analyzed, but as the amount of data for reconstruction of a gene tree ratchets downward, the number of nodes in the gene tree that need to be resolved ratchets upward. Some advocates of shortcut coalescence methods have attempted to address problems with inaccurate gene trees by concatenating multiple coalescence-genes to yield "gene trees" that better match the species tree. However, this hybrid concatenation/coalescence approach, "concatalescence," contradicts the most basic biological rationale for performing a coalescence analysis in the first place. We discuss this reality in the context of recent simulation work that also suggests inaccurate reconstruction of gene trees is more problematic for shortcut coalescence methods than deep coalescence of independently segregating loci is for concatenation methods. Copyright © 2014 Elsevier Inc. All rights reserved.

SPACE PROPULSION SYSTEM PHASED-MISSION PROBABILITY ANALYSIS USING CONVENTIONAL PRA METHODS

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

Curtis Smith; James Knudsen

As part of a series of papers on the topic of advance probabilistic methods, a benchmark phased-mission problem has been suggested. This problem consists of modeling a space mission using an ion propulsion system, where the mission consists of seven mission phases. The mission requires that the propulsion operate for several phases, where the configuration changes as a function of phase. The ion propulsion system itself consists of five thruster assemblies and a single propellant supply, where each thruster assembly has one propulsion power unit and two ion engines. In this paper, we evaluate the probability of mission failure usingmore » the conventional methodology of event tree/fault tree analysis. The event tree and fault trees are developed and analyzed using Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE). While the benchmark problem is nominally a "dynamic" problem, in our analysis the mission phases are modeled in a single event tree to show the progression from one phase to the next. The propulsion system is modeled in fault trees to account for the operation; or in this case, the failure of the system. Specifically, the propulsion system is decomposed into each of the five thruster assemblies and fed into the appropriate N-out-of-M gate to evaluate mission failure. A separate fault tree for the propulsion system is developed to account for the different success criteria of each mission phase. Common-cause failure modeling is treated using traditional (i.e., parametrically) methods. As part of this paper, we discuss the overall results in addition to the positive and negative aspects of modeling dynamic situations with non-dynamic modeling techniques. One insight from the use of this conventional method for analyzing the benchmark problem is that it requires significant manual manipulation to the fault trees and how they are linked into the event tree. The conventional method also requires editing the resultant cut sets to obtain the correct results. While conventional methods may be used to evaluate a dynamic system like that in the benchmark, the level of effort required may preclude its use on real-world problems.« less

Analysis and out-year forecast of beetle, borer, and drought-induced tree mortality in California

Treesearch

Haiganoush K. Preisler; Nancy E. Grulke; Zachary Heath; Sheri L. Smith

2017-01-01

The level of tree mortality and drought observed over the past decade in North America has been described as ‘unparalleled’ in our modern history, in particular in the Sierra Nevada, California. Forest managers could use early warning of where and how much tree mortality to expect in the very near future to plan and prioritize hazard tree removal, pest suppression...

Assessing urban forest effects and values, Washington, D.C.'s urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Jack C. Stevens; Jeffrey T. Walton

2006-01-01

An analysis of trees in Washington, D.C. reveals that this city has about 1,928,000 trees with canopies that cover 28.6 percent of the area. The most common tree species are American beech, red maple, and boxelder. The urban forest currently store about 526,000 tons of carbon valued at $9.7 million. In addition, these trees remove about 16,200 tons of carbon per year...

Modeling time-to-event (survival) data using classification tree analysis.

PubMed

Linden, Ariel; Yarnold, Paul R

2017-12-01

Time to the occurrence of an event is often studied in health research. Survival analysis differs from other designs in that follow-up times for individuals who do not experience the event by the end of the study (called censored) are accounted for in the analysis. Cox regression is the standard method for analysing censored data, but the assumptions required of these models are easily violated. In this paper, we introduce classification tree analysis (CTA) as a flexible alternative for modelling censored data. Classification tree analysis is a "decision-tree"-like classification model that provides parsimonious, transparent (ie, easy to visually display and interpret) decision rules that maximize predictive accuracy, derives exact P values via permutation tests, and evaluates model cross-generalizability. Using empirical data, we identify all statistically valid, reproducible, longitudinally consistent, and cross-generalizable CTA survival models and then compare their predictive accuracy to estimates derived via Cox regression and an unadjusted naïve model. Model performance is assessed using integrated Brier scores and a comparison between estimated survival curves. The Cox regression model best predicts average incidence of the outcome over time, whereas CTA survival models best predict either relatively high, or low, incidence of the outcome over time. Classification tree analysis survival models offer many advantages over Cox regression, such as explicit maximization of predictive accuracy, parsimony, statistical robustness, and transparency. Therefore, researchers interested in accurate prognoses and clear decision rules should consider developing models using the CTA-survival framework. © 2017 John Wiley & Sons, Ltd.

[Changes of Forest Canopy Spectral Reflectance with Seasons in Lang Ya Mountains].

PubMed

Li, Wei-tao; Peng, Dao-li; Zhang, Yan; Wu, Jian; Chen, Tai-sheng

2015-08-01

The physiological mechanism and ecological structure of forest trees can change with the changes of years. In a certain extent, the changes were expressed through the canopy spectral features. The mastery of changing rules about spectral characteristics of trees over the years is benefit to remote sensing interpretation and provide scientific basis for the classification of different trees. The study adopted high-resolution spectrometer to measure the canopy spectral characteristics for seven major deciduous trees and seven evergreen trees to gain the spectrum curve of four different ages and calculate the first derivative curve. The analysis of changing rules about spectral characteristics of different deciduous trees and evergreen trees and the comparison of changes about spectrum of various trees in the visible and infrared band could find the best year and best band for identification of trees. The results showed that the canopy spectral reflectance of deciduous and evergreen trees increases with the increase of age. And the spectral changes of two species were most obvious in the near infrared band.

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

PubMed

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

2013-08-01

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. Despite the significance of ToF, forest and other natural resource inventory programs and geospatial land cover datasets that are available at a national scale do not include comprehensive information regarding ToF in the United States. Additional ground-based data collection and acquisition of specialized imagery to inventory these resources are expensive alternatives. As a potential solution, we identified two remote sensing-based approaches that use free high-resolution aerial imagery from the National Agriculture Imagery Program (NAIP) to map all tree cover in an agriculturally dominant landscape. We compared the results obtained using an unsupervised per-pixel classifier (independent component analysis-[ICA]) and an object-based image analysis (OBIA) procedure in Steele County, Minnesota, USA. Three types of accuracy assessments were used to evaluate how each method performed in terms of: (1) producing a county-level estimate of total tree-covered area, (2) correctly locating tree cover on the ground, and (3) how tree cover patch metrics computed from the classified outputs compared to those delineated by a human photo interpreter. Both approaches were found to be viable for mapping tree cover over a broad spatial extent and could serve to supplement ground-based inventory data. The ICA approach produced an estimate of total tree cover more similar to the photo-interpreted result, but the output from the OBIA method was more realistic in terms of describing the actual observed spatial pattern of tree cover.

Temperature and rainfall strongly drive temporal growth variation in Asian tropical forest trees.

PubMed

Vlam, Mart; Baker, Patrick J; Bunyavejchewin, Sarayudh; Zuidema, Pieter A

2014-04-01

Climate change effects on growth rates of tropical trees may lead to alterations in carbon cycling of carbon-rich tropical forests. However, climate sensitivity of broad-leaved lowland tropical trees is poorly understood. Dendrochronology (tree-ring analysis) provides a powerful tool to study the relationship between tropical tree growth and annual climate variability. We aimed to establish climate-growth relationships for five annual-ring forming tree species, using ring-width data from 459 canopy and understory trees from a seasonal tropical forest in western Thailand. Based on 183/459 trees, chronologies with total lengths between 29 and 62 years were produced for four out of five species. Bootstrapped correlation analysis revealed that climate-growth responses were similar among these four species. Growth was significantly negatively correlated with current-year maximum and minimum temperatures, and positively correlated with dry-season precipitation levels. Negative correlations between growth and temperature may be attributed to a positive relationship between temperature and autotrophic respiration rates. The positive relationship between growth and dry-season precipitation levels likely reflects the strong water demand during leaf flush. Mixed-effect models yielded results that were consistent across species: a negative effect of current wet-season maximum temperatures on growth, but also additive positive effects of, for example, prior dry-season maximum temperatures. Our analyses showed that annual growth variability in tropical trees is determined by a combination of both temperature and precipitation variability. With rising temperature, the predominantly negative relationship between temperature and growth may imply decreasing growth rates of tropical trees as a result of global warming.

Tree Canopy Cover Mapping Using LiDAR in Urban Barangays of Cebu City, Central Philippines

NASA Astrophysics Data System (ADS)

Ejares, J. A.; Violanda, R. R.; Diola, A. G.; Dy, D. T.; Otadoy, J. B.; Otadoy, R. E. S.

2016-06-01

This paper investigates tree canopy cover mapping of urban barangays (smallest administrative division in the Philippines) in Cebu City using LiDAR (Light Detection and Ranging). Object-Based Image Analysis (OBIA) was used to extract tree canopy cover. Multi-resolution segmentation and a series of assign-class algorithm in eCognition software was also performed to extract different land features. Contextual features of tree canopies such as height, area, roundness, slope, length-width and elliptic fit were also evaluated. The results showed that at the time the LiDAR data was collected (June 24, 2014), the tree cover was around 25.11 % (or 15,674,341.8 m2) of the city's urban barangays (or 62,426,064.6 m2). Among all urban barangays in Cebu City, Barangay Busay had the highest cover (55.79 %) while barangay Suba had the lowest (0.8 %). The 16 barangays with less than 10 % tree cover were generally located in the coastal area, presumably due to accelerated urbanization. Thirty-one barangays have tree cover ranging from 10.59--27.3 %. Only 3 barangays (i.e., Lahug, Talamban, and Busay) have tree cover greater than 30 %. The overall accuracy of the analysis was 96.6 % with the Kappa Index of Agreement or KIA of 0.9. From the study, a grouping can be made of the city's urban barangays with regards to tree cover. The grouping will be useful to urban planners not only in allocating budget to the tree planting program of the city but also in planning and creation of urban parks and playgrounds.

Seismic Investigation of the Glacier de la Plaine Morte, Switzerland

NASA Astrophysics Data System (ADS)

Laske, Gabi; Lindner, Fabian; Walter, Fabian; Krage, Manuel

2017-04-01

Glacier de la Plaine Morte is a plateau glacier along the border between Valais and Berne cantons. It covers a narrow elevation range and is extremely vulnerable to climate change. During snow melt, it feeds three marginal lakes that have experienced sudden subglacial drainage in recent years, thereby causing flooding in the Simme Valley below. Of greatest concern is Lac des Faverges at the southeastern end of the glacier that has drained near the end of July in recent years, with flood levels reaching capacity of flood control systems downstream. The lake levels are carefully monitored but precise prediction has not yet been achieved. In the search for precursory ice fracturing to the lake drainage to improve forecast, four seismic arrays comprised of five short-period borehole seismometers provided by Eidgenössische Technische Hochschule (ETH), Zürich as well as fifteen 3-component geophones from the Geophysical Instrument Pool Potsdam (GIPP) collected continuous seismic data for about seven weeks during the summer of 2016. We present initial results on discharge dynamics as well as changing noise levels and seismicity before, during and after the drainage of Lac des Faverges. Compared to previous recent years, the 2016 drainage of Lac des Faverges occurred unusually late on August 28. With an aperture between 100 and 200 m, the small arrays recorded many hundred ice quakes per day. A majority of the events exhibits clearly dispersed, high-frequency Rayleigh waves at about 10 Hz and higher. A wide distribution of events allows us to study azimuthal anisotropy and its relationship with the orientation of glacial crevasses.

Dual impacts of climate change: forest migration and turnover through life history.

PubMed

Zhu, Kai; Woodall, Christopher W; Ghosh, Souparno; Gelfand, Alan E; Clark, James S

2014-01-01

Tree species are predicted to track future climate by shifting their geographic distributions, but climate-mediated migrations are not apparent in a recent continental-scale analysis. To better understand the mechanisms of a possible migration lag, we analyzed relative recruitment patterns by comparing juvenile and adult tree abundances in climate space. One would expect relative recruitment to be higher in cold and dry climates as a result of tree migration with juveniles located further poleward than adults. Alternatively, relative recruitment could be higher in warm and wet climates as a result of higher tree population turnover with increased temperature and precipitation. Using the USDA Forest Service's Forest Inventory and Analysis data at regional scales, we jointly modeled juvenile and adult abundance distributions for 65 tree species in climate space of the eastern United States. We directly compared the optimal climate conditions for juveniles and adults, identified the climates where each species has high relative recruitment, and synthesized relative recruitment patterns across species. Results suggest that for 77% and 83% of the tree species, juveniles have higher optimal temperature and optimal precipitation, respectively, than adults. Across species, the relative recruitment pattern is dominated by relatively more abundant juveniles than adults in warm and wet climates. These different abundance-climate responses through life history are consistent with faster population turnover and inconsistent with the geographic trend of large-scale tree migration. Taken together, this juvenile-adult analysis suggests that tree species might respond to climate change by having faster turnover as dynamics accelerate with longer growing seasons and higher temperatures, before there is evidence of poleward migration at biogeographic scales.

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

PubMed Central

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

FAULT TREE ANALYSIS FOR EXPOSURE TO REFRIGERANTS USED FOR AUTOMOTIVE AIR CONDITIONING IN THE U.S.

EPA Science Inventory

A fault tree analysis was used to estimate the number of refrigerant exposures of automotive service technicians and vehicle occupants in the United States. Exposures of service technicians can occur when service equipment or automotive air-conditioning systems leak during servic...

A Fault Tree Approach to Analysis of Organizational Communication Systems.

ERIC Educational Resources Information Center

Witkin, Belle Ruth; Stephens, Kent G.

Fault Tree Analysis (FTA) is a method of examing communication in an organization by focusing on: (1) the complex interrelationships in human systems, particularly in communication systems; (2) interactions across subsystems and system boundaries; and (3) the need to select and "prioritize" channels which will eliminate noise in the…

[Health assessment of individual trees in natural Larix gmelinii forest in Great Xing' an Mountains of China].

PubMed

Zhu, Yu; Liu, Zhao-Gang; Jin, Guang-Ze

2013-05-01

To integrate the health assessment results of individual trees into the health assessment of subcompartment (or stand) scale could improve the accuracy of subcompartment (or stand) scale health assessment, and realize the coupling process between the individual tree scale and the subcompartment (or stand) scale, providing a theoretical basis for the realization of forest health management. Taking the natural Larix gmelinii forest in Great Xing' an Mountains as the object, a health assessment indicators system of individual trees was established, which included root state, canopy defoliation degree, crown transparency, crown overlap, crown dieback ratio, live crown ratio, crown skewness, and vertical competition index. The principal component analysis (PCA) was employed to eliminate the correlations, the entropy value method was adopted to confirm the weight of each indicator, and the health status of individual L. gmelinii was assessed by fuzzy synthetic evaluation (FSE) method. Based on the health assessment results, a prediction model of the individual tree health was established by discriminant analysis (DA) method. The results showed that the trees in sub-healthy gradation were up to 36.7%, and those in healthy gradation only reached 12.9%. The proportion of the trees in unhealthy gradation exceeded that of the trees in healthy gradation, occupying 21.1% of the total. The prediction accuracy of the established model was 86.3%. More rational and effective management measures should be taken to improve the tree health grade.

Tree crown conditions in Missouri, 2000-2003

Treesearch

KaDonna C. Randolph; W. Keith Moser

2009-01-01

The Forest Service, U.S. Department of Agriculture, Forest Inventory and Analysis (FIA) Program uses visual assessments of tree crown condition to monitor changes and trends in forest health. This report describes three FIA tree crown condition indicators (crown dieback, crown density, and foliage transparency) and sapling crown vigor measured in Missouri between 2000...

Desert Southwest Community Tree Guide: Benefits, Costs and Strategic Planting

Treesearch

Greg McPherson; J.R. Simpson; P.J. Peper; S.E. Maco; Q. Xiao; E. Mulrean

2004-01-01

This report quantifies benefits and costs for typical large-, medium-, small-stature, deciduous trees (Fraxinus uhdei, Prosopis chilensis, Acacia farnesiana), as well as a conifer (Pinus halapensis). The analysis assumed that trees were planted in a residential yard site or a public (street/park) site, a 40-year time frame, and...

City of Charleston, South Carolina Municipal Forest Resource Analysis

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.L. Gardner; K.E. Vargas; S.E. Maco; Q. Xiao

2006-01-01

Charleston, a charming Southern city appreciated for its rich history and culture, maintains trees as an integral component of the urban infrastructure (Figure 1). Research indicates that healthy trees can lessen impacts associated with the built environment by reducing stormwater runoff, energy consumption, and air pollutants. Trees improve urban life, making...

City of Charlotte, North Carolina Municipal Forest Resource Analysis

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.L. Gardner; K.E. Vargas; S.E. Maco; Q. Xiao

2005-01-01

Charlotte, a vibrant Southern city appreciated for its rich history and cultural wealth, maintains trees as an integral component of the urban infrastructure (Figure 1). Research indicates that healthy trees can lessen impacts associated with the built environment by reducing stormwater runoff, energy consumption, and air pollutants. Trees improve urban life, making...

City of Boulder, Colorado Municipal Tree Resource Analysis

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.L. Gardner; K.E. Vargas; Q. Xiao

2005-01-01

Boulder is a vibrant city, renowned for its livability and cultural wealth and well known for its Smart Growth policies that protect and restore environmental quality while enhancing economic opportunity. The city maintains trees as an integral component of the urban infrastructure. Research indicates that healthy trees can mitigate impacts associated with the built...

A critical analysis of methods for rapid and nondestructive determination of wood density in standing trees

Treesearch

Shan Gao; Xiping Wang; Michael C. Wiemann; Brian K. Brashaw; Robert J. Ross; Lihai Wang

2017-01-01

Key message Field methods for rapid determination of wood density in trees have evolved from increment borer, torsiometer, Pilodyn, and nail withdrawal into sophisticated electronic tools of resistance drilling measurement. A partial resistance drilling approach coupled with knowledge of internal tree density distribution may...

Characterization and Discrimination of Oueslati Virgin Olive Oils from Adult and Young Trees in Different Ripening Stages Using Sterols, Pigments, and Alcohols in Tandem with Chemometrics.

PubMed

Chtourou, Fatma; Jabeur, Hazem; Lazzez, Ayda; Bouaziz, Mohamed

2017-05-03

Dynamics of squalene, sterol, aliphatic alcohol, pigment, and triterpenic diol accumulations in olive oils from adult and young trees of the Oueslati cultivar were studied for two consecutive years, 2013-2014 and 2014-2015. Data were compared statistically for differences by age of trees, maturation of olive, and year of harvesting. Results showed that the mean campesterol content in olive oil from adult trees at the green stage of maturation was significantly (p < 0.02) above the limit established by IOC legislation. However, the mean values of campesterol and Δ-7-stigmastenol were significantly (p < 0.01) above the limits in oils from young trees at the black stage of ripening. Principal component analysis was applied to alcohols, squalene, pigments, and sterols having noncompliance with the legislation. Then, data of 36 samples were subjected to a discriminant analysis with "maturation" as grouping variable and principal components as input variables. The model revealed clear discrimination of each tree age/maturation stage group.

Analyzing tree-shape anatomical structures using topological descriptors of branching and ensemble of classifiers.

PubMed

Skoura, Angeliki; Bakic, Predrag R; Megalooikonomou, Vasilis

2013-01-01

The analysis of anatomical tree-shape structures visualized in medical images provides insight into the relationship between tree topology and pathology of the corresponding organs. In this paper, we propose three methods to extract descriptive features of the branching topology; the asymmetry index, the encoding of branching patterns using a node labeling scheme and an extension of the Sholl analysis. Based on these descriptors, we present classification schemes for tree topologies with respect to the underlying pathology. Moreover, we present a classifier ensemble approach which combines the predictions of the individual classifiers to optimize the classification accuracy. We applied the proposed methodology to a dataset of x-ray galactograms, medical images which visualize the breast ductal tree, in order to recognize images with radiological findings regarding breast cancer. The experimental results demonstrate the effectiveness of the proposed framework compared to state-of-the-art techniques suggesting that the proposed descriptors provide more valuable information regarding the topological patterns of ductal trees and indicating the potential of facilitating early breast cancer diagnosis.

Analyzing tree-shape anatomical structures using topological descriptors of branching and ensemble of classifiers

PubMed Central

Skoura, Angeliki; Bakic, Predrag R.; Megalooikonomou, Vasilis

2014-01-01

The analysis of anatomical tree-shape structures visualized in medical images provides insight into the relationship between tree topology and pathology of the corresponding organs. In this paper, we propose three methods to extract descriptive features of the branching topology; the asymmetry index, the encoding of branching patterns using a node labeling scheme and an extension of the Sholl analysis. Based on these descriptors, we present classification schemes for tree topologies with respect to the underlying pathology. Moreover, we present a classifier ensemble approach which combines the predictions of the individual classifiers to optimize the classification accuracy. We applied the proposed methodology to a dataset of x-ray galactograms, medical images which visualize the breast ductal tree, in order to recognize images with radiological findings regarding breast cancer. The experimental results demonstrate the effectiveness of the proposed framework compared to state-of-the-art techniques suggesting that the proposed descriptors provide more valuable information regarding the topological patterns of ductal trees and indicating the potential of facilitating early breast cancer diagnosis. PMID:25414850

treespace: Statistical exploration of landscapes of phylogenetic trees.

PubMed

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

2017-11-01

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

Reliability database development for use with an object-oriented fault tree evaluation program

NASA Technical Reports Server (NTRS)

Heger, A. Sharif; Harringtton, Robert J.; Koen, Billy V.; Patterson-Hine, F. Ann

1989-01-01

A description is given of the development of a fault-tree analysis method using object-oriented programming. In addition, the authors discuss the programs that have been developed or are under development to connect a fault-tree analysis routine to a reliability database. To assess the performance of the routines, a relational database simulating one of the nuclear power industry databases has been constructed. For a realistic assessment of the results of this project, the use of one of existing nuclear power reliability databases is planned.

A new approach to enhance the performance of decision tree for classifying gene expression data.

PubMed

Hassan, Md; Kotagiri, Ramamohanarao

2013-12-20

Gene expression data classification is a challenging task due to the large dimensionality and very small number of samples. Decision tree is one of the popular machine learning approaches to address such classification problems. However, the existing decision tree algorithms use a single gene feature at each node to split the data into its child nodes and hence might suffer from poor performance specially when classifying gene expression dataset. By using a new decision tree algorithm where, each node of the tree consists of more than one gene, we enhance the classification performance of traditional decision tree classifiers. Our method selects suitable genes that are combined using a linear function to form a derived composite feature. To determine the structure of the tree we use the area under the Receiver Operating Characteristics curve (AUC). Experimental analysis demonstrates higher classification accuracy using the new decision tree compared to the other existing decision trees in literature. We experimentally compare the effect of our scheme against other well known decision tree techniques. Experiments show that our algorithm can substantially boost the classification performance of the decision tree.

Multi-decadal carbon and water relations of African tropical humid forests: a tree-ring stable isotope analysis

NASA Astrophysics Data System (ADS)

Hufkens, Koen; Helle, Gerd; Beeckman, Hans; de Haulleville, Thales; Kearsley, Elizabeth; Boeckx, Pascal

2013-04-01

Little is known about the temporal dynamics of the carbon sequestering capacity and dynamics of African tropical humid forest ecosystems in response to various environmental drivers. This lack of knowledge is mainly due to the absence of ecosystem scale flux measurements of gas exchange. However, tree growth often displays itself as alternating pattern of visible rings due to the seasonally varying growth speed of the vascular cambium. Consequently, analysis of tree growth through tree-ring analysis provides us with insights into past responses of the carbon sequestering capacity of key species to abrupt ecosystem disturbances and, while slower, a changing climate. Not only does the width and density of growth rings reflect annual growth but their isotopic composition of 13C/12C and 18O/16O isotopes also reveal the environmental conditions in which the trees were growing. In particular, stable isotope ratios in tree-rings of carbon are influenced by fractionation through carboxylation during photosynthesis and changes in leaf stomatal conductance. Similarly, fractionation of oxygen isotopes of soil water occurs at the leaf level through evapo-transipiration. As a consequence, 18O/16O (δ18O) values in wood cores will reflect both the signal of the source water as well as that of for example summer humidity. Therefore, both C and O stable isotopes might not only be valuable as proxy data for past climatic conditions but they also serve as an important tool in understanding carbon and water relations within a tropical forest ecosystems. To this end we correlate long term climate records (1961 - present) with tree ring measurement of incremental growth and high resolution analysis of tree-core stable isotope composition(δ13C , δ18O) at a tropical humid forests in the DR Congo. The Yangambi Man And Biosphere (MAB) reserve is located in the north-eastern part of DR Congo, with a distinct tropical rainforest climate. In addition to the tree-core data records and extensive meteorological records collected at both sites, observations on green leaf phenology of key species will provide us with additional information on potential carbon sequestration dynamics. Because, phenology is a first order control on plant productivity. In this unique study, using detailed tree-ring analyses together with auxiliary data, we explore the temporal dynamics of carbon and water relations and the influence on carbon sequestration of key tree species in African tropical humid forests.

Fault tree analysis for system modeling in case of intentional EMI

NASA Astrophysics Data System (ADS)

Genender, E.; Mleczko, M.; Döring, O.; Garbe, H.; Potthast, S.

2011-08-01

The complexity of modern systems on the one hand and the rising threat of intentional electromagnetic interference (IEMI) on the other hand increase the necessity for systematical risk analysis. Most of the problems can not be treated deterministically since slight changes in the configuration (source, position, polarization, ...) can dramatically change the outcome of an event. For that purpose, methods known from probabilistic risk analysis can be applied. One of the most common approaches is the fault tree analysis (FTA). The FTA is used to determine the system failure probability and also the main contributors to its failure. In this paper the fault tree analysis is introduced and a possible application of that method is shown using a small computer network as an example. The constraints of this methods are explained and conclusions for further research are drawn.

Estimates of biomass in logging residue and standing residual inventory following tree-harvest activity on timberland acres in the southern region

Treesearch

Roger C. Conner; Tony G. Johnson

2011-01-01

This report provides estimates of biomass (green tons) in logging residue and standing residual inventory on timberland acres with evidence of tree cutting. Biomass as defined by Forest Inventory and Analysis is the aboveground dry weight of wood in the bole and limbs of live trees ≥ 1-inch diameter at breast height (d.b.h.), and excludes tree foliage, seedlings, and...

Growth of Pinus caribaea hondurensis relative to spacing and trunk diameter on two soils in Puerto Rico

Treesearch

F.H. Wadsworth

2008-01-01

Analysis of 19-year-old planted Pinus caribaea var. hondurensis on clay and sandy soils in the mountains of Puerto Rico showed the suitability of both sites for tree growth to commercial size. Growth rates were compared with tree densities ranging from 278 to 2,500 trees per hectare and tree dbh’s (trunk diameters outside bark at breast height, 1.4 meters above ground...

Association Analysis with One Scan of Databases

DTIC Science & Technology

2006-01-01

frequency list . 2. After the first and only scan of the database, we sort according to item supports. The restructure of the P- tree consists of similar...tree can be created in two steps: Step 1: Construct a P-tree and obtain the item frequency list . (1) Root (2) (3) For each transaction in...those infrequent items from item frequency list . Next, we prune the P-tree to exclude the infrequent nodes by checking the frequency of each node

Simulation of Tsunami Resistance of a Pinus Thunbergii tree in Coastal Forest in Japan

NASA Astrophysics Data System (ADS)

Nanko, K.; Suzuki, S.; Noguchi, H.; Hagino, H.

2015-12-01

Forests reduce fluid force of tsunami, whereas extreme tsunami sometimes breaks down the forest trees. It is difficult to estimate the interactive relationship between the fluid and the trees because fluid deform tree architecture and deformed tree changes flow field. Dynamic tree deformation and fluid behavior should be clarified by fluid-structure interaction analysis. For the initial step, we have developed dynamic simulation of tree sway and breakage caused by tsunami based on a vibrating system with multiple degrees of freedom. The target specie of the simulation was Japanese black pine (pinus thunbergii), which is major specie in the coastal forest to secure livelihood area from the damage by blown sand and salt in Japanese coastal area. For the simulation, a tree was segmented into 0.2 m long circular truncated cones. Turning moment induced by tsunami and self-weight was calculated at each segment bottom. Tree deformation was computed on multi-degree-of-freedom vibration equation. Tree sway was simulated by iterative calculation of the tree deformation with time step 0.05 second with temporally varied flow velocity of tsunami. From the calculation of bending stress and turning moment at tree base, we estimated resistance of a Pinus thunbergii tree from tsunami against tree breakage.

Bioinformatics in proteomics: application, terminology, and pitfalls.

PubMed

Wiemer, Jan C; Prokudin, Alexander

2004-01-01

Bioinformatics applies data mining, i.e., modern computer-based statistics, to biomedical data. It leverages on machine learning approaches, such as artificial neural networks, decision trees and clustering algorithms, and is ideally suited for handling huge data amounts. In this article, we review the analysis of mass spectrometry data in proteomics, starting with common pre-processing steps and using single decision trees and decision tree ensembles for classification. Special emphasis is put on the pitfall of overfitting, i.e., of generating too complex single decision trees. Finally, we discuss the pros and cons of the two different decision tree usages.

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

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

2007-05-07

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

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

PubMed

Stephens, Timothy G; Bhattacharya, Debashish; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

Benefits of tree mixes in carbon plantings

NASA Astrophysics Data System (ADS)

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

2013-10-01

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

High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

NASA Astrophysics Data System (ADS)

MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

2012-01-01

Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

Soft error evaluation and vulnerability analysis in Xilinx Zynq-7010 system-on chip

NASA Astrophysics Data System (ADS)

Du, Xuecheng; He, Chaohui; Liu, Shuhuan; Zhang, Yao; Li, Yonghong; Xiong, Ceng; Tan, Pengkang

2016-09-01

Radiation-induced soft errors are an increasingly important threat to the reliability of modern electronic systems. In order to evaluate system-on chip's reliability and soft error, the fault tree analysis method was used in this work. The system fault tree was constructed based on Xilinx Zynq-7010 All Programmable SoC. Moreover, the soft error rates of different components in Zynq-7010 SoC were tested by americium-241 alpha radiation source. Furthermore, some parameters that used to evaluate the system's reliability and safety were calculated using Isograph Reliability Workbench 11.0, such as failure rate, unavailability and mean time to failure (MTTF). According to fault tree analysis for system-on chip, the critical blocks and system reliability were evaluated through the qualitative and quantitative analysis.

Quantitative and qualitative characteristics of cell wall components and prenyl lipids in the leaves of Tilia x euchlora trees growing under salt stress.

PubMed

Milewska-Hendel, Anna; Baczewska, Aneta H; Sala, Katarzyna; Dmuchowski, Wojciech; Brągoszewska, Paulina; Gozdowski, Dariusz; Jozwiak, Adam; Chojnacki, Tadeusz; Swiezewska, Ewa; Kurczynska, Ewa

2017-01-01

The study was focused on assessing the presence of arabinogalactan proteins (AGPs) and pectins within the cell walls as well as prenyl lipids, sodium and chlorine content in leaves of Tilia x euchlora trees. The leaves that were analyzed were collected from trees with and without signs of damage that were all growing in the same salt stress conditions. The reason for undertaking these investigations was the observations over many years that indicated that there are trees that present a healthy appearance and trees that have visible symptoms of decay in the same habitat. Leaf samples were collected from trees growing in the median strip between roadways that have been intensively salted during the winter season for many years. The sodium content was determined using atomic spectrophotometry, chloride using potentiometric titration and poly-isoprenoids using HPLC/UV. AGPs and pectins were determined using immunohistochemistry methods. The immunohistochemical analysis showed that rhamnogalacturonans I (RG-I) and homogalacturonans were differentially distributed in leaves from healthy trees in contrast to leaves from injured trees. In the case of AGPs, the most visible difference was the presence of the JIM16 epitope. Chemical analyses of sodium and chloride showed that in the leaves from injured trees, the level of these ions was higher than in the leaves from healthy trees. Based on chromatographic analysis, four poly-isoprenoid alcohols were identified in the leaves of T. x euchlora. The levels of these lipids were higher in the leaves from healthy trees. The results suggest that the differences that were detected in the apoplast and symplasm may be part of the defensive strategy of T. x euchlora trees to salt stress, which rely on changes in the chemical composition of the cell wall with respect to the pectic and AGP epitopes and an increased synthesis of prenyl lipids.

Quantitative and qualitative characteristics of cell wall components and prenyl lipids in the leaves of Tilia x euchlora trees growing under salt stress

PubMed Central

Milewska-Hendel, Anna; Baczewska, Aneta H.; Sala, Katarzyna; Dmuchowski, Wojciech; Brągoszewska, Paulina; Gozdowski, Dariusz; Jozwiak, Adam; Chojnacki, Tadeusz; Swiezewska, Ewa; Kurczynska, Ewa

2017-01-01

The study was focused on assessing the presence of arabinogalactan proteins (AGPs) and pectins within the cell walls as well as prenyl lipids, sodium and chlorine content in leaves of Tilia x euchlora trees. The leaves that were analyzed were collected from trees with and without signs of damage that were all growing in the same salt stress conditions. The reason for undertaking these investigations was the observations over many years that indicated that there are trees that present a healthy appearance and trees that have visible symptoms of decay in the same habitat. Leaf samples were collected from trees growing in the median strip between roadways that have been intensively salted during the winter season for many years. The sodium content was determined using atomic spectrophotometry, chloride using potentiometric titration and poly-isoprenoids using HPLC/UV. AGPs and pectins were determined using immunohistochemistry methods. The immunohistochemical analysis showed that rhamnogalacturonans I (RG-I) and homogalacturonans were differentially distributed in leaves from healthy trees in contrast to leaves from injured trees. In the case of AGPs, the most visible difference was the presence of the JIM16 epitope. Chemical analyses of sodium and chloride showed that in the leaves from injured trees, the level of these ions was higher than in the leaves from healthy trees. Based on chromatographic analysis, four poly-isoprenoid alcohols were identified in the leaves of T. x euchlora. The levels of these lipids were higher in the leaves from healthy trees. The results suggest that the differences that were detected in the apoplast and symplasm may be part of the defensive strategy of T. x euchlora trees to salt stress, which rely on changes in the chemical composition of the cell wall with respect to the pectic and AGP epitopes and an increased synthesis of prenyl lipids. PMID:28234963

Cost-Benefit Analysis for Biological Control Programs That Targeted Insect Pests of Eucalypts in Urban Landscapes of California.

PubMed

Paine, T D; Millar, J G; Hanks, L M; Gould, J; Wang, Q; Daane, K; Dahlsten, D L; Mcpherson, E G

2015-12-01

As well as being planted for wind breaks, landscape trees, and fuel wood, eucalypts are also widely used as urban street trees in California. They now are besieged by exotic insect herbivores of four different feeding guilds. The objective of the current analysis was to determine the return on investment from biological control programs that have targeted these pests. Independent estimates of the total number of eucalypt street trees in California ranged from a high of 476,527 trees (based on tree inventories from 135 California cities) to a low of 190,666 trees (based on 49 tree inventories). Based on a survey of 3,512 trees, the estimated mean value of an individual eucalypt was US$5,978. Thus, the total value of eucalypt street trees in California ranged from more than US$1.0 billion to more than US$2.8 billion. Biological control programs that targeted pests of eucalypts in California have cost US$2,663,097 in extramural grants and University of California salaries. Consequently, the return derived from protecting the value of this resource through the biological control efforts, per dollar expended, ranged from US$1,070 for the high estimated number of trees to US$428 for the lower estimate. The analyses demonstrate both the tremendous value of urban street trees, and the benefits that stem from successful biological control programs aimed at preserving these trees. Economic analyses such as this, which demonstrate the substantial rates of return from successful biological control of invasive pests, may play a key role in developing both grass-roots and governmental support for future urban biological control efforts. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Inter- and intraannual growth patterns of urban small-leaved lime (Tilia cordata mill.) at two public squares with contrasting microclimatic conditions.

PubMed

Moser, Astrid; Rahman, Mohammad A; Pretzsch, Hans; Pauleit, Stephan; Rötzer, Thomas

2017-06-01

The effects of urban conditions on tree growth have been investigated in an increasing number of studies over the last decades, emphasizing the harsh environment of cities. Urban trees often grow in highly paved, compacted sites with consequently less soil moisture, higher soil temperatures, and greater vapor pressure deficits. However, there is still a knowledge gap regarding the impact of harsh paved environments on urban tree growth during drought years on the growth patterns of urban trees. The present study investigated the structure and growth of the common urban tree species small-leaved lime (Tilia cordata) at a highly paved public square (CPS) compared with a contrasting more open, greener square (OGS). Continuously, measured high precision dendrometer data along with meteorological data of the extreme dry and warm summer 2015 as well as dendrochronological data of the sampled trees were investigated to analyze tree growth during a drought year. The results highlight different tree dimensions and growth patterns of the trees at both sites, influenced by tree age and distinct site conditions. While the trees at OGS grew up to 2.5 mm from July until mid of August, the trees at CPS had only 0.4-mm diameter increment. After the initial expansion at CPS, tree diameter contracted again during summer to the point of shrinkage (up to 0.8 mm) at the end of our investigation. Further drought year analysis confirmed the patterns of significant stem growth reductions in the consecutive two years following the drought. A correlation analysis revealed that transpiration, air temperature, and vapor pressure deficit were negatively correlated with the daily diameter growth, whereas precipitation had a strong positive effect. Due to high transpiration rates associated with anisohydric water use behavior, T. cordata was able to provide evaporative cooling even during drought. However, this anisohydric behavior resulted in substantial growth decline afterwards especially at paved sites like CPS. Our results suggest selection of tree species, such as those with isohydric water use behavior, which may achieve a better balance between growth, transpiration, and hence evaporative cooling.

Using Tree-Ring Data to Develop Critical Scientific and Mathematical Thinking Skills in Undergraduate Students

NASA Astrophysics Data System (ADS)

Fiondella, F.; Davi, N. K.; Wattenberg, F.; Pringle, P. T.; Greidanus, I.; Oelkers, R.

2015-12-01

Tree-ring science provides an engaging, intuitive, and relevant entryway into understanding both climate change and environmental research. It also sheds light on the process of science--from inspiration, to fieldwork, to analysis, to publishing and communication. The basic premise of dendrochronology is that annual rings reflect year-to-year environmental conditions and that by studying long-lived trees we can learn about environmental and climatic conditions going back hundreds to thousands of years. Conceptually, this makes tree-ring studies accessible to students and faculty for a number of reasons. First, in order to collect their data, dendrochronologists often launch expeditions to stunningly picturesque and remote places in search of long-lived, climate sensitive trees. The exciting stories and images that scientists bring back from the field can help connect students to the studies, their motivation, and the data collected. Second, tree rings can be more easily explained as a proxy for climate than ice cores, speleothems and others. Most people have prior knowledge about trees and annual growth rings. It is even possible, for example, for non-expert audiences to see climate variability through time with the naked eye by looking at climate-sensitive tree cores. Third, tree rings are interdisciplinary and illustrate the interplay between the mathematical sciences, the biological sciences, and the geosciences—that is, they show that the biosphere is a fundamental component of the Earth system. Here, we present online, multi-media learning modules for undergraduates that introduce students to several foundational studies in tree-ring science. These include evaluating tree-ring cores from ancient hemlock trees growing on a talus slope in New Paltz, NY to learn about drought in the Northeastern US, evaluating long-term streamflow and drought of the Colorado River based on tree-ring records, and using tree-ring dating techniques to develop construction histories of cliff dwellings and pueblos in the US Southwest. Our modules are designed to give undergraduate students a sense of the scientific process, from fieldwork and logistics, to data processing and data analysis.

Fault trees for decision making in systems analysis

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

Lambert, Howard E.

1975-10-09

The application of fault tree analysis (FTA) to system safety and reliability is presented within the framework of system safety analysis. The concepts and techniques involved in manual and automated fault tree construction are described and their differences noted. The theory of mathematical reliability pertinent to FTA is presented with emphasis on engineering applications. An outline of the quantitative reliability techniques of the Reactor Safety Study is given. Concepts of probabilistic importance are presented within the fault tree framework and applied to the areas of system design, diagnosis and simulation. The computer code IMPORTANCE ranks basic events and cut setsmore » according to a sensitivity analysis. A useful feature of the IMPORTANCE code is that it can accept relative failure data as input. The output of the IMPORTANCE code can assist an analyst in finding weaknesses in system design and operation, suggest the most optimal course of system upgrade, and determine the optimal location of sensors within a system. A general simulation model of system failure in terms of fault tree logic is described. The model is intended for efficient diagnosis of the causes of system failure in the event of a system breakdown. It can also be used to assist an operator in making decisions under a time constraint regarding the future course of operations. The model is well suited for computer implementation. New results incorporated in the simulation model include an algorithm to generate repair checklists on the basis of fault tree logic and a one-step-ahead optimization procedure that minimizes the expected time to diagnose system failure.« less

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

PubMed

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

2011-01-01

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

What Satisfies Students?: Mining Student-Opinion Data with Regression and Decision Tree Analysis

ERIC Educational Resources Information Center

Thomas, Emily H.; Galambos, Nora

2004-01-01

To investigate how students' characteristics and experiences affect satisfaction, this study uses regression and decision tree analysis with the CHAID algorithm to analyze student-opinion data. A data mining approach identifies the specific aspects of students' university experience that most influence three measures of general satisfaction. The…

Using Fault Trees to Advance Understanding of Diagnostic Errors.

PubMed

Rogith, Deevakar; Iyengar, M Sriram; Singh, Hardeep

2017-11-01

Diagnostic errors annually affect at least 5% of adults in the outpatient setting in the United States. Formal analytic techniques are only infrequently used to understand them, in part because of the complexity of diagnostic processes and clinical work flows involved. In this article, diagnostic errors were modeled using fault tree analysis (FTA), a form of root cause analysis that has been successfully used in other high-complexity, high-risk contexts. How factors contributing to diagnostic errors can be systematically modeled by FTA to inform error understanding and error prevention is demonstrated. A team of three experts reviewed 10 published cases of diagnostic error and constructed fault trees. The fault trees were modeled according to currently available conceptual frameworks characterizing diagnostic error. The 10 trees were then synthesized into a single fault tree to identify common contributing factors and pathways leading to diagnostic error. FTA is a visual, structured, deductive approach that depicts the temporal sequence of events and their interactions in a formal logical hierarchy. The visual FTA enables easier understanding of causative processes and cognitive and system factors, as well as rapid identification of common pathways and interactions in a unified fashion. In addition, it enables calculation of empirical estimates for causative pathways. Thus, fault trees might provide a useful framework for both quantitative and qualitative analysis of diagnostic errors. Future directions include establishing validity and reliability by modeling a wider range of error cases, conducting quantitative evaluations, and undertaking deeper exploration of other FTA capabilities. Copyright © 2017 The Joint Commission. Published by Elsevier Inc. All rights reserved.

Ultrasonographic Diagnosis of Biliary Atresia Based on a Decision-Making Tree Model.

PubMed

Lee, So Mi; Cheon, Jung-Eun; Choi, Young Hun; Kim, Woo Sun; Cho, Hyun-Hae; Cho, Hyun-Hye; Kim, In-One; You, Sun Kyoung

2015-01-01

To assess the diagnostic value of various ultrasound (US) findings and to make a decision-tree model for US diagnosis of biliary atresia (BA). From March 2008 to January 2014, the following US findings were retrospectively evaluated in 100 infants with cholestatic jaundice (BA, n = 46; non-BA, n = 54): length and morphology of the gallbladder, triangular cord thickness, hepatic artery and portal vein diameters, and visualization of the common bile duct. Logistic regression analyses were performed to determine the features that would be useful in predicting BA. Conditional inference tree analysis was used to generate a decision-making tree for classifying patients into the BA or non-BA groups. Multivariate logistic regression analysis showed that abnormal gallbladder morphology and greater triangular cord thickness were significant predictors of BA (p = 0.003 and 0.001; adjusted odds ratio: 345.6 and 65.6, respectively). In the decision-making tree using conditional inference tree analysis, gallbladder morphology and triangular cord thickness (optimal cutoff value of triangular cord thickness, 3.4 mm) were also selected as significant discriminators for differential diagnosis of BA, and gallbladder morphology was the first discriminator. The diagnostic performance of the decision-making tree was excellent, with sensitivity of 100% (46/46), specificity of 94.4% (51/54), and overall accuracy of 97% (97/100). Abnormal gallbladder morphology and greater triangular cord thickness (> 3.4 mm) were the most useful predictors of BA on US. We suggest that the gallbladder morphology should be evaluated first and that triangular cord thickness should be evaluated subsequently in cases with normal gallbladder morphology.

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality

PubMed Central

Vergara, Pablo M.; Soto, Gerardo E.; Rodewald, Amanda D.; Meneses, Luis O.; Pérez-Hernández, Christian G.

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox’s proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales. PMID:27416115

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality.

PubMed

Vergara, Pablo M; Soto, Gerardo E; Moreira-Arce, Darío; Rodewald, Amanda D; Meneses, Luis O; Pérez-Hernández, Christian G

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox's proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales.

Causation mechanism analysis for haze pollution related to vehicle emission in Guangzhou, China by employing the fault tree approach.

PubMed

Huang, Weiqing; Fan, Hongbo; Qiu, Yongfu; Cheng, Zhiyu; Xu, Pingru; Qian, Yu

2016-05-01

Recently, China has frequently experienced large-scale, severe and persistent haze pollution due to surging urbanization and industrialization and a rapid growth in the number of motor vehicles and energy consumption. The vehicle emission due to the consumption of a large number of fossil fuels is no doubt a critical factor of the haze pollution. This work is focused on the causation mechanism of haze pollution related to the vehicle emission for Guangzhou city by employing the Fault Tree Analysis (FTA) method for the first time. With the establishment of the fault tree system of "Haze weather-Vehicle exhausts explosive emission", all of the important risk factors are discussed and identified by using this deductive FTA method. The qualitative and quantitative assessments of the fault tree system are carried out based on the structure, probability and critical importance degree analysis of the risk factors. The study may provide a new simple and effective tool/strategy for the causation mechanism analysis and risk management of haze pollution in China. Copyright © 2016 Elsevier Ltd. All rights reserved.

An analysis of tree mortality using high resolution remotely-sensed data for mixed-conifer forests in San Diego county

NASA Astrophysics Data System (ADS)

Freeman, Mary Pyott

ABSTRACT An Analysis of Tree Mortality Using High Resolution Remotely-Sensed Data for Mixed-Conifer Forests in San Diego County by Mary Pyott Freeman The montane mixed-conifer forests of San Diego County are currently experiencing extensive tree mortality, which is defined as dieback where whole stands are affected. This mortality is likely the result of the complex interaction of many variables, such as altered fire regimes, climatic conditions such as drought, as well as forest pathogens and past management strategies. Conifer tree mortality and its spatial pattern and change over time were examined in three components. In component 1, two remote sensing approaches were compared for their effectiveness in delineating dead trees, a spatial contextual approach and an OBIA (object based image analysis) approach, utilizing various dates and spatial resolutions of airborne image data. For each approach transforms and masking techniques were explored, which were found to improve classifications, and an object-based assessment approach was tested. In component 2, dead tree maps produced by the most effective techniques derived from component 1 were utilized for point pattern and vector analyses to further understand spatio-temporal changes in tree mortality for the years 1997, 2000, 2002, and 2005 for three study areas: Palomar, Volcan and Laguna mountains. Plot-based fieldwork was conducted to further assess mortality patterns. Results indicate that conifer mortality was significantly clustered, increased substantially between 2002 and 2005, and was non-random with respect to tree species and diameter class sizes. In component 3, multiple environmental variables were used in Generalized Linear Model (GLM-logistic regression) and decision tree classifier model development, revealing the importance of climate and topographic factors such as precipitation and elevation, in being able to predict areas of high risk for tree mortality. The results from this study highlight the importance of multi-scale spatial as well as temporal analyses, in order to understand mixed-conifer forest structure, dynamics, and processes of decline, which can lead to more sustainable management of forests with continued natural and anthropogenic disturbance.

Modeling vertebrate diversity in Oregon using satellite imagery

NASA Astrophysics Data System (ADS)

Cablk, Mary Elizabeth

Vertebrate diversity was modeled for the state of Oregon using a parametric approach to regression tree analysis. This exploratory data analysis effectively modeled the non-linear relationships between vertebrate richness and phenology, terrain, and climate. Phenology was derived from time-series NOAA-AVHRR satellite imagery for the year 1992 using two methods: principal component analysis and derivation of EROS data center greenness metrics. These two measures of spatial and temporal vegetation condition incorporated the critical temporal element in this analysis. The first three principal components were shown to contain spatial and temporal information about the landscape and discriminated phenologically distinct regions in Oregon. Principal components 2 and 3, 6 greenness metrics, elevation, slope, aspect, annual precipitation, and annual seasonal temperature difference were investigated as correlates to amphibians, birds, all vertebrates, reptiles, and mammals. Variation explained for each regression tree by taxa were: amphibians (91%), birds (67%), all vertebrates (66%), reptiles (57%), and mammals (55%). Spatial statistics were used to quantify the pattern of each taxa and assess validity of resulting predictions from regression tree models. Regression tree analysis was relatively robust against spatial autocorrelation in the response data and graphical results indicated models were well fit to the data.

Characterizing individual particles on tree leaves using computer automated scanning electron microscopy

Treesearch

D. L. Johnson; D. J. Nowak; V. A. Jouraeva

1999-01-01

Leaves from twenty-three deciduous tree species and five conifer species were collected within a limited geographic range (1 km radius) and evaluated for possible application of scanning electron microscopy and X-ray microanalysis techniques of individual particle analysis (IPA). The goal was to identify tree species with leaves suitable for the automated...

Optimal tree increment models for the Northeastern United Statesq

Treesearch

Don C. Bragg

2003-01-01

used the potential relative increment (PRI) methodology to develop optimal tree diameter growth models for the Northeastern United States. Thirty species from the Eastwide Forest Inventory Database yielded 69,676 individuals, which were then reduced to fast-growing subsets for PRI analysis. For instance, only 14 individuals from the greater than 6,300-tree eastern...

Optimal Tree Increment Models for the Northeastern United States

Treesearch

Don C. Bragg

2005-01-01

I used the potential relative increment (PRI) methodology to develop optimal tree diameter growth models for the Northeastern United States. Thirty species from the Eastwide Forest Inventory Database yielded 69,676 individuals, which were then reduced to fast-growing subsets for PRI analysis. For instance, only 14 individuals from the greater than 6,300-tree eastern...

Tree planting in the United States - 1997

Treesearch

Robert J. Moulton

1997-01-01

This annual report summarizes tree planting, timber stand improvement, and nursery production activities across all ownerships of forest land in the United States. It includes state-by-state and ownership breakdowns, regional totals, as well as analysis of the trends in the data. It does not include tree planting in urban and community environments. As far as we...

A framework for reporting tree cover attributes in agricultural landscapes

Treesearch

Dacia M. Meneguzzo; Greg C. Liknes

2012-01-01

The definition of forest land used by the USDA Forest Service’s Forest Inventory and Analysis program includes area, width, and density requirements. These requirements frequently exclude from the inventory any trees occupyingnarrow riparian corridors or linear tree plantings (e.g., windbreaks and shelterbelts). With recent attention being paid to such topics as bio-...

Tree failures and accidents in recreation areas: a guide to data management for hazard control

Treesearch

Lee A. Paine; James W. Clarke

1978-01-01

A data management system has been developed for storage and retrieval of tree failure and hazard data, with provision for computer analyses and presentation of results in useful tables. This system emphasizes important relationships between tree characteristics, environmental factors, and the resulting hazard. The analysis programs permit easy selection of subsets of...

Ecological Technologies for Small-Diameter Tree Harvesting

Treesearch

Bryce J. Stokes; John F. Klepac

1997-01-01

Production, costs, and merchantable chip recovery values were developed for a tree-length, flail/chip, and cut-to-length system. The systems were evaluated for three representative stands: early thinning, late thinning, and a clearcut. A sensitivity analysis was completed for the three systems over a range of tree diameters. Recovery was affected by stand type and...

Midwest community tree guide: benefits, costs, and strategic planting

Treesearch

E. Gregory McPherson; James R. Simpson; Paula J. Peper; Scott E. Maco; Shelley L. Gardner; Shauna K. Cozad; Qingfu Xiao

2006-01-01

This report quantifies benefits and costs for typical small, medium, and large deciduous (losing their leaves every autumn) trees: crabapple, red oak, and hackberry (see "Common and Scientific Names" section). The analysis assumed that trees were planted in a residential yard or public site (streetside or park) with a 60 percent survival rate over a 40-year...

Dendrochemistry of multiple releases of chlorinated solvents at a former industrial site

Treesearch

Jean Christophe ​Balouet; Joel G. Burken; Frank Karg; Don Vroblesky; Kevin T. Smith; Håkan Grudd; Anders Rindby; François Beaujard; Michel Chalot

2012-01-01

Trees can take up and assimilate contaminants from soil, subsurface, and groundwater. Contaminants in the transpiration stream can become bound or incorporated into the annual rings formed in trees of the temperate zones. The chemical analysis of precisely dated tree rings, called dendrochemistry, can be used to interpret past plant interactions with contaminants. This...

Optimal tree-stem bucking of northeastern species of China

Treesearch

Jingxin Wang; Chris B. LeDoux; Joseph McNeel

2004-01-01

An application of optimal tree-stem bucking to the northeastern tree species of China is reported. The bucking procedures used in this region are summarized, which are the basic guidelines for the optimal bucking design. The directed graph approach was adopted to generate the bucking patterns by using the network analysis labeling algorithm. A computer-based bucking...

Prioritizing preferable locations for increasing urban tree canopy in New York City

Treesearch

Dexter Locke; J. Morgan Grove; Jacqueline W.T. Lu; Austin Troy; Jarlath P.M. O' Neil-Dunne; Brian Beck

2010-01-01

This paper presents a set of Geographic Information System (GIS) methods for identifying and prioritizing tree planting sites in urban environments. It uses an analytical approach created by a University of Vermont service-learning class called "GIS Analysis of New York City's Ecology" that was designed to provide research support to the MillionTreesNYC...

Tree nut consumption improves nutrient intake and diet quality in US adults: an analysis of National Health and Nutrition Examination Survey (NHANES) 1999-2004

USDA-ARS?s Scientific Manuscript database

Recent epidemiologic studies assessing tree nut (almonds, Brazil nuts, cashews, hazelnuts, macadamia nuts, pecans, pine nuts, pistachios, and walnuts) consumption and the association with nutrient intake and diet quality are lacking. This study determined the association of tree nut consumption and ...

Goal Programming: A New Tool for the Christmas Tree Industry

Treesearch

Bruce G. Hansen

1977-01-01

Goal programing (GP) can be useful for decision making in the natural Christmas tree industry. Its usefulness is demonstrated through an analysis of a hypothetical problem in which two potential growers decide how to use 10 acres in growing Christmas trees. Though the physical settings are identical, distinct differences between their goals significantly influence the...

"Whoa! We're Going Deep in the Trees!": Patterns of Collaboration around an Interactive Information Visualization Exhibit

ERIC Educational Resources Information Center

Davis, Pryce; Horn, Michael; Block, Florian; Phillips, Brenda; Evans, E. Margaret; Diamond, Judy; Shen, Chia

2015-01-01

In this paper we present a qualitative analysis of natural history museum visitor interaction around a multi-touch tabletop exhibit called "DeepTree" that we designed around concepts of evolution and common descent. DeepTree combines several large scientific datasets and an innovative visualization technique to display a phylogenetic…

Descriptive statistics of tree crown condition in California, Oregon, and Washington

Treesearch

KaDonna C. Randolph; Sally J. Campbell; Glenn Christensen

2010-01-01

The U.S. Forest Service Forest Inventory and Analysis (FIA) Program uses visual assessments of tree crown condition to monitor changes and trends in forest health. This report describes four tree crown condition indicators (crown dieback, crown density, foliage transparency, and sapling crown vigor) measured in California, Oregon, and Washington between 1996 and 1999....

Alabama, 2010 forest inventory and analysis factsheet

Treesearch

Andrew J. Hartsell

2011-01-01

FIA was initially established to monitor the Nation’s timber supply and the amount of commercially available resources. These early surveys were not concerned with the forests, species, and tree sizes that were not considered commercially viable. Early FIA reported only on growing-stock trees on timberlands, i.e., commercially important tree species and sizes on...

Reliability computation using fault tree analysis

NASA Technical Reports Server (NTRS)

Chelson, P. O.

1971-01-01

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

Landscape-scale analysis of aboveground tree carbon stocks affected by mountain pine beetles in Idaho

Treesearch

Benjamin Bright; J. A. Hicke; A. T. Hudak

2012-01-01

Bark beetle outbreaks kill billions of trees in western North America, and the resulting tree mortality can significantly impact local and regional carbon cycling. However, substantial variability in mortality occurs within outbreak areas. Our objective was to quantify landscape-scale effects of beetle infestations on aboveground carbon (AGC) stocks using field...

Applying survival analysis to a large-scale forest inventory for assessment of tree mortality in Minnesota

Treesearch

C.W. Woodall; P.L. Grambsch; W. Thomas

2005-01-01

Tree mortality has traditionally been assessed in forest inventories through summaries of mortality by location, species, and causal agents. Although these methods have historically constituted the majority of tree mortality summarizations, they have had limited use in assessing mortality trends and dynamics. This study proposed a novel method of applying survival...

A benefit-cost analysis of ten tree species in Modesto, California, U.S.A

Treesearch

E.G. McPherson

2003-01-01

Tree work records for ten species were analyzed to estimate average annual management costs by dbh class for six activity areas. Average annual benefits were calculated by dbh class for each species with computer modeling. Average annual net benefits per tree were greatest for London plane (Platanus acerifolia) ($178.57), hackberry (...

Potential redistribution of tree species habitat under five climate change scenarios in the eastern US

Treesearch

Louis R. Iverson; Anantha M. Prasad; Anantha M. Prasad

2002-01-01

Global climate change could have profound effects on the Earth's biota, including large redistributions of tree species and forest types. We used DISTRIB, a deterministic regression tree analysis model, to examine environmental drivers related to current forest-species distributions and then model potential suitable habitat under five climate change scenarios...

Tree improvement opportunities in the North-Central States related to economic trends, a problem analysis.

Treesearch

David H. Dawson; John A. Pitcher

1970-01-01

Economic trends are interpreted and related to planning applied forest tree-improvement programs for the North-Central Region. Projected demands for forest products are considered in light of the forest resource and alternatives for its use. Suggestions are given for tree-improvement programs for seven conifer and three hardwood species.

Tree planting in the United States - 1998

Treesearch

R.J. Moulton; G. Hernandez

2000-01-01

This annual report summarizes tree planting, timber stand improvement, and nursery production activities across all ownerships of forest land in the United States. It includes State-by-State and ownership breakdowns, regional totals, as well as analysis of trends in the data. It does not include tree planting in urban and community environments. As far as we know, it...

Impacts of age-dependent tree sensitivity and dating approaches on dendrogeomorphic time series of landslides

NASA Astrophysics Data System (ADS)

Šilhán, Karel; Stoffel, Markus

2015-05-01

Different approaches and thresholds have been utilized in the past to date landslides with growth ring series of disturbed trees. Past work was mostly based on conifer species because of their well-defined ring boundaries and the easy identification of compression wood after stem tilting. More recently, work has been expanded to include broad-leaved trees, which are thought to produce less and less evident reactions after landsliding. This contribution reviews recent progress made in dendrogeomorphic landslide analysis and introduces a new approach in which landslides are dated via ring eccentricity formed after tilting. We compare results of this new and the more conventional approaches. In addition, the paper also addresses tree sensitivity to landslide disturbance as a function of tree age and trunk diameter using 119 common beech (Fagus sylvatica L.) and 39 Crimean pine (Pinus nigra ssp. pallasiana) trees growing on two landslide bodies. The landslide events reconstructed with the classical approach (reaction wood) also appear as events in the eccentricity analysis, but the inclusion of eccentricity clearly allowed for more (162%) landslides to be detected in the tree-ring series. With respect to tree sensitivity, conifers and broad-leaved trees show the strongest reactions to landslides at ages comprised between 40 and 60 years, with a second phase of increased sensitivity in P. nigra at ages of ca. 120-130 years. These phases of highest sensitivities correspond with trunk diameters at breast height of 6-8 and 18-22 cm, respectively (P. nigra). This study thus calls for the inclusion of eccentricity analyses in future landslide reconstructions as well as for the selection of trees belonging to different age and diameter classes to allow for a well-balanced and more complete reconstruction of past events.

Structure of a forested urban park: implications for strategic management.

PubMed

Millward, Andrew A; Sabir, Senna

2010-11-01

Informed management of urban parks can provide optimal conditions for tree establishment and growth and thus maximize the ecological and aesthetic benefits that trees provide. This study assesses the structure, and its implications for function, of the urban forest in Allan Gardens, a 6.1 ha downtown park in the City of Toronto, Canada, using the Street Tree Resource Analysis Tool for Urban Forest Managers (STRATUM). Our goal is to present a framework for collection and analysis of baseline data that can inform a management strategy that would serve to protect and enhance this significant natural asset. We found that Allan Garden's tree population, while species rich (43), is dominated by maple (Acer spp.) (48% of all park trees), making it reliant on very few species for the majority of its ecological and aesthetic benefits and raising disease and pest-related concerns. Age profiles (using size as a proxy) showed a dominance of older trees with an inadequate number of individuals in the young to early middle age cohort necessary for short- to medium-term replacement. Because leaf area represents the single-most important contributor to urban tree benefits modelling, we calculated it separately for every park tree, using hemispheric photography, to document current canopy condition. These empirical measurements were lower than estimates produced by STRATUM, especially when trees were in decline and lacked full canopies, highlighting the importance of individual tree condition in determining leaf area and hence overall forest benefits. Stewardship of natural spaces within cities demands access to accurate and timely resource-specific data. Our work provides an uncomplicated approach to the acquisition and interpretation of these data in the context of a forested urban park. Copyright 2010 Elsevier Ltd. All rights reserved.

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

PubMed

Zwickl, Derrick J; Stein, Joshua C; Wing, Rod A; Ware, Doreen; Sanderson, Michael J

2014-09-01

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development of a Prognostic Marker for Lung Cancer Using Analysis of Tumor Evolution

DTIC Science & Technology

2016-08-01

construct evolutionary trees , the characteristics of which will be used to predict whether a tumor will metastasize or not. We established a procedure for...of populations, the evolution of tumor cells within a tumor can be diagrammed on a phylogenetic tree . The more diverse a tumor’s phylogenetic tree ...individual tumor cells from the tumors of a training set of patients (half early stage, half late stage). We will reconstruct each tumor’s phylogenetic tree

Introduction in IND and recursive partitioning

NASA Technical Reports Server (NTRS)

Buntine, Wray; Caruana, Rich

1991-01-01

This manual describes the IND package for learning tree classifiers from data. The package is an integrated C and C shell re-implementation of tree learning routines such as CART, C4, and various MDL and Bayesian variations. The package includes routines for experiment control, interactive operation, and analysis of tree building. The manual introduces the system and its many options, gives a basic review of tree learning, contains a guide to the literature and a glossary, and lists the manual pages for the routines and instructions on installation.

The use of gas-sensor arrays in the detection of bole and root decays in living trees: development of a new non-invasive method of sampling and analysis

Treesearch

Manuela Baietto; Sofia Aquaro; Dan Wilson; Letizia Pozzi; Danieli Bassi

2015-01-01

Wood rot is a serious fungal disease of trees. Wood decay fungi penetrate and gain entry into trees through pruning cuts or open wounds using extracellular digestive enzymes to attack all components of the cell wall, leading to the destruction of sapwood which compromises wood strength and stability. On living trees, it is often difficult to diagnose wood rot disease,...

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

PubMed Central

Chen, Shaoping; Tu, Yi-Cheng; Xia, Yuni

2011-01-01

Many scientific and engineering fields produce large volume of spatiotemporal data. The storage, retrieval, and analysis of such data impose great challenges to database systems design. Analysis of scientific spatiotemporal data often involves computing functions of all point-to-point interactions. One such analytics, the Spatial Distance Histogram (SDH), is of vital importance to scientific discovery. Recently, algorithms for efficient SDH processing in large-scale scientific databases have been proposed. These algorithms adopt a recursive tree-traversing strategy to process point-to-point distances in the visited tree nodes in batches, thus require less time when compared to the brute-force approach where all pairwise distances have to be computed. Despite the promising experimental results, the complexity of such algorithms has not been thoroughly studied. In this paper, we present an analysis of such algorithms based on a geometric modeling approach. The main technique is to transform the analysis of point counts into a problem of quantifying the area of regions where pairwise distances can be processed in batches by the algorithm. From the analysis, we conclude that the number of pairwise distances that are left to be processed decreases exponentially with more levels of the tree visited. This leads to the proof of a time complexity lower than the quadratic time needed for a brute-force algorithm and builds the foundation for a constant-time approximate algorithm. Our model is also general in that it works for a wide range of point spatial distributions, histogram types, and space-partitioning options in building the tree. PMID:21804753

Simulation-Based Acquisition of the Future Air-Land Combat System (acquisition par la simulation des systemes futurs de combat aeroterresire)

DTIC Science & Technology

2003-11-01

de défense sur des matériels, des hommes et des doctrines préexistants, mais part au contraire d’une analyse des menaces et du... hommes et les doctrines. Comme on le verra ultérieurement, cette nouvelle démarche d’ingénierie du système de défense, qui se veut proactive et non...résolvent sous des contraintes de zéro mort ou tout au moins de pertes minimales, dont l ’« acceptabilité » est essentiellement facteur de

High-Throughput 3-D Monitoring of Agricultural-Tree Plantations with Unmanned Aerial Vehicle (UAV) Technology

PubMed Central

Torres-Sánchez, Jorge; López-Granados, Francisca; Serrano, Nicolás; Arquero, Octavio; Peña, José M.

2015-01-01

The geometric features of agricultural trees such as canopy area, tree height and crown volume provide useful information about plantation status and crop production. However, these variables are mostly estimated after a time-consuming and hard field work and applying equations that treat the trees as geometric solids, which produce inconsistent results. As an alternative, this work presents an innovative procedure for computing the 3-dimensional geometric features of individual trees and tree-rows by applying two consecutive phases: 1) generation of Digital Surface Models with Unmanned Aerial Vehicle (UAV) technology and 2) use of object-based image analysis techniques. Our UAV-based procedure produced successful results both in single-tree and in tree-row plantations, reporting up to 97% accuracy on area quantification and minimal deviations compared to in-field estimations of tree heights and crown volumes. The maps generated could be used to understand the linkages between tree grown and field-related factors or to optimize crop management operations in the context of precision agriculture with relevant agro-environmental implications. PMID:26107174

High-Throughput 3-D Monitoring of Agricultural-Tree Plantations with Unmanned Aerial Vehicle (UAV) Technology.

PubMed

Torres-Sánchez, Jorge; López-Granados, Francisca; Serrano, Nicolás; Arquero, Octavio; Peña, José M

2015-01-01

The geometric features of agricultural trees such as canopy area, tree height and crown volume provide useful information about plantation status and crop production. However, these variables are mostly estimated after a time-consuming and hard field work and applying equations that treat the trees as geometric solids, which produce inconsistent results. As an alternative, this work presents an innovative procedure for computing the 3-dimensional geometric features of individual trees and tree-rows by applying two consecutive phases: 1) generation of Digital Surface Models with Unmanned Aerial Vehicle (UAV) technology and 2) use of object-based image analysis techniques. Our UAV-based procedure produced successful results both in single-tree and in tree-row plantations, reporting up to 97% accuracy on area quantification and minimal deviations compared to in-field estimations of tree heights and crown volumes. The maps generated could be used to understand the linkages between tree grown and field-related factors or to optimize crop management operations in the context of precision agriculture with relevant agro-environmental implications.

Modelling and in-situ measurements of intense currents during a winter storm in the Gulf of Aigues-Mortes (NW Mediterranean Sea)

NASA Astrophysics Data System (ADS)

Michaud, Héloïse; Leredde, Yann; Estournel, Claude; Berthebaud, Éric; Marsaleix, Patrick

2013-09-01

While oceanic circulation in the Gulf of Lion (GoL) has often been studied in calm weather or with northerly winds (Tramontane or Mistral) through observations and numerical circulation models, few studies have focused on southeasterly storm events. Yet, correct representation of the circulation during storms is crucial if the suspension of sediments is to be correctly modelled throughout the Gulf. The purpose of this paper is to describe the hydrodynamics in the Gulf of Aigues-Mortes (NW of the GoL) during the storm of 18 February 2007 by using a set of data from an ADCP station placed at a depth of 65 m on the sea bed off the coast at Sète, supplemented by the ocean circulation model SYMPHONIE. This storm was characterized by a moderate south-easterly wind (15 m . s-1) and waves of up to 5 m of significant height at its apex. At the ADCP, strong currents of up to 0.8 m . s-1 near the surface and 0.5 m . s-1 near the bottom were recorded, parallel to the coast, flowing towards the south-west. The simulated currents were widely underestimated, even taking the effect of waves into account in the model. It was suspected that the representation of the wind in the atmospheric model was an underestimation. A new simulation was therefore run with an arbitrarily chosen stronger wind and its results were in much better agreement with the measurements. A simplified theoretical analysis successfully isolated the wind-induced processes, responsible for the strong currents measured during the apex and the strong vertical shear that occurred at the beginning of the storm. These processes were: 1/ the barotropic geostrophic current induced by a wind parallel to the coast and 2/ the Ekman spiral. The duration of the storm (about 36 h at the apex) explains the continuous increase of the current as predicted by the theory. The frictionally induced Ekman transport explains the current shear in the surface layer in the rising stage of the storm, and the addition of high waves and strong wind at the apex is more in favour of strong vertical mixing in the surface layer.

Understanding tree growth in response to moisture variability: Linking 32 years of satellite based soil moisture observations with tree rings

NASA Astrophysics Data System (ADS)

Albrecht, Franziska; Dorigo, Wouter; Gruber, Alexander; Wagner, Wolfgang; Kainz, Wolfgang

2014-05-01

Climate change induced drought variability impacts global forest ecosystems and forest carbon cycle dynamics. Physiological drought stress might even become an issue in regions generally not considered water-limited. The water balance at the soil surface is essential for forest growth. Soil moisture is a key driver linking precipitation and tree development. Tree ring based analyses are a potential approach to study the driving role of hydrological parameters for tree growth. However, at present two major research gaps are apparent: i) soil moisture records are hardly considered and ii) only a few studies are linking tree ring chronologies and satellite observations. Here we used tree ring chronologies obtained from the International Tree ring Data Bank (ITRDB) and remotely sensed soil moisture observations (ECV_SM) to analyze the moisture-tree growth relationship. The ECV_SM dataset, which is being distributed through ESA's Climate Change Initiative for soil moisture covers the period 1979 to 2010 at a spatial resolution of 0.25°. First analyses were performed for Mongolia, a country characterized by a continental arid climate. We extracted 13 tree ring chronologies suitable for our analysis from the ITRDB. Using monthly satellite based soil moisture observations we confirmed previous studies on the seasonality of soil moisture in Mongolia. Further, we investigated the relationship between tree growth (as reflected by tree ring width index) and remotely sensed soil moisture records by applying correlation analysis. In terms of correlation coefficient a strong response of tree growth to soil moisture conditions of current April to August was observed, confirming a strong linkage between tree growth and soil water storage. The highest correlation was found for current April (R=0.44), indicating that sufficient water supply is vital for trees at the beginning of the growing season. To verify these results, we related the chronologies to reanalysis precipitation and temperature datasets. Precipitation was important during both the current and previous growth season. Temperature showed the strongest correlation for previous (R=0.12) and current October (R=0.21). Hence, our results demonstrated that water supply is most likely limiting tree growth during the growing season, while temperature is determining its length. We are confident that long-term satellite based soil moisture observations can bridge spatial and temporal limitations that are inherent to in situ measurements, which are traditionally used for tree ring research. Our preliminary results are a foundation for further studies linking remotely sensed datasets and tree ring chronologies, an approach that has not been widely investigated among the scientific community.

A transportable magnetic resonance imaging system for in situ measurements of living trees: the Tree Hugger.

PubMed

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

2012-05-01

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

Tree Islands of the Florida Everglades - A Disappearing Resource

USGS Publications Warehouse

,

2003-01-01

Until recently, the timing and cause of tree island formation have been poorly understood, with estimates of initial tree-island development as early as thousands of years ago to as recently as the last few decades. To increase our knowledge about the origins of these features, sediment cores were collected on and around tree islands. These cores were dated using radioisotopic techniques, including carbon-14 dating, which provides reliable dates from ~40,000 to ~300 years ago, and lead-210 dating, which provides age models for the last century. These age models were paired with vegetational reconstruction based on pollen analysis from cores to identify the timing of tree-island formation and assess past tree-island response to hydrologic changes in the 20th century.

Multispectral color photography for mineral exploration by the remote sensing of biogeochemical anomalies

NASA Technical Reports Server (NTRS)

Yost, E.

1975-01-01

Selected band multispectral photography was evaluated as a mineral exploration tool by detecting stress on trees caused by underground mineralization. Ground truth consisted of two test sites in the Prescott National Forest within which the mineralization had been established by a drilling program. Species of trees were categorized as background, intermediate, and anomalous based upon where they grew with respect to this underlying mineralization. Soil geochemistry and the metal content of ashed samples of the trees were studied in relation to the inferred locus of mineralization. Computer analysis of the reflectance spectra of mineralized trees confirmed that the relative percent reflectance differences of trees growing in anomalous areas was less than that of the same tree species growing in background areas.

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

PubMed

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

2015-01-01

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

An advancement in removing extraneous color from wood for low-magnification reflected-light image analysis of conifer tree rings

Treesearch

Paul R. Sheppard; Alex Wiedenhoeft

2007-01-01

This paper describes the removal of extraneous color from increment cores of conifers prior to reflected-light image analysis of tree rings. Ponderosa pine in central New Mexico was chosen for study. Peroxide bleaching was used as a pretreatment to remove extraneous color and still yield usable wood for image analysis. The cores were bleached in 3% peroxide raised to...

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript.

PubMed

Shearman, Jeremy R; Sangsrakru, Duangjai; Ruang-Areerate, Panthita; Sonthirod, Chutima; Uthaipaisanwong, Pichahpuk; Yoocha, Thippawan; Poopear, Supannee; Theerawattanasuk, Kanikar; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

2014-02-10

The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherited from the variety GT 1. We constructed the rubber tree mitochondrial genome of a cytoplasmic male sterile variety, BPM 24, using 454 sequencing, including 8 kb paired-end libraries, plus Illumina paired-end sequencing. We annotated this mitochondrial genome with the aid of Illumina RNA-seq data and performed comparative analysis. We then compared the sequence of BPM 24 to the contigs of the published rubber tree, variety RRIM 600, and identified a rearrangement that is unique to BPM 24 resulting in a novel transcript containing a portion of atp9. The novel transcript is consistent with changes that cause cytoplasmic male sterility through a slight reduction to ATP production efficiency. The exhaustive nature of the search rules out alternative causes and supports previous findings of novel transcripts causing cytoplasmic male sterility.

Climate Controls on Tree Growth Across Species and Sites in Northeastern Arizona

NASA Astrophysics Data System (ADS)

Schwan, M. R.; Guiterman, C. H.; Anchukaitis, K. J.

2016-12-01

Understanding how forests will respond to ongoing climate change is important for conservation and resource management. Conifer forests in the US Southwest are predicted to be particularly at risk from increased drought and higher temperatures projected to occur in the region. Tree-ring studies shed light on how trees respond to climate, but there remains considerable uncertainty as to which climate factors are most important, and which species are most at risk. Confounding climate and environmental factors, biological differences among species, and biogeography often complicate cross-species analysis. Here we present a multi-species, multivariate analysis of tree growth response to climate variability. We analyze data from three coexisting conifer tree species at two sites near Canyon de Chelly, Arizona. We use a high-resolution PRISM gridded climate dataset to determine the growth responses across species and sites to temperature and precipitation. We identify both common and differential responses in our data and use these to infer possible risks these forest communities may face under a changing climate.

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

Spatial statistical analysis of tree deaths using airborne digital imagery

NASA Astrophysics Data System (ADS)

Chang, Ya-Mei; Baddeley, Adrian; Wallace, Jeremy; Canci, Michael

2013-04-01

High resolution digital airborne imagery offers unprecedented opportunities for observation and monitoring of vegetation, providing the potential to identify, locate and track individual vegetation objects over time. Analytical tools are required to quantify relevant information. In this paper, locations of trees over a large area of native woodland vegetation were identified using morphological image analysis techniques. Methods of spatial point process statistics were then applied to estimate the spatially-varying tree death risk, and to show that it is significantly non-uniform. [Tree deaths over the area were detected in our previous work (Wallace et al., 2008).] The study area is a major source of ground water for the city of Perth, and the work was motivated by the need to understand and quantify vegetation changes in the context of water extraction and drying climate. The influence of hydrological variables on tree death risk was investigated using spatial statistics (graphical exploratory methods, spatial point pattern modelling and diagnostics).

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

PubMed

Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

2015-12-01

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

Element concentrations in growth rings of trees near an abandoned wood-preserving plant site at Jackson, Tennessee

USGS Publications Warehouse

Yanosky, T.M.; Carmichael, J.K.

1993-01-01

Multielement analysis was performed on individual annual rings of trees growing at and near an abandoned wood-preserving plant site in Jackson, Tennessee, that operated from the early 1930's until 1981. Numerous organic compounds associated with the wood-preserving process have been detected in soils, ground water, and surface water within much of the site. Tree-ring investigations were conducted prior to investigations of ground water downgradient from the site to determine if trees preserved an areal and temporal record of contaminant movement into offsite areas. Increment cores were collected from trees on the abandoned plant site, in downgradient areas west and south of the site, and at two locations presumably unaffected by contamination from the site. Multielement analysis by proton-induced X-ray emission was performed on 5 to 15 individual growth rings from each of 34 trees that ranged in age from about 5 to 50 years. Concentrations of 16 elements were evaluated by analyzing average concentrations within the 1987, 1989, and 1990 rings of all trees; analyzing element-concentration trends along entire core radii; and analyzing element correlations between and among trees. Concentrations of some nutrients and trace metals were elevated in the outermost sapwood rings of some trees that grow south and southwest of the most contaminated part of the site; small trees on the main part of the site and larger trees to the west generally contained fewer rings with elevated concentrations, particularly of trace metals. Concentrations of several elements elevated in tree rings also were elevated in water samples collected from the reach of a stream that flows near the southwestern part of the site. Multielement analysis of each ring of a willow growing along the southern boundary of the site detected extremely large concentrations of chromium, nickel, and iron in rings that formed in 1986 and thereafter. Relative increases in the concentrations of these elements also were detected in a silver maple growing next to the willow, but not in another silver maple growing 150 meters farther to the west. An oak growing in the southwestern part of the study area contained large concentrations of calcium and several trace elements, and some trees south of the abandoned site contained large concentrations of phosphorus or potassium. Concentrations of trace metals and nutrients in some trees may be related to wood-preserving activities at the site and possibly to remedial efforts conducted during the early to mid 1980's.However, the possibility cannot be discounted that large concentrations of some elements are from sources other than the wood-preserving facility, or in part from flooding of the South Fork Forked Deer River.

The Ring-Barking Experiment: Analysis of Forest Vitality Using Multi-Temporal Hyperspectral Data

NASA Astrophysics Data System (ADS)

Reichmuth, Anne; Bachmann, Martin; Heiden, Uta; Pinnel, Nicole; Holzwarth, Stefanie; Muller, Andreas; Henning, Lea; Einzmann, Kathrin; Immitzer, Markus; Seitz, Rudolf

2016-08-01

Through new operational optical spaceborne sensors (En- MAP and Sentinel-2) the impact analysis of climate change on forest ecosystems will be fostered. This analysis examines the potential of high spectral, spatial and temporal resolution data for detecting forest vegetation parameters, in particular Chlorophyll and Canopy Water content. The study site is a temperate spruce forest in Germany where in 2013 several trees were Ring-barked for a controlled die-off. During this experiment Ring- barked and Control trees were observed. Twelve airborne hyperspectral HySpex VNIR (Visible/Near Infrared) and SWIR (Shortwave Infrared) data with 1m spatial and 416 bands spectral resolution were acquired during the vegetation periods of 2013 and 2014. Additional laboratory spectral measurements of collected needle samples from Ring-barked and Control trees are available for needle level analysis. Index analysis of the laboratory measurements and image data are presented in this study.

Phylogeny, host-parasite relationship and zoogeography

PubMed Central

1999-01-01

Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates. PMID:10634036

Mines Systems Safety Improvement Using an Integrated Event Tree and Fault Tree Analysis

NASA Astrophysics Data System (ADS)

Kumar, Ranjan; Ghosh, Achyuta Krishna

2017-04-01

Mines systems such as ventilation system, strata support system, flame proof safety equipment, are exposed to dynamic operational conditions such as stress, humidity, dust, temperature, etc., and safety improvement of such systems can be done preferably during planning and design stage. However, the existing safety analysis methods do not handle the accident initiation and progression of mine systems explicitly. To bridge this gap, this paper presents an integrated Event Tree (ET) and Fault Tree (FT) approach for safety analysis and improvement of mine systems design. This approach includes ET and FT modeling coupled with redundancy allocation technique. In this method, a concept of top hazard probability is introduced for identifying system failure probability and redundancy is allocated to the system either at component or system level. A case study on mine methane explosion safety with two initiating events is performed. The results demonstrate that the presented method can reveal the accident scenarios and improve the safety of complex mine systems simultaneously.

Protection of individual ash trees from emerald ash borer (Coleoptera: Buprestidae) with basal soil applications of imidacloprid.

PubMed

Smitley, D R; Rebek, E J; Royalty, R N; Davis, T W; Newhouse, K F

2010-02-01

We conducted field trials at five different locations over a period of 6 yr to investigate the efficacy of imidacloprid applied each spring as a basal soil drench for protection against emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). Canopy thinning and emerald ash borer larval density were used to evaluate efficacy for 3-4 yr at each location while treatments continued. Test sites included small urban trees (5-15 cm diameter at breast height [dbh]), medium to large (15-65 cm dbh) trees at golf courses, and medium to large street trees. Annual basal drenches with imidacloprid gave complete protection of small ash trees for three years. At three sites where the size of trees ranged from 23 to 37 cm dbh, we successfully protected all ash trees beginning the test with <60% canopy thinning. Regression analysis of data from two sites reveals that tree size explains 46% of the variation in efficacy of imidacloprid drenches. The smallest trees (<30 cm dbh) remained in excellent condition for 3 yr, whereas most of the largest trees (>38 cm dbh) declined to a weakened state and undesirable appearance. The five-fold increase in trunk and branch surface area of ash trees as the tree dbh doubles may account for reduced efficacy on larger trees, and suggests a need to increase treatment rates for larger trees.

Forest Watch: a K-12 Outreach Program to Engage Young Students in Authentic, Hands-On Science

NASA Astrophysics Data System (ADS)

Rock, B. N.; Gagnon, M.

2008-12-01

The Forest Watch Program is a K-12 science outreach program developed at the University of New Hampshire (UNH) in 1991. The program engages pre-college teachers and their students in assisting researchers at UNH in the assessment of the state-of-health of white pine (Pinus strobus), a known bio- indicator species for exposure to elevated levels of ground-level ozone. Students participate in three types of activities: 1. selection, collection, and analysis of needle samples from five permanently tagged white pine trees near their school; 2. Study of needles in their classroom and sending a set of needles to UNH for spectral analysis; and 3. analysis of remote sensing data (Landsat TM) provided of their local area using freeware software (MultiSpec). Student-derived foliar symptomology, needle length, needle retention, and tree biometrics, plus the spectral indices, allow UNH researchers to characterize annual variations in tree state-of-health, and to correlate that state-of-health with annual summer ozone levels collected by the EPA and state environmental monitoring networks. The results suggest that regional air quality and state- of-health of trees has improved since 1991. Annual student data and the yearly spectral variations, for the same trees, suggest that white pine health has improved dramatically since 1997/8. This improvement in tree health corresponds with improved regional air quality. An evaluation of student data reliability has been conducted and suggests that the DBH measurements are a most reliable indicator of tree growth. Student data are more reliable if multiple sets of measurements are made and averaged together, compared with single sets of measurements. Based on both student data and spectral analysis of student-provided branch samples, the greatest damage (chlorosis) occurs in trees located along the seacoast areas. Participation in Forest Watch introduces students to the scientific method via an authentic research program. The program is designed in partnership with participating teachers, and thus meets New England state science and mathematics curricula for K-12 education. Student participation in Forest Watch has resulted in an improved understanding of inter-annual white pine state-of-health response to improved air quality across the New England region.

Climate signal detected in sub-fossil and living oak trees data. An analysis of signal frequency components

NASA Astrophysics Data System (ADS)

Constantin, Nechita; Francisca, Chiriloaei; Maria, Radoane; Ionel, Popa; Nicoae, Radoane

2016-04-01

This study is focused on analysis the frequency components of the signal detected in living and sub-fossil tree ring series from different time periods. The investigation is oriented to analyze signal frequency components (low and high) of the two categories of trees. The interpretation technique of tree ring width is the instrument most often used to elaborate past climatic reconstructions. The annual resolution, but also, the high capacity of trees to accumulate climatic information are attributes which confer to palaeo-environmental reconstructions the biggest credibility. The main objective of the study refers to the evaluation of climatic signal characteristics, both present day climate and palaeo-climate (last 7000 years BP). Modern dendrochronological methods were applied on 350 samples of sub-fossil trees and 400 living trees. The subfossil trunks were sampled from different fluvial environments (Siret, Suceava, Moldova). Their age was determined using radiocarbon, varying from under 100 years to almost 7000 years BP. The subfossil tree species investigated were Quercus, Alnus, Ulmus. Considering living trees, these were identified on eastern part of Romania, in different actual physico-geographical conditions. The studied living tree species consisted in Quercus species (robur and petraea). Each site was investigated regarding stress factors of the sampled tree. The working methods were applied to the total wood series, both late and early, to detect intra-annual level climate information. Each series has been tested to separate individual trees with climatic signal of other trees with different signals (noises determined by competition between individuals or site stress, or anthropic impact). Comparing dendrochronological series (sub-fossil and living trees) we want to identify what significant causes determined the difference in the signal frequencies. Especially, the human interventions registered in the last 2 centuries will be evaluated by these different types of signal in the tree rings. In order to evaluate this aspect we used time series which were standardized to avoid the non-climatic signal. This type of investigation is the first of its kind to Eastern Europe, an area so large (over 50 000 km2) and a high number of sites and individuals studied (about 1000). The obtained results will help us to understand the palaeo-environment evolution in the last Holocene and when human intervention has been really significant.

A Fault Tree Approach to Analysis of Behavioral Systems: An Overview.

ERIC Educational Resources Information Center

Stephens, Kent G.

Developed at Brigham Young University, Fault Tree Analysis (FTA) is a technique for enhancing the probability of success in any system by analyzing the most likely modes of failure that could occur. It provides a logical, step-by-step description of possible failure events within a system and their interaction--the combinations of potential…

Identification of Sexually Abused Female Adolescents at Risk for Suicidal Ideations: A Classification and Regression Tree Analysis

ERIC Educational Resources Information Center

Brabant, Marie-Eve; Hebert, Martine; Chagnon, Francois

2013-01-01

This study explored the clinical profiles of 77 female teenager survivors of sexual abuse and examined the association of abuse-related and personal variables with suicidal ideations. Analyses revealed that 64% of participants experienced suicidal ideations. Findings from classification and regression tree analysis indicated that depression,…

What Satisfies Students? Mining Student-Opinion Data with Regression and Decision-Tree Analysis. AIR 2002 Forum Paper.

ERIC Educational Resources Information Center

Thomas, Emily H.; Galambos, Nora

To investigate how students' characteristics and experiences affect satisfaction, this study used regression and decision-tree analysis with the CHAID algorithm to analyze student opinion data from a sample of 1,783 college students. A data-mining approach identifies the specific aspects of students' university experience that most influence three…

Long-term sustainability in Davis Late Successional Reserve

Treesearch

Jim Stone; Joan Kittrell

2004-01-01

A pilot watershed analysis along with the Davis Late Successional Reserve analysis in the range of the northern spotted owl identified potential loss of suitable habitat, reduction in the numbers of large trees, and lack of replacements for large trees. A variety of silvicultural thinning techniques has been used to address these important issues and to move toward a...

On the use of cartographic projections in visualizing phylo-genetic tree space

PubMed Central

2010-01-01

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets. PMID:20529355

Analysis of sounds produced by Rhynchophorus ferrugineus and Oryctes elegans larvae and adults in data palm trees and offshoots in Saudi Arabian commercial orchards

USDA-ARS?s Scientific Manuscript database

Sounds produced by larval and adult palm tree pests in Saudi Arabian date palm orchards were recorded using commercially available insect acoustic detection instruments. The trees and offshoots were inspected for presence/absence of insects and other visual signs of infestation. Subsequently, the sp...

Relating FIA data to habitat classifications via tree-based models of canopy cover

Treesearch

Mark D. Nelson; Brian G. Tavernia; Chris Toney; Brian F. Walters

2012-01-01

Wildlife species-habitat matrices are used to relate lists of species with abundance of their habitats. The Forest Inventory and Analysis Program provides data on forest composition and structure, but these attributes may not correspond directly with definitions of wildlife habitats. We used FIA tree data and tree crown diameter models to estimate canopy cover, from...

An evaluation of the STEMS tree growth projection system.

Treesearch

Margaret R. Holdaway; Gary J. Brand

1983-01-01

STEMS (Stand and Tree Evaluation and Modeling System) is a tree growth projection system. This paper (1) compares the performance of the current version of STEMS developed for the Lake States with that of the original model and (2) reports the results of an analysis of the current model over a wide range of conditions and identifies its main strengths and weaknesses...

Inventory methods for trees in nonforest areas in the Great Plains States

Treesearch

Andrew J. Lister; Charles T. Scott; Steven Rasmussen

2012-01-01

The US Forest Service's Forest Inventory and Analysis (FIA) program collects information on trees in areas that meet its definition of forest. However, the inventory excludes trees in areas that do not meet this definition, such as those found in urban areas, in isolated patches, in areas with sparse or predominantly herbaceous vegetation, in narrow strips (e.g.,...

Pervasive hydrologic effects on freshwater mussels and riparian trees in southeastern floodplain ecosystems

Treesearch

Andrew L. Rypel; Wendell R. Haag; Robert H. Findlay

2009-01-01

We present long-term growth trends for 13 freshwater mussel species from two unregulated rivers and one regulated river in the southeastern U.S. Coastal Plain. We also collected baldcypress (Taxodium distichum (L.) Rich.) tree cores adjacent to mussel collection sites in one river and directly compared tree and mussel chronologies in this river. To extend our analysis...

Modeling potential future individual tree-species distributions in the eastern United States under a climate change scenario: a case study with Pinus virginiana

Treesearch

Louis R. Iverson; Anantha Prasad; Mark W. Schwartz; Mark W. Schwartz

1999-01-01

We are using a deterministic regression tree analysis model (DISTRIB) and a stochastic migration model (SHIFT) to examine potential distributions of ~66 individual species of eastern US trees under a 2 x CO2 climate change scenario. This process is demonstrated for Virginia pine (Pinus virginiana).

European settlement-era vegetation of the Monongahela National Forest, West Virginia

Treesearch

Melissa A. Thomas-Van Gundy; Michael P. Strager

2012-01-01

Forest restoration would be greatly helped by understanding just what forests looked like a century or more ago. One source of information on early forests is found in old deeds or surveys, where boundary corners were described by noting nearby trees known as witness trees. This paper describes the creation and analysis of a database of witness trees from original...

Forest composition of Maine: an analysis using number of trees

Treesearch

Douglas S. Powell

1985-01-01

Number-of-trees data compiled by the USDA Forest Service from three periodic statewide inventories of Maine's forest resources are used to analyze the composition of the state's timberland in terms of species, tree class, and size. Conditions are compared and contrasted for periods from 1959 to 1971 to 1982 across different regions and counties of the state....

West Coast tree improvement programs: a break-even, cost-benefit analysis

Treesearch

F. Thomas Ledig; Richard L Porterfield

1981-01-01

Three tree improvement programs were analyzed by break-even, cost-benefit technique: one for ponderosa pine in the Pacific Northwest, and two for Douglas-fir in the Pacific Northwest-one of low intensity and the other of high intensity. A return of 8 percent on investment appears feasible by using short rotations or by accompanying tree improvement with thinning....

Potential Changes in Tree Species Richness and Forest Community Types following Climate Change

Treesearch

Louis R. Iverson; Anantha M. Prasad

2001-01-01

Potential changes in tree species richness and forest community types were evaluated for the eastern United States according to five scenarios of future climate change resulting from a doubling of atmospheric carbon dioxide (CO2). DISTRIB, an empirical model that uses a regression tree analysis approach, was used to generate suitable habitat, or potential future...

Probability of infestation and extent of mortality associated with the Douglas-fir beetle in the Colorado Front Range

Treesearch

Jose F. Negron

1998-01-01

Infested and uninfested areas within Douglas fir, Pseudotsuga menziesii Mirb.. Franco, stands affected by the Douglas-fir beetle, Dendroctonus pseudotsugae Hopk. were sampled in the Colorado Front Range, CO. Classification tree models were built to predict probabilities of infestation. Regression trees and linear regression analysis were used to model amount of tree...

Estimating tree crown widths for the primary Acadian species in Maine

Treesearch

Matthew B. Russell; Aaron R. Weiskittel

2012-01-01

In this analysis, data for seven conifer and eight hardwood species were gathered from across the state of Maine for estimating tree crown widths. Maximum and largest crown width equations were developed using tree diameter at breast height as the primary predicting variable. Quantile regression techniques were used to estimate the maximum crown width and a constrained...

A comparison of tree crown condition in areas with and without gypsy moth activity

Treesearch

KaDonna C. Randolph

2005-01-01

This study compared the crown condition of trees within and outside areas of gypsy moth defoliation in Virginia via hypothesis tests of mean differences for five U.S. Department of Agriculture (USDA) Forest Service Forest Inventory and Analysis phase 3 crown condition indicators. Significant differences were found between the trees located within and outside gypsy moth...

A comparison of tree crown condition in areas with and without gypsy moth activity

Treesearch

KaDonna C. Randolph

2007-01-01

This study compared the crown condition of trees within and outside areas of gypsy moth defoliation in Virginia via hypothesis tests of mean differences for five U.S. Department of Agriculture (USDA) Forest Service Forest Inventory and Analysis phase 3 crown condition indicators. Significant differences were found between the trees located within and outside gypsy moth...

Tree migration detection through comparisons of historic and current forest inventories

Treesearch

Christopher W. Woodall; Christopher M. Oswalt; James A. Westfall; Charles H. Perry; Mark N. Nelson

2009-01-01

Changes in tree species distributions are a potential impact of climate change on forest ecosystems. The examination of tree species shifts in forests of the eastern United States largely has been limited to modeling activities with little empirical analysis of long-term forest inventory datasets. The goal of this study was to compare historic and current spatial...

Site Productivity and Tree Mortality on New Frontiers of Gypsy Moth Infestation

Treesearch

David A. Gansner; David A. Gansner

1987-01-01

Recent analysis of forest stand losses to gypsy moth has provided basic information for analyzing the relationship between forest site productivity and tree mortality on new frontiers of infestation. Poor timber-growing sites had the lowest rates of mortality. Oak mortality (number of trees) amounted to 18 percent on poor sites compared with 26 percent on medium and 28...

Comparison of protein profiles of beech bark disease-resistant or beech bark disease-susceptible American beech

Treesearch

Mary E. Mason; Marek Krasowski; Judy Loo; Jennifer. Koch

2011-01-01

Proteomic analysis of beech bark proteins from trees resistant and susceptible to beech bark disease (BBD) was conducted. Sixteen trees from eight geographically isolated stands, 10 resistant (healthy) and 6 susceptible (diseased/infested) trees, were studied. The genetic complexity of the sample unit, the sampling across a wide geographic area, and the complexity of...

Project CAPTURE: using forest inventory and analysis data to prioritize tree species for conservation, management, and restoration

Treesearch

Kevin M. Potter; Barbara S. Crane; William W. Hargrove

2015-01-01

A variety of threats, most importantly climate change and insect and disease infestation, will increase the likelihood that forest tree species could experience population-level extirpation or species-level extinction during the next century. Project CAPTURE (Conservation Assessment and Prioritization of Forest Trees Under Risk of Extirpation) is a cooperative effort...

Production analysis of two tree-bucking and product-sorting methods for hardwoods

Treesearch

John E. Baumgras; Chris B. LeDoux

1989-01-01

This paper documents the results of a study to determine the cost and productivity of two tree-bucking and product-sorting methods used by West Virginia loggers harvesting three to four types of roundwood products. The methods include manual chainsaw bucking and bucking with a hydraulically powered chainsaw slasher. Results show that chain saw bucking of trees...

Inventory of trees in nonforest areas in the Great Plains states

Treesearch

Andrew Lister; Chip Scott; Steve Rasmussen

2009-01-01

The U.S. Forest Service's Forest Inventory and Analysis (FIA) program collects information on trees in areas that meet its definition of forest. However, the inventory excludes trees in areas that do not meet this definition, such as those found in isolated patches, in areas with sparse or predominantly herbaceous vegetation, in narrow strips (e.g., shelterbelts...

Past and ongoing shifts in Joshua tree distribution support future modeled range contraction

Treesearch

Kenneth L. Cole; Kirsten Ironside; Jon Eischeid; Gregg Garfin; Phillip B. Duffy; Chris Toney

2011-01-01

The future distribution of the Joshua tree (Yucca brevifolia) is projected by combining a geostatistical analysis of 20th-century climates over its current range, future modeled climates, and paleoecological data showing its response to a past similar climate change. As climate rapidly warmed ~11 700 years ago, the range of Joshua tree contracted, leaving only the...

Sampling tree tops by helicopter...special pole pruner cuts branchlets

Treesearch

John F. Wear; Robert G. Winterfeld

1966-01-01

A new technique for sampling tops of tall Douglas-fir trees by using a special pole pruner from a helicopter has been developed and field-tested. Thee pole pruner cuts and holds a branchlet. Foliage samples collected will be compared by spectral analysis to show the type of aerial imagery that best differentiates healthy trees from those attacked by root rot.

Accuracy assessment of the vegetation continuous field tree cover product using 3954 ground plots in the southwestern USA

Treesearch

M. A. White; J. D. Shaw; R. D. Ramsey

2005-01-01

An accuracy assessment of the Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation continuous field (VCF) tree cover product using two independent ground-based tree cover databases was conducted. Ground data included 1176 Forest Inventory and Analysis (FIA) plots for Arizona and 2778 Southwest Regional GAP (SWReGAP) plots for Utah and western Colorado....

Modeling the effect of competition on tree diameter growth as applied in STEMS.

Treesearch

Margaret R. Holdaway

1984-01-01

The modifier function used in STEMS (Stand and Tree Evaluation and Modeling System) mathematically represents the effect that the surrounding forest community has on the growth of an individual tree. This paper 1) develops the most recent modifier function, 2) discusses its form, 3) reports the results of the analysis with biological considerations and 4) evaluates the...

Decision tree analysis in subarachnoid hemorrhage: prediction of outcome parameters during the course of aneurysmal subarachnoid hemorrhage using decision tree analysis.

PubMed

Hostettler, Isabel Charlotte; Muroi, Carl; Richter, Johannes Konstantin; Schmid, Josef; Neidert, Marian Christoph; Seule, Martin; Boss, Oliver; Pangalu, Athina; Germans, Menno Robbert; Keller, Emanuela

2018-01-19

OBJECTIVE The aim of this study was to create prediction models for outcome parameters by decision tree analysis based on clinical and laboratory data in patients with aneurysmal subarachnoid hemorrhage (aSAH). METHODS The database consisted of clinical and laboratory parameters of 548 patients with aSAH who were admitted to the Neurocritical Care Unit, University Hospital Zurich. To examine the model performance, the cohort was randomly divided into a derivation cohort (60% [n = 329]; training data set) and a validation cohort (40% [n = 219]; test data set). The classification and regression tree prediction algorithm was applied to predict death, functional outcome, and ventriculoperitoneal (VP) shunt dependency. Chi-square automatic interaction detection was applied to predict delayed cerebral infarction on days 1, 3, and 7. RESULTS The overall mortality was 18.4%. The accuracy of the decision tree models was good for survival on day 1 and favorable functional outcome at all time points, with a difference between the training and test data sets of < 5%. Prediction accuracy for survival on day 1 was 75.2%. The most important differentiating factor was the interleukin-6 (IL-6) level on day 1. Favorable functional outcome, defined as Glasgow Outcome Scale scores of 4 and 5, was observed in 68.6% of patients. Favorable functional outcome at all time points had a prediction accuracy of 71.1% in the training data set, with procalcitonin on day 1 being the most important differentiating factor at all time points. A total of 148 patients (27%) developed VP shunt dependency. The most important differentiating factor was hyperglycemia on admission. CONCLUSIONS The multiple variable analysis capability of decision trees enables exploration of dependent variables in the context of multiple changing influences over the course of an illness. The decision tree currently generated increases awareness of the early systemic stress response, which is seemingly pertinent for prognostication.

[RS estimation of inventory parameters and carbon storage of moso bamboo forest based on synergistic use of object-based image analysis and decision tree].

PubMed

Du, Hua Qiang; Sun, Xiao Yan; Han, Ning; Mao, Fang Jie

2017-10-01

By synergistically using the object-based image analysis (OBIA) and the classification and regression tree (CART) methods, the distribution information, the indexes (including diameter at breast, tree height, and crown closure), and the aboveground carbon storage (AGC) of moso bamboo forest in Shanchuan Town, Anji County, Zhejiang Province were investigated. The results showed that the moso bamboo forest could be accurately delineated by integrating the multi-scale ima ge segmentation in OBIA technique and CART, which connected the image objects at various scales, with a pretty good producer's accuracy of 89.1%. The investigation of indexes estimated by regression tree model that was constructed based on the features extracted from the image objects reached normal or better accuracy, in which the crown closure model archived the best estimating accuracy of 67.9%. The estimating accuracy of diameter at breast and tree height was relatively low, which was consistent with conclusion that estimating diameter at breast and tree height using optical remote sensing could not achieve satisfactory results. Estimation of AGC reached relatively high accuracy, and accuracy of the region of high value achieved above 80%.

Genetic diversity analysis of tree peony germplasm using iPBS markers.

PubMed

Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

2015-07-06

We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties.

Structural Analysis Of CD59 Of Chinese Tree Shrew: A New Reference Molecule For Human Immune System Specific CD59 Drug Discovery.

PubMed

Panda, Subhamay; Kumari, Leena; Panda, Santamay

2017-11-17

Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquires shared common as well as unique characteristics, and hence offers a genetic basis for employing this animal as a prospective model for biomedical research. CD59 glycoprotein, commonly referred to as MAC-inhibitory protein (MAC-IP), membrane inhibitor of reactive lysis (MIRL), or protectin, is encoded by the CD59 gene in human beings. It is the member of the LY6/uPAR/alpha-neurotoxin protein family. With this initial point the objective of this study was to determine a comparative composite based structure of CD59 of Chinese tree shrew. The additional objective of this study was to examine the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the assistance of several bioinformatical analytical tools. CD59 Amino acid sequence of Chinese tree shrew collected from the online database system of National Centre for Biotechnology Information. SignalP 4.0 online server was employed for detection of signal peptide instance within the protein sequence of CD59. Molecular model structure of CD59 protein was generated by the Iterative Threading ASSEmbly Refinement (I-TASSER) suite. The confirmation for three-dimensional structural model was evaluated by structure validation tools. Location of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of Chimera tool. Electrostatic potential analysis was carried out with the adaptive Poisson-Boltzmann solver package. Subsequently validated model was used for the functionally critical amino acids and active site prediction. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) was determined using the COACH program. Analysis of Ramachandran plot for Chinese tree shrew depicted that overall, 100% of the residues in homology model were observed in allowed and favored regions, sequentially leading to the validation of the standard of generated protein structural model. In case of CD59 of Chinese tree shrew, the total score of G-factor was found to be -0.66 that was generally larger than the acceptable value. This approach suggests the significance and acceptability of the modeled structure of CD59 of Chinese tree shrew. The molecular model data in cooperation to other relevant post model analysis data put forward molecular insight to protecting activity of CD59 protein molecule of Chinese tree shrew. In the present study, we have proposed the first molecular model structure of uncharted CD59 of Chinese tree shrew by significantly utilizing the comparative composite modeling approach. Therefore, the development of a structural model of the CD59 protein was carried out and analyzed further for deducing molecular enrichment technique. The collaborative effort of molecular model and other relevant data of post model analysis carry forward molecular understanding to protecting activity of CD59 functions towards better insight of features of this natural lead compound. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny.

PubMed

Lambert, Shea M; Reeder, Tod W; Wiens, John J

2015-01-01

Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, andsuggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling. Copyright © 2014 Elsevier Inc. All rights reserved.

Lethal trap trees: a potential option for emerald ash borer (Agrilus planipennis Fairmaire) management.

PubMed

McCullough, Deborah G; Poland, Therese M; Lewis, Phillip A

2016-05-01

Economic and ecological impacts of ash (Fraxinus spp.) mortality resulting from emerald ash borer (EAB) (Agrilus planipennis Fairmaire) invasion are severe in forested, residential and urban areas. Management options include girdling ash trees to attract ovipositing adult beetles and then destroying infested trees before larvae develop or protecting ash with a highly effective, systemic emamectin benzoate insecticide. Injecting this insecticide and then girdling injected trees a few weeks later could effectively create lethal trap trees, similar to a bait-and-kill tactic, if girdling does not interfere with insecticide translocation. We compared EAB larval densities on girdled trees, trees injected with the emamectin benzoate insecticide, trees injected with the insecticide and then girdled 18-21 days later and untreated controls at multiple sites. Pretreatment larval densities did not differ among treatments. Current-year larval densities were higher on girdled and control trees than on any trees treated with insecticide at all sites. Foliar residue analysis and adult EAB bioassays showed that girdling trees after insecticide injections did not reduce insecticide translocation. Girdling ash trees to attract adult EAB did not reduce efficacy of emamectin benzoate trunk injections applied ≥ 18 days earlier and could potentially be used in integrated management programs to slow EAB population growth. © 2015 Society of Chemical Industry.

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

PubMed

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.

Aerodynamic effects of trees on pollutant concentration in street canyons.

PubMed

Buccolieri, Riccardo; Gromke, Christof; Di Sabatino, Silvana; Ruck, Bodo

2009-09-15

This paper deals with aerodynamic effects of avenue-like tree planting on flow and traffic-originated pollutant dispersion in urban street canyons by means of wind tunnel experiments and numerical simulations. Several parameters affecting pedestrian level concentration are investigated, namely plant morphology, positioning and arrangement. We extend our previous work in this novel aspect of research to new configurations which comprise tree planting of different crown porosity and stand density, planted in two rows within a canyon of street width to building height ratio W/H=2 with perpendicular approaching wind. Sulfur hexafluoride was used as tracer gas to model the traffic emissions. Complementary to wind tunnel experiments, 3D numerical simulations were performed with the Computational Fluid Dynamics (CFD) code FLUENT using a Reynolds Stress turbulence closure for flow and the advection-diffusion method for concentration calculations. In the presence of trees, both measurements and simulations showed considerable larger pollutant concentrations near the leeward wall and slightly lower concentrations near the windward wall in comparison with the tree-less case. Tree stand density and crown porosity were found to be of minor importance in affecting pollutant concentration. On the other hand, the analysis indicated that W/H is a more crucial parameter. The larger the value of W/H the smaller is the effect of trees on pedestrian level concentration regardless of tree morphology and arrangement. A preliminary analysis of approaching flow velocities showed that at low wind speed the effect of trees on concentrations is worst than at higher speed. The investigations carried out in this work allowed us to set up an appropriate CFD modelling methodology for the study of the aerodynamic effects of tree planting in street canyons. The results obtained can be used by city planners for the design of tree planting in the urban environment with regard to air quality issues.

A novel dendrochronological approach reveals drivers of carbon sequestration in tree species of riparian forests across spatiotemporal scales.

PubMed

Rieger, Isaak; Kowarik, Ingo; Cherubini, Paolo; Cierjacks, Arne

2017-01-01

Aboveground carbon (C) sequestration in trees is important in global C dynamics, but reliable techniques for its modeling in highly productive and heterogeneous ecosystems are limited. We applied an extended dendrochronological approach to disentangle the functioning of drivers from the atmosphere (temperature, precipitation), the lithosphere (sedimentation rate), the hydrosphere (groundwater table, river water level fluctuation), the biosphere (tree characteristics), and the anthroposphere (dike construction). Carbon sequestration in aboveground biomass of riparian Quercus robur L. and Fraxinus excelsior L. was modeled (1) over time using boosted regression tree analysis (BRT) on cross-datable trees characterized by equal annual growth ring patterns and (2) across space using a subsequent classification and regression tree analysis (CART) on cross-datable and not cross-datable trees. While C sequestration of cross-datable Q. robur responded to precipitation and temperature, cross-datable F. excelsior also responded to a low Danube river water level. However, CART revealed that C sequestration over time is governed by tree height and parameters that vary over space (magnitude of fluctuation in the groundwater table, vertical distance to mean river water level, and longitudinal distance to upstream end of the study area). Thus, a uniform response to climatic drivers of aboveground C sequestration in Q. robur was only detectable in trees of an intermediate height class and in taller trees (>21.8m) on sites where the groundwater table fluctuated little (≤0.9m). The detection of climatic drivers and the river water level in F. excelsior depended on sites at lower altitudes above the mean river water level (≤2.7m) and along a less dynamic downstream section of the study area. Our approach indicates unexploited opportunities of understanding the interplay of different environmental drivers in aboveground C sequestration. Results may support species-specific and locally adapted forest management plans to increase carbon dioxide sequestration from the atmosphere in trees. Copyright © 2016 Elsevier B.V. All rights reserved.

Revealing critical mechanisms of BR-mediated apple nursery tree growth using iTRAQ-based proteomic analysis.

PubMed

Zheng, Liwei; Ma, Juanjuan; Zhang, Lizhi; Gao, Cai; Zhang, Dong; Zhao, Caiping; Han, Mingyu

2018-02-20

Brassinosteroid is identified as an important hormone. However, information about brassinosteroid has not been fully elucidated, and few studies concerned its role in apple. The aim of this work was to study the role of brassinosteroid for apple tree growth. In our study, the effect of brassinosteroid on apple nursery tree was analyzed. The biomass, cell size and xylem content of apple nursery tree were obviously evaluated by brassinosteroid treatment; mineral elements contents, photosynthesis indexes, carbohydrate level and hormone contents were significantly high in brassinosteroid treated trees. To explore the molecular mechanisms of these phenotypic differences, iTRAQ-based quantitative proteomics were used to identify the expression profiles of proteins in apple nursery tree shoot tips in response to brassinosteroid at a key period (14days after brassinosteroid treatment). A total of 175 differentially expressed proteins were identified. They were mainly involved in chlorophyII biosynthesis, photosynthesis, carbohydrate metabolism, glycolysis, citric acid cycle, respiratory action, hormone signal, cell growth and ligin metabolism. The findings in this study indicate that brassinosteroid mediating apple nursery tree growth may be mainly through energy metabolism. Important biological processes identified here can be useful theoretical basis and provide new insights into the molecular mechanisms of brassinosteroid. Brassinosteroid is very important for plant growth and development. However, the molecular mechanism of brassinosteroid mediating growth process is not perfectly clear in plant, especially in apple nursery tree. We used a combination of physiological and bioinformatics analysis to investigate the effects of brassinosteroid on apple nursery tree growth and development. The data reported here demonstrated that brassinosteroid regulates apple nursery tree growth mainly through energy metabolism. Therefore it can provide a theoretical basis from energy points for developing dwarfed or compact apple trees. This will benefit for low orchard management cost as well as early bearing, and high fruit yield as well as quality. Copyright © 2017 Elsevier B.V. All rights reserved.

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

Probabilistic Risk Assessment of Hydraulic Fracturing in Unconventional Reservoirs by Means of Fault Tree Analysis: An Initial Discussion

NASA Astrophysics Data System (ADS)

Rodak, C. M.; McHugh, R.; Wei, X.

2016-12-01

The development and combination of horizontal drilling and hydraulic fracturing has unlocked unconventional hydrocarbon reserves around the globe. These advances have triggered a number of concerns regarding aquifer contamination and over-exploitation, leading to scientific studies investigating potential risks posed by directional hydraulic fracturing activities. These studies, balanced with potential economic benefits of energy production, are a crucial source of information for communities considering the development of unconventional reservoirs. However, probabilistic quantification of the overall risk posed by hydraulic fracturing at the system level are rare. Here we present the concept of fault tree analysis to determine the overall probability of groundwater contamination or over-exploitation, broadly referred to as the probability of failure. The potential utility of fault tree analysis for the quantification and communication of risks is approached with a general application. However, the fault tree design is robust and can handle various combinations of regional-specific data pertaining to relevant spatial scales, geological conditions, and industry practices where available. All available data are grouped into quantity and quality-based impacts and sub-divided based on the stage of the hydraulic fracturing process in which the data is relevant as described by the USEPA. Each stage is broken down into the unique basic events required for failure; for example, to quantify the risk of an on-site spill we must consider the likelihood, magnitude, composition, and subsurface transport of the spill. The structure of the fault tree described above can be used to render a highly complex system of variables into a straightforward equation for risk calculation based on Boolean logic. This project shows the utility of fault tree analysis for the visual communication of the potential risks of hydraulic fracturing activities on groundwater resources.

Slope Stability Analysis of Mountain Pine Beetle Impacted Areas

NASA Astrophysics Data System (ADS)

Bogenschuetz, N. M.; Bearup, L. A.; Maxwell, R. M.; Santi, P. M.

2015-12-01

The mountain pine beetle (MPB), Dendroctonus ponderosae, has caused significant tree mortality within North America. Specifically, the MPB affects ponderosa pine and lodgepole pine forests within the Rocky Mountains with approximately 3.4 million acres of forest impacted over the past 20 years. The full impacts of such unprecedented tree mortality on hydrology and slope stability is not well understood. This work studies the affects of MPB infestation on slope instability. A large-scale statistical analysis of MPB and slope stability is combined with a more in-depth analysis of the factors that contribute to slope stability. These factors include: slope aspect, slope angle, root decay, regrowth and hydrologic properties, such as water table depth and soil moisture. Preliminary results show that MPB may affect a greater number of north- and east-facing slopes. This is in accordance with more water availability and a higher MPB impacted tree density on north-facing slopes which, in turn, could potentially increase the probability of slope failure. Root strength is predicted to decrease as the roots stop transpiring 3-4 years proceeding infestation. However, this effect on the hillslope is likely being counterbalanced by the regrowth of grasses, forbs, shrubs, and trees. In addition, the increase in water table height from the lack of transpiring trees is adding a driving force to the slopes. The combination of all these factors will be used in order to assess the effects of MPB tree mortality on slope stability.

Arctic tree rings as recorders of variations in light availability

PubMed Central

Stine, A. R.; Huybers, P.

2014-01-01

Annual growth ring variations in Arctic trees are often used to reconstruct surface temperature. In general, however, the growth of Arctic vegetation is limited both by temperature and light availability, suggesting that variations in atmospheric transmissivity may also influence tree-ring characteristics. Here we show that Arctic tree-ring density is sensitive to changes in light availability across two distinct phenomena: explosive volcanic eruptions (P<0.01) and the recent epoch of global dimming (P<0.01). In each case, the greatest response is found in the most light-limited regions of the Arctic. Essentially no late 20th century decline in tree-ring density relative to temperature is seen in the least light-limited regions of the Arctic. Consistent results follow from analysis of tree-ring width and from individually analysing each of seven tree species. Light availability thus appears an important control, opening the possibility for using tree rings to reconstruct historical changes in surface light intensity. PMID:24805143

Climate change accelerates growth of urban trees in metropolises worldwide.

PubMed

Pretzsch, Hans; Biber, Peter; Uhl, Enno; Dahlhausen, Jens; Schütze, Gerhard; Perkins, Diana; Rötzer, Thomas; Caldentey, Juan; Koike, Takayoshi; Con, Tran van; Chavanne, Aurélia; Toit, Ben du; Foster, Keith; Lefer, Barry

2017-11-13

Despite the importance of urban trees, their growth reaction to climate change and to the urban heat island effect has not yet been investigated with an international scope. While we are well informed about forest growth under recent conditions, it is unclear if this knowledge can be simply transferred to urban environments. Based on tree ring analyses in ten metropolises worldwide, we show that, in general, urban trees have undergone accelerated growth since the 1960s. In addition, urban trees tend to grow more quickly than their counterparts in the rural surroundings. However, our analysis shows that climate change seems to enhance the growth of rural trees more than that of urban trees. The benefits of growing in an urban environment seem to outweigh known negative effects, however, accelerated growth may also mean more rapid ageing and shortened lifetime. Thus, city planners should adapt to the changed dynamics in order to secure the ecosystem services provided by urban trees.

Geospatial Technologies and i-Tree Echo Inventory for Predicting Climate Change on Urban Environment

NASA Astrophysics Data System (ADS)

Sriharan, S.; Robinson, L.; Ghariban, N.; Comar, M.; Pope, B.; Frey, G.

2015-12-01

Urban forests can be useful both in mitigating climate change and in helping cities adapt to higher temperatures and other impacts of climate change. Understanding and managing the impacts of climate change on the urban forest trees and natural communities will help us maintain their environmental, cultural, and economic benefits. Tree Inventory can provide important information on tree species, height, crown width, overall condition, health and maintenance needs. This presentation will demonstrate that a trees database system is necessary for developing a sustainable urban tree program. Virginia State University (VSU) campus benefits from large number and diversity of trees that are helping us by cleaning the air, retaining water, and providing shade on the buildings to reduce energy cost. The objectives of this study were to develop campus inventory of the trees, identify the tree species, map the locations of the trees with user-friendly tools such as i-Tree Eco and geospatial technologies by assessing the cost/benefit of employing student labor for training and ground validation of the results, and help campus landscape managers implement adaptive responses to climate change impacts. Data was collected on the location, species, and size of trees by using i-Tree urban forestry analysis software. This data was transferred to i-Tree inventory system for demonstrating types of trees, diameter of the trees, height of the trees, and vintage of the trees. The study site was mapped by collecting waypoints with GPS (Global Positioning System) at the trees and uploading these waypoints in ArcMap. The results of this study showed that: (i) students make good field crews, (ii) if more trees were placed in the proper area, the heating and cooling costs will reduce, and (iii) trees database system is necessary for planning, designing, planting, and maintenance, and removal of campus trees Research sponsored by the NIFA Grant, "Urban Forestry Management" (2012-38821-20153).

Population structure and fruit production of Pyrus bourgaeana D. are affected by land-use

NASA Astrophysics Data System (ADS)

Arenas-Castro, Salvador; Fernández-Haeger, Juan; Jordano-Barbudo, Diego

2016-11-01

The Iberian wild pear (Pyrus bourgaeana D.) is a rare, fleshy-fruited tree restricted to dehesas and evergreen sclerophyllous Mediterranean forests in the southwestern Iberian Peninsula. It produces palatable fruits and leaves attractive to different species groups, playing an important trophic role in the ecological networks of Mediterranean ecosystems. However, the intensification in the traditional land-use linked to these areas could threaten the stability of the wild pear populations in the short/medium-term. In order to determine the population dynamics of this relevant species in relation to the land-use history, we selected two populations (southern Spain) subjected to different land-use management, dehesa (D) and abandoned olive grove (AOG). An analysis of 122 adult trees reported an overall density of 0.6 trees ha-1. The tree age was estimated by tree-rings analysis in all adult trees. Dendrometric parameters, reproductive features, and germination rates were also measured. Regeneration was clearly biased, as evidenced by the truncated age structure. A low correlation (R2 = 34%) between age and DBH (diameter at breast height) (244 cores analysed) showed that diameter seems not to be a reliable predictor of tree age. Trees from AOG populations had significantly-higher values of DBH, height and crown diameter, but were less productive in terms of fruits and seeds. Nested analysis of variance showed significant variation in fruit production, fruit size, dry mass, water content and seed viability. There were also significant differences in masting. No evidence was found to demonstrate that fruit production, seed viability, or germination rate influence the low natural recruitment of this species. These findings indicate that the traditional agrosilvopastoral practices carried out in the study area for decades, and its subsequent intensification, have strongly influenced the ecological structure of the Iberian wild pear populations at the local scale, which could compromise its stability in the near future.

How different are the results acquired from mathematical and subjective methods in dendrogeomorphology? Insights from landslide movements

NASA Astrophysics Data System (ADS)

Šilhán, Karel

2016-01-01

Knowledge of past landslide activity is crucial for understanding landslide behaviour and for modelling potential future landslide occurrence. Dendrogeomorphic approaches represent the most precise methods of landslide dating (where trees annually create tree-rings in the timescale of up to several hundred years). Despite the advantages of these methods, many open questions remain. One of the less researched uncertainties, and the focus of this study, is the impact of two common methods of geomorphic signal extraction on the spatial and temporal results of landslide reconstruction. In total, 93 Norway spruce (Picea abies (L.) Karst.) trees were sampled at one landslide location dominated by block-type movements in the forefield of the Orlické hory Mts., Bohemian Massif. Landslide signals were examined by the classical subjective method based on reaction (compression) wood analysis and by a numerical method based on eccentric growth analysis. The chronology of landslide movements obtained by the mathematical method resulted in twice the number of events detected compared to the subjective method. This finding indicates that eccentric growth is a more accurate indicator for landslide movements than the classical analysis of reaction wood. The reconstructed spatial activity of landslide movements shows a similar distribution of recurrence intervals (Ri) for both methods. The differences (maximally 30% of the total Ri ranges) in results obtained by both methods may be caused by differences in the ability of trees to react to tilting of their stems by a specific growth response (reaction wood formation or eccentric growth). Finally, the ability of trees to record tilting events (by both growth responses) in their tree-ring series was analysed for different decades of tree life. The highest sensitivity to external tilting events occurred at tree ages from 70 to 80 years for reaction wood formation and from 80 to 90 years for eccentric growth response. This means that the ability of P. abies to record geomorphic signals varies with not only eccentric growth responses but also with age.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

PubMed Central

Minh, Bui Quang; von Haeseler, Arndt

2015-01-01

Abstract In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original “full” terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference. PMID:26448206

Introduction to IND and recursive partitioning, version 1.0

NASA Technical Reports Server (NTRS)

Buntine, Wray; Caruana, Rich

1991-01-01

This manual describes the IND package for learning tree classifiers from data. The package is an integrated C and C shell re-implementation of tree learning routines such as CART, C4, and various MDL and Bayesian variations. The package includes routines for experiment control, interactive operation, and analysis of tree building. The manual introduces the system and its many options, gives a basic review of tree learning, contains a guide to the literature and a glossary, lists the manual pages for the routines, and instructions on installation.

Crown-level tree species classification from AISA hyperspectral imagery using an innovative pixel-weighting approach

NASA Astrophysics Data System (ADS)

Liu, Haijian; Wu, Changshan

2018-06-01

Crown-level tree species classification is a challenging task due to the spectral similarity among different tree species. Shadow, underlying objects, and other materials within a crown may decrease the purity of extracted crown spectra and further reduce classification accuracy. To address this problem, an innovative pixel-weighting approach was developed for tree species classification at the crown level. The method utilized high density discrete LiDAR data for individual tree delineation and Airborne Imaging Spectrometer for Applications (AISA) hyperspectral imagery for pure crown-scale spectra extraction. Specifically, three steps were included: 1) individual tree identification using LiDAR data, 2) pixel-weighted representative crown spectra calculation using hyperspectral imagery, with which pixel-based illuminated-leaf fractions estimated using a linear spectral mixture analysis (LSMA) were employed as weighted factors, and 3) representative spectra based tree species classification was performed through applying a support vector machine (SVM) approach. Analysis of results suggests that the developed pixel-weighting approach (OA = 82.12%, Kc = 0.74) performed better than treetop-based (OA = 70.86%, Kc = 0.58) and pixel-majority methods (OA = 72.26, Kc = 0.62) in terms of classification accuracy. McNemar tests indicated the differences in accuracy between pixel-weighting and treetop-based approaches as well as that between pixel-weighting and pixel-majority approaches were statistically significant.

A novel approach to internal crown characterization for coniferous tree species classification

NASA Astrophysics Data System (ADS)

Harikumar, A.; Bovolo, F.; Bruzzone, L.

2016-10-01

The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Biochemical analysis of 'kerosene tree' Hymenaea courbaril L. under heat stress.

PubMed

Gupta, Dinesh; Eldakak, Moustafa; Rohila, Jai S; Basu, Chhandak

2014-01-01

Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, β ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.

Complexity of major UK companies between 2006 and 2010: Hierarchical structure method approach

NASA Astrophysics Data System (ADS)

Ulusoy, Tolga; Keskin, Mustafa; Shirvani, Ayoub; Deviren, Bayram; Kantar, Ersin; Çaǧrı Dönmez, Cem

2012-11-01

This study reports on topology of the top 40 UK companies that have been analysed for predictive verification of markets for the period 2006-2010, applying the concept of minimal spanning tree and hierarchical tree (HT) analysis. Construction of the minimal spanning tree (MST) and the hierarchical tree (HT) is confined to a brief description of the methodology and a definition of the correlation function between a pair of companies based on the London Stock Exchange (LSE) index in order to quantify synchronization between the companies. A derivation of hierarchical organization and the construction of minimal-spanning and hierarchical trees for the 2006-2008 and 2008-2010 periods have been used and the results validate the predictive verification of applied semantics. The trees are known as useful tools to perceive and detect the global structure, taxonomy and hierarchy in financial data. From these trees, two different clusters of companies in 2006 were detected. They also show three clusters in 2008 and two between 2008 and 2010, according to their proximity. The clusters match each other as regards their common production activities or their strong interrelationship. The key companies are generally given by major economic activities as expected. This work gives a comparative approach between MST and HT methods from statistical physics and information theory with analysis of financial markets that may give new valuable and useful information of the financial market dynamics.

Chi-squared Automatic Interaction Detection Decision Tree Analysis of Risk Factors for Infant Anemia in Beijing, China

PubMed Central

Ye, Fang; Chen, Zhi-Hua; Chen, Jie; Liu, Fang; Zhang, Yong; Fan, Qin-Ying; Wang, Lin

2016-01-01

Background: In the past decades, studies on infant anemia have mainly focused on rural areas of China. With the increasing heterogeneity of population in recent years, available information on infant anemia is inconclusive in large cities of China, especially with comparison between native residents and floating population. This population-based cross-sectional study was implemented to determine the anemic status of infants as well as the risk factors in a representative downtown area of Beijing. Methods: As useful methods to build a predictive model, Chi-squared automatic interaction detection (CHAID) decision tree analysis and logistic regression analysis were introduced to explore risk factors of infant anemia. A total of 1091 infants aged 6–12 months together with their parents/caregivers living at Heping Avenue Subdistrict of Beijing were surveyed from January 1, 2013 to December 31, 2014. Results: The prevalence of anemia was 12.60% with a range of 3.47%–40.00% in different subgroup characteristics. The CHAID decision tree model has demonstrated multilevel interaction among risk factors through stepwise pathways to detect anemia. Besides the three predictors identified by logistic regression model including maternal anemia during pregnancy, exclusive breastfeeding in the first 6 months, and floating population, CHAID decision tree analysis also identified the fourth risk factor, the maternal educational level, with higher overall classification accuracy and larger area below the receiver operating characteristic curve. Conclusions: The infant anemic status in metropolis is complex and should be carefully considered by the basic health care practitioners. CHAID decision tree analysis has demonstrated a better performance in hierarchical analysis of population with great heterogeneity. Risk factors identified by this study might be meaningful in the early detection and prompt treatment of infant anemia in large cities. PMID:27174328

Chi-squared Automatic Interaction Detection Decision Tree Analysis of Risk Factors for Infant Anemia in Beijing, China.

PubMed

Ye, Fang; Chen, Zhi-Hua; Chen, Jie; Liu, Fang; Zhang, Yong; Fan, Qin-Ying; Wang, Lin

2016-05-20

In the past decades, studies on infant anemia have mainly focused on rural areas of China. With the increasing heterogeneity of population in recent years, available information on infant anemia is inconclusive in large cities of China, especially with comparison between native residents and floating population. This population-based cross-sectional study was implemented to determine the anemic status of infants as well as the risk factors in a representative downtown area of Beijing. As useful methods to build a predictive model, Chi-squared automatic interaction detection (CHAID) decision tree analysis and logistic regression analysis were introduced to explore risk factors of infant anemia. A total of 1091 infants aged 6-12 months together with their parents/caregivers living at Heping Avenue Subdistrict of Beijing were surveyed from January 1, 2013 to December 31, 2014. The prevalence of anemia was 12.60% with a range of 3.47%-40.00% in different subgroup characteristics. The CHAID decision tree model has demonstrated multilevel interaction among risk factors through stepwise pathways to detect anemia. Besides the three predictors identified by logistic regression model including maternal anemia during pregnancy, exclusive breastfeeding in the first 6 months, and floating population, CHAID decision tree analysis also identified the fourth risk factor, the maternal educational level, with higher overall classification accuracy and larger area below the receiver operating characteristic curve. The infant anemic status in metropolis is complex and should be carefully considered by the basic health care practitioners. CHAID decision tree analysis has demonstrated a better performance in hierarchical analysis of population with great heterogeneity. Risk factors identified by this study might be meaningful in the early detection and prompt treatment of infant anemia in large cities.

Pneumomédiastin compliquant une crise d’éclampsie: à propos d'un cas

PubMed Central

Doumiri, Mouhssine; Motiaa, Youssef; Oudghiri, Nezha; Saoud, Anas Tazi

2014-01-01

Le pneumomédiastin associé à l'emphysème sous cutané et le pneumothorax, sont des complications rares de la grossesse et surviennent au cours du travail obstétrical. Nous rapportons l'observation d'une parturiente de 25ans, sans antécédent pathologique particulier, admise pour une crise d’éclampsie à 36 semaines d'aménorrhées avec une mort fœtale et trouble de la conscience. L'examen clinique a montré un emphysème sous cutané étendu du visage jusqu’à l'abdomen sans notion de traumatisme et un score de Glasgow à 10. Après mise en condition, traitement de la crise d’éclampsie, stabilisation de la tension artérielle et retour à l’état de conscience, une TDM cervico-thoraco-abdominale a été demandée et a révélé la présence d'un pneumomédiastin important avec un discret pneumothorax droit postérieur et un pneumopéritoine important qui n'ont pas nécessité de drainage pleural. Deux jours après son admission, la patiente a expulsé un mort-né d'un poids de 1800 grammes avec forceps et sans efforts d'expulsions sous analgésie péridurale. Le contrôle radiologique à une semaine a noté une nette diminution de l'emphysème sous cutané et du pneumomédiastin. La patiente a quitté l'hôpital après dix jours. PMID:25838864

A molecular phylogeny of the Canidae based on six nuclear loci.

PubMed

Bardeleben, Carolyne; Moore, Rachael L; Wayne, Robert K

2005-12-01

We have reconstructed the phylogenetic relationships of 23 species in the dog family, Canidae, using DNA sequence data from six nuclear loci. Individual gene trees were generated with maximum parsimony (MP) and maximum likelihood (ML) analysis. In general, these individual gene trees were not well resolved, but several identical groupings were supported by more than one locus. Phylogenetic analysis with a data set combining the six nuclear loci using MP, ML, and Bayesian approaches produced a more resolved tree that agreed with previously published mitochondrial trees in finding three well-defined clades, including the red fox-like canids, the South American foxes, and the wolf-like canids. In addition, the nuclear data set provides novel indel support for several previously inferred clades. Differences between trees derived from the nuclear data and those from the mitochondrial data include the grouping of the bush dog and maned wolf into a clade with the South American foxes, the grouping of the side-striped jackal (Canis adustus) and black-backed jackal (Canis mesomelas) and the grouping of the bat-eared fox (Otocyon megalotis) with the raccoon dog (Nycteruetes procyonoides). We also analyzed the combined nuclear+mitochondrial tree. Many nodes that were strongly supported in the nuclear tree or the mitochondrial tree remained strongly supported in the nuclear+mitochondrial tree. Relationships within the clades containing the red fox-like canids and South American canids are well resolved, whereas the relationships among the wolf-like canids remain largely undetermined. The lack of resolution within the wolf-like canids may be due to their recent divergence and insufficient time for the accumulation of phylogenetically informative signal.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

PubMed Central

Chesters, Douglas

2017-01-01

Abstract Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. PMID:27798407

The structure of western warbler assemblages: Analysis of foraging behavior and habitat selection in Oregon

USGS Publications Warehouse

Morrison, Michael L.

1981-01-01

This study examines the foraging behavior and habitat selection of a MacGillivray's (Oporornis tolmiei)-Orange-crowned (Vermivora celata)-Wilson's (Wilsonia pusilla) warbler assemblage that occurred on early-growth clearcuts in western Oregon during breeding. Sites were divided into two groups based on the presence or absence of deciduous trees. Density estimates for each species were nearly identical between site classes except for Wilson's, whose density declined on nondeciduous tree sites. Analysis of vegetation parameters within the territories of the species identified deciduous tree cover as the variable of primary importance in the separation of warblers on each site, so that the assemblage could be arranged on a continuum of increasing deciduous tree cover. MacGillivray's and Wilson's extensively used shrub cover and deciduous tree cover, respectively; Orange-crowns were associated with both vegetation types. When the deciduous tree cover was reduced, Orange-crowns concentrated foraging activities in shrub cover and maintained nondisturbance densities. Indices of foraging-height diversity showed a marked decrease after the removal of deciduous trees. All species except MacGillivray's foraged lower in the vegatative substrate on the nondeciduous tree sites; MacGillivray's concentrated foraging activities in the low shrub cover on both sites. Indices of foraging overlap revealed a general pattern of decreased segregation by habitat after removal of deciduous trees. I suggest that the basic patterns of foraging behavior and habitat selection evidenced today in western North America were initially developed by ancestral warblers before their invasion of the west. Species successfully colonizing western habitats were probably preadapted to the conditions they encountered, with new habitats occupied without obvious evolutionary modifications.

Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri).

PubMed

Zheng, Yu; Yun, Chenxia; Wang, Qihui; Smith, Wanli W; Leng, Jing

2015-02-01

The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

Electrical treeing behaviors in silicone rubber under an impulse voltage considering high temperature

NASA Astrophysics Data System (ADS)

Yunxiao, ZHANG; Yuanxiang, ZHOU; Ling, ZHANG; Zhen, LIN; Jie, LIU; Zhongliu, ZHOU

2018-05-01

In this paper, work was conducted to reveal electrical tree behaviors (initiation and propagation) of silicone rubber (SIR) under an impulse voltage with high temperature. Impulse frequencies ranging from 10 Hz to 1 kHz were applied and the temperature was controlled between 30 °C and 90 °C. Experimental results show that tree initiation voltage decreases with increasing pulse frequency, and the descending amplitude is different in different frequency bands. As the pulse frequency increases, more frequent partial discharges occur in the channel, increasing the tree growth rate and the final shape intensity. As for temperature, the initiation voltage decreases and the tree shape becomes denser as the temperature gets higher. Based on differential scanning calorimetry results, we believe that partial segment relaxation of SIR at high temperature leads to a decrease in the initiation voltage. However, the tree growth rate decreases with increasing temperature. Carbonization deposition in the channel under high temperature was observed under microscope and proven by Raman analysis. Different tree growth models considering tree channel characteristics are proposed. It is believed that increasing the conductivity in the tree channel restrains the partial discharge, holding back the tree growth at high temperature.

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

Investigation into calculating tree biomass and carbon in the FIADB using a biomass expansion factor approach

Treesearch

Linda S. Heath; Mark Hansen; James E. Smith; Patrick D. Miles

2009-01-01

The official U.S. forest carbon inventories (U.S. EPA 2008) have relied on tree biomass estimates that utilize diameter based prediction equations from Jenkins and others (2003), coupled with U.S. Forest Service, Forest Inventory and Analysis (FIA) sample tree measurements and forest area estimates. However, these biomass prediction equations are not the equations used...

Genome-wide analysis of oleosin gene family in 22 tree species: An accelerator for metabolic engineering of biofuel crops and agrigenomics industrial applications?

USDA-ARS?s Scientific Manuscript database

Triacylglycerols (TAGs) are the major molecules of energy storage in eukaryotes. Trees contribute to part of enormous plant oil reserves because fruits and kernels of many trees contain up to 50-80% of oil. TAGs accumulate in oil bodies in plants, similar to oil droplets in animals. Oleosins (OLEs) ...

An empirical, hierarchical typology of tree species assemblages for assessing forest dynamics under global change scenarios

Treesearch

Jennifer K. Costanza; John W. Coulston; David N. Wear

2017-01-01

The composition of tree species occurring in a forest is important and can be affected by global change drivers such as climate change. To inform assessment and projection of global change impacts at broad extents, we used hierarchical cluster analysis and over 120,000 recent forest inventory plots to empirically define forest tree assemblages across the U.S., and...

New machine learning tools for predictive vegetation mapping after climate change: Bagging and Random Forest perform better than Regression Tree Analysis

Treesearch

L.R. Iverson; A.M. Prasad; A. Liaw

2004-01-01

More and better machine learning tools are becoming available for landscape ecologists to aid in understanding species-environment relationships and to map probable species occurrence now and potentially into the future. To thal end, we evaluated three statistical models: Regression Tree Analybib (RTA), Bagging Trees (BT) and Random Forest (RF) for their utility in...

Equations for predicting biomass in 2- to 6-year-old Eucalyptus saligna in Hawaii

Treesearch

Craig D. Whitesell; Susan C. Miyasaka; Robert F. Strand; Thomas H. Schubert; Katharine E. McDuffie

1988-01-01

Eucalyptus saligna trees grown in short-rotation plantations on the island of Hawaii were measured, harvested, and weighed to provide data for developing regression equations using non-destructive stand measurements. Regression analysis of the data from 190 trees in the 2.0- to 3.5-year range and 96 trees in the 4- to 6-year range related stem-only...

Using inventory data to determine the impact of drought on tree mortality

Treesearch

Greg C. Liknes; Christopher W. Woodall; Charles H. Perry

2012-01-01

Drought has been the subject of numerous recent studies that hint at an acceleration of tree mortality due to climate change. In particular, a recent global survey of tree mortality events implicates drought as the cause of quaking aspen mortality in Minnesota, USA in 2007. In this study, data from the Forest Inventory and Analysis program of the USDA Forest Service...

Estimating probabilities of infestation and extent of damage by the roundheaded pine beetle in ponderosa pine in the Sacramento Mountains, New Mexico

Treesearch

Jose Negron

1997-01-01

Classification trees and linear regression analysis were used to build models to predict probabilities of infestation and amount of tree mortality in terms of basal area resulting from roundheaded pine beetle, Dendroctonus adjunctus Blandford, activity in ponderosa pine, Pinus ponderosa Laws., in the Sacramento Mountains, New Mexico. Classification trees were built for...

Probability of Damage to Sidewalks and Curbs by Street Trees in the Tropics

Treesearch

John K. Francis; Bernard R. Parresol; Juana Marin de Patino

1996-01-01

For 75 trees each of 12 species growing along streets in San Juan, Puerto Rico and Merida, Mexico, diameter at breast height and distance to sidewalk or curb was measured and damage (cracking or raising) was evaluated. Logistic analysis was used to construct a model to predict probability of damage to sidewalk or curb. Distance to the pavement, diameter of the tree,...

An Extension of CART's Pruning Algorithm. Program Statistics Research Technical Report No. 91-11.

ERIC Educational Resources Information Center

Kim, Sung-Ho

Among the computer-based methods used for the construction of trees such as AID, THAID, CART, and FACT, the only one that uses an algorithm that first grows a tree and then prunes the tree is CART. The pruning component of CART is analogous in spirit to the backward elimination approach in regression analysis. This idea provides a tool in…

New Approaches to FIA data for understanding distribution, abundance, and response to climate change

Treesearch

Kai Zhu; Souparno Ghosh; Alan E. Gelfand; James S. Clark

2012-01-01

We are using Forest Inventory and Analysis data to examine evidence for tree responses to climate change. By comparing seedling and tree occurrence data, we found that there is not yet evidence that tree populations in the eastern half of the United States are shifting geographic ranges to higher latitude in response to warming temperature. We are developing novel...

A GIS-based tool for estimating tree canopy cover on fixed-radius plots using high-resolution aerial imagery

Treesearch

Sara A. Goeking; Greg C. Liknes; Erik Lindblom; John Chase; Dennis M. Jacobs; Robert. Benton

2012-01-01

Recent changes to the Forest Inventory and Analysis (FIA) Program's definition of forest land precipitated the development of a geographic information system (GIS)-based tool for efficiently estimating tree canopy cover for all FIA plots. The FIA definition of forest land has shifted from a density-related criterion based on stocking to a 10 percent tree canopy...

Monitoring nontimber forest products using forest inventory data: an example with slippery elm bark

Treesearch

Jobriath S. Kauffman; Stephen P. Prisley; James L. Chamberlain

2015-01-01

The USDA Forest Service Forest Inventory and Analysi (FIA) program collects data on a wealth of variables related to trees in forests. Some of these trees produce nontimber forest products (NTFPs) (e.g., fruit, bark and sap) that are harvested for culinary, decorative, building, and medicinal purposes. At least 11 tree species inventoried by FIA are valued for their...

Assessing urban forest effects and values, Scranton's urban forest

Treesearch

David J. Nowak; Robert E. III Hoehn; Daniel E. Crane; Jack C. Stevens; Vincent Cotrone

2010-01-01

An analysis of trees in the urbanized portion of Scranton, PA, reveals that this area has about 1.2 million trees with canopies that cover 22.0 percent of the area. The most common tree species are red maple, gray birch, black cherry, northern red oak, and quaking aspen. Scranton's urban forest currently store about 93,300 tons of carbon valued at $1.9 million. In...

City of Cheyenne, Wyoming Municipal Tree Resource Analysis

Treesearch

P.J. Peper; Greg McPherson; J.R. Simpson; S.E. Maco; Q. Xiao

2004-01-01

Street trees in Cheyenne are comprised of two distinct populations, those managed by the city’s Urban Forestry Division (UFD) and those inspected by the UFD but managed by private property owners. Over the years Cheyenne has invested millions in its municipal forest. The primary question that this study asks is whether the accrued benefits from Cheyenne’s street trees...

Impact of ecological and socioeconomic determinants on the spread of tallow tree in southern forest lands

Treesearch

Yuan Tan; Joseph Z. Fan; Christopher M. Oswalt

2010-01-01

Based on USDA Forest Service Forest Inventory and Analysis (FIA) database, relationships between the presence of tallow tree and related driving variables including forest landscape metrics, stand and site conditions, as well as natural and anthropogenic disturbances were analyzed for the southern states infested by tallow trees. Of the 9,966 re-measured FIA plots in...

Is there a better metric than site index to indicate the productivity of forested lands?

Treesearch

Maria E. Blanco Martin; Michael Hoppus; Andrew Lister; James A. Westfall

2009-01-01

The Forest Service, U.S. Department of Agriculture's Forest Inventory and Analysis (FIA) program selects site trees for each plot that are used to measure site productivity. The ability of a site to produce wood volume is indicated indirectly by comparing total tree height with tree age. This comparison assumes that the rate of height growth is strongly related to...

Inventory-based sensitivity analysis of the Large Tree Diameter Growth Submodel of the Southern Variant of the FVS

Treesearch

Giorgio Vacchiano; John D. Shaw; R. Justin DeRose; James N. Long

2008-01-01

Diameter increment is an important variable in modeling tree growth. Most facets of predicted tree development are dependent in part on diameter or diameter increment, the most commonly measured stand variable. The behavior of the Forest Vegetation Simulator (FVS) largely relies on the performance of the diameter increment model and the subsequent use of predicted dbh...

A novel method of fuzzy fault tree analysis combined with VB program to identify and assess the risk of coal dust explosions

PubMed Central

Li, Jia; Wang, Deming; Huang, Zonghou

2017-01-01

Coal dust explosions (CDE) are one of the main threats to the occupational safety of coal miners. Aiming to identify and assess the risk of CDE, this paper proposes a novel method of fuzzy fault tree analysis combined with the Visual Basic (VB) program. In this methodology, various potential causes of the CDE are identified and a CDE fault tree is constructed. To overcome drawbacks from the lack of exact probability data for the basic events, fuzzy set theory is employed and the probability data of each basic event is treated as intuitionistic trapezoidal fuzzy numbers. In addition, a new approach for calculating the weighting of each expert is also introduced in this paper to reduce the error during the expert elicitation process. Specifically, an in-depth quantitative analysis of the fuzzy fault tree, such as the importance measure of the basic events and the cut sets, and the CDE occurrence probability is given to assess the explosion risk and acquire more details of the CDE. The VB program is applied to simplify the analysis process. A case study and analysis is provided to illustrate the effectiveness of this proposed method, and some suggestions are given to take preventive measures in advance and avoid CDE accidents. PMID:28793348

Reliability analysis of airship remote sensing system

NASA Astrophysics Data System (ADS)

Qin, Jun

1998-08-01

Airship Remote Sensing System (ARSS) for obtain the dynamic or real time images in the remote sensing of the catastrophe and the environment, is a mixed complex system. Its sensor platform is a remote control airship. The achievement of a remote sensing mission depends on a series of factors. For this reason, it is very important for us to analyze reliability of ARSS. In first place, the system model was simplified form multi-stage system to two-state system on the basis of the result of the failure mode and effect analysis and the failure tree failure mode effect and criticality analysis. The failure tree was created after analyzing all factors and their interrelations. This failure tree includes four branches, e.g. engine subsystem, remote control subsystem, airship construction subsystem, flying metrology and climate subsystem. By way of failure tree analysis and basic-events classing, the weak links were discovered. The result of test running shown no difference in comparison with theory analysis. In accordance with the above conclusions, a plan of the reliability growth and reliability maintenance were posed. System's reliability are raised from 89 percent to 92 percent with the reformation of the man-machine interactive interface, the augmentation of the secondary better-groupie and the secondary remote control equipment.

A novel method of fuzzy fault tree analysis combined with VB program to identify and assess the risk of coal dust explosions.

PubMed

Wang, Hetang; Li, Jia; Wang, Deming; Huang, Zonghou

2017-01-01

Coal dust explosions (CDE) are one of the main threats to the occupational safety of coal miners. Aiming to identify and assess the risk of CDE, this paper proposes a novel method of fuzzy fault tree analysis combined with the Visual Basic (VB) program. In this methodology, various potential causes of the CDE are identified and a CDE fault tree is constructed. To overcome drawbacks from the lack of exact probability data for the basic events, fuzzy set theory is employed and the probability data of each basic event is treated as intuitionistic trapezoidal fuzzy numbers. In addition, a new approach for calculating the weighting of each expert is also introduced in this paper to reduce the error during the expert elicitation process. Specifically, an in-depth quantitative analysis of the fuzzy fault tree, such as the importance measure of the basic events and the cut sets, and the CDE occurrence probability is given to assess the explosion risk and acquire more details of the CDE. The VB program is applied to simplify the analysis process. A case study and analysis is provided to illustrate the effectiveness of this proposed method, and some suggestions are given to take preventive measures in advance and avoid CDE accidents.

A Hierarchical Analysis of Tree Growth and Environmental Drivers Across Eastern US Temperate Forests

NASA Astrophysics Data System (ADS)

Mantooth, J.; Dietze, M.

2014-12-01

Improving predictions of how forests in the eastern United States will respond to future global change requires a better understanding of the drivers of variability in tree growth rates. Current inventory data lack the temporal resolution to characterize interannual variability, while existing growth records lack the extent required to assess spatial scales of variability. Therefore, we established a network of forest inventory plots across ten sites across the eastern US, and measured growth in adult trees using increment cores. Sites were chosen to maximize climate space explored, while within sites, plots were spread across primary environmental gradients to explore landscape-level variability in growth. Using the annual growth record available from tree cores, we explored the responses of trees to multiple environmental covariates over multiple spatial and temporal scales. We hypothesized that within and across sites growth rates vary among species, and that intraspecific growth rates increase with temperature along a species' range. We also hypothesized that trees show synchrony in growth responses to landscape-scale climatic changes. Initial analyses of growth increments indicate that across sites, trees with intermediate shade tolerance, e.g. Red Oak (Quercus rubra), tend to have the highest growth rates. At the site level, there is evidence for synchrony in response to large-scale climatic events (e.g. prolonged drought and above average temperatures). However, growth responses to climate at the landscape scale have yet to be detected. Our current analysis utilizes hierarchical Bayesian state-space modeling to focus on growth responses of adult trees to environmental covariates at multiple spatial and temporal scales. This predictive model of tree growth currently incorporates observed effects at the individual, plot, site, and landscape scale. Current analysis using this model shows a potential slowing of growth in the past decade for two sites in the northeastern US (Harvard Forest and Bartlett Experimental Forest), however more work is required to determine the robustness of this trend. Finally, these observations are being incorporated into ecosystem models using the Brown Dog informatics tools and the Predictive Ecosystem Analyzer (PEcAn) data assimilation workflow.

D.B.H. and Survival Analysis: A New Methodology for Assessing Forest Inventory Mortality

Treesearch

Christopher W. Woodall; Patricia L. Grambsch; William Thomas

2005-01-01

Tree mortality has typically been assessed in Forest Inventory and Analysis (FIA) studies through summaries of mortality by location, species, and causal agents. Although these methods have historically been used for most of FIA's tree mortality analyses, they are inadequate for robust assessment of mortality trends and dynamics. To offer a new method of analyzing...

UFORE (i-Tree Eco) Analysis of Chicago

Treesearch

Cherie LeBlanc Fisher; David Nowak

2010-01-01

The USDA Forest Service and City of Chicago conducted a UFORE (now called i-Tree Eco) analysis of Chicago's urban forest in the summer of 2007. The UFORE (Urban FORest Effects) model developed by the Forest Service uses on-the-ground sampling data to understand the composition of on urban forest and calculate the forest's impacts on air pollution and energy...

Method of center localization for objects containing concentric arcs

NASA Astrophysics Data System (ADS)

Kuznetsova, Elena G.; Shvets, Evgeny A.; Nikolaev, Dmitry P.

2015-02-01

This paper proposes a method for automatic center location of objects containing concentric arcs. The method utilizes structure tensor analysis and voting scheme optimized with Fast Hough Transform. Two applications of the proposed method are considered: (i) wheel tracking in video-based system for automatic vehicle classification and (ii) tree growth rings analysis on a tree cross cut image.

Vermont's use-value appraisal property tax program: a forest inventory and analysis

Treesearch

Paul E. Sendak; Donald F. Dennis; Donald F. Dennis

1989-01-01

A statistical report and analysis of the timberland enrolled in the Vermont Use Value Appraisal (UVA) property tax program. The study was conducted using data collected in the fourth forest survey of Vermont (1983). Estimates are presented on land area, timber volumes, tree quality, numbers of live trees, and biomass for timberland enrolled in the UVA program and for...

A stem-map model for predicting tree canopy cover of Forest Inventory and Analysis (FIA) plots

Treesearch

Chris Toney; John D. Shaw; Mark D. Nelson

2009-01-01

Tree canopy cover is an important stand characteristic that affects understory light, fuel moisture, decomposition rates, wind speed, and wildlife habitat. Canopy cover also is a component of most definitions of forest land used by US and international agencies. The USDA Forest Service Forest Inventory and Analysis (FIA) Program currently does not provide a national...

Water-Tree Modelling and Detection for Underground Cables

NASA Astrophysics Data System (ADS)

Chen, Qi

In recent years, aging infrastructure has become a major concern for the power industry. Since its inception in early 20th century, the electrical system has been the cornerstone of an industrial society. Stable and uninterrupted delivery of electrical power is now a base necessity for the modern world. As the times march-on, however, the electrical infrastructure ages and there is the inevitable need to renew and replace the existing system. Unfortunately, due to time and financial constraints, many electrical systems today are forced to operate beyond their original design and power utilities must find ways to prolong the lifespan of older equipment. Thus, the concept of preventative maintenance arises. Preventative maintenance allows old equipment to operate longer and at better efficiency, but in order to implement preventative maintenance, the operators must know minute details of the electrical system, especially some of the harder to assess issues such water-tree. Water-tree induced insulation degradation is a problem typically associated with older cable systems. It is a very high impedance phenomenon and it is difficult to detect using traditional methods such as Tan-Delta or Partial Discharge. The proposed dissertation studies water-tree development in underground cables, potential methods to detect water-tree location and water-tree severity estimation. The dissertation begins by developing mathematical models of water-tree using finite element analysis. The method focuses on surface-originated vented tree, the most prominent type of water-tree fault in the field. Using the standard operation parameters of North American electrical systems, the water-tree boundary conditions are defined. By applying finite element analysis technique, the complex water-tree structure is broken down to homogeneous components. The result is a generalized representation of water-tree capacitance at different stages of development. The result from the finite element analysis is used to model water-tree in large system. Both empirical measurements and the mathematical model show that the impedance of early-stage water-tree is extremely large. As the result, traditional detection methods such Tan-Delta or Partial Discharge are not effective due to the excessively high accuracy requirement. A high-frequency pulse detection method is developed instead. The water-tree impedance is capacitive in nature and it can be reduced to manageable level by high-frequency inputs. The method is able to determine the location of early-stage water-tree in long-distance cables using economically feasible equipment. A pattern recognition method is developed to estimate the severity of water-tree using its pulse response from the high-frequency test method. The early-warning system for water-tree appearance is a tool developed to assist the practical implementation of the high-frequency pulse detection method. Although the equipment used by the detection method is economically feasible, it is still a specialized test and not designed for constant monitoring of the system. The test also place heavy stress on the cable and it is most effective when the cable is taken offline. As the result, utilities need a method to estimate the likelihood of water-tree presence before subjecting the cable to the specialized test. The early-warning system takes advantage of naturally occurring high-frequency events in the system and uses a deviation-comparison method to estimate the probability of water-tree presence on the cable. If the likelihood is high, then the utility can use the high-frequency pulse detection method to obtain accurate results. Specific pulse response patterns can be used to calculate the capacitance of water-tree. The calculated result, however, is subjected to margins of error due to limitations from the real system. There are both long-term and short-term methods to improve the accuracy. Computation algorithm improvement allows immediate improvement on accuracy of the capacitance estimation. The probability distribution of the calculation solution showed that improvements in waveform time-step measurement allow fundamental improves to the overall result.

On the Number of Non-equivalent Ancestral Configurations for Matching Gene Trees and Species Trees.

PubMed

Disanto, Filippo; Rosenberg, Noah A

2017-09-14

An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation. We examine the largest number of non-equivalent ancestral configurations possible for a given tree size n. Whereas the smallest number of non-equivalent ancestral configurations increases polynomially with n, we show that the largest number increases with [Formula: see text], where k is a constant that satisfies [Formula: see text]. Under a uniform distribution on the set of binary labeled trees with a given size n, the mean number of non-equivalent ancestral configurations grows exponentially with n. The results refine an earlier analysis of the number of ancestral configurations considered without applying the equivalence relation, showing that use of the equivalence relation does not alter the exponential nature of the increase with tree size.

Discriminant forest classification method and system

DOEpatents

Chen, Barry Y.; Hanley, William G.; Lemmond, Tracy D.; Hiller, Lawrence J.; Knapp, David A.; Mugge, Marshall J.

2012-11-06

A hybrid machine learning methodology and system for classification that combines classical random forest (RF) methodology with discriminant analysis (DA) techniques to provide enhanced classification capability. A DA technique which uses feature measurements of an object to predict its class membership, such as linear discriminant analysis (LDA) or Andersen-Bahadur linear discriminant technique (AB), is used to split the data at each node in each of its classification trees to train and grow the trees and the forest. When training is finished, a set of n DA-based decision trees of a discriminant forest is produced for use in predicting the classification of new samples of unknown class.

[Infrared Spectrum Analysis of Propolis and Tree Gum Collected from Different Areas].

PubMed

Luo, Huo-lin; Liu, Xing-xing; Gong, Shang-ji; Guo, Xia-li; Luo, Li-ping

2015-11-01

Propolis possesses functions of antibacterial, antiviral, anticancer, and liver protection, and is known as the "purple gold", however, the phenomenon which making and selling of counterfeit are growing in intensity. In order to establish a authenticity and quality of propolis evaluation model, in this paper, forty-one Chinese propolis, one proplis from United States and two tree gums were used for experimental materials. The infrared spectrum collection was performed by Fourier transform infrared spectrometer, and principal component analysis (PCA) was used for data analysis. The result showed that, the intrared spectrum of propolis and tree gum were significantly different. The propolis characteristic peak only appeared in 2500-3500 and 400-1800 cm⁻¹. All propolis had two frequency region of characteristic peaks, 2849.08-2848.53 and 2917.74- 2916.76 cm⁻¹, but tree gum did not have characteristic peak in this region. The characteristic peaks of gum were in 1150-1300 and 1550-1650 cm⁻¹. Differences in these aspects can be used to distinguish propolis and gum, and can be used to identify true and false propolis. We use Qinghai propolis as a standard sample, in 42 samples, the matching degree of other propolis is > 80%. In addition, the result of PCA shows that tree gum and the propolis from different climate zone, or with different colors could be distinguished well. This paper firstly performed analysis on different propolis and gum by infrared spectrum, and a new method, for authenticity and quality of propolis identification, could be developed.

Applications of Photogrammetry for Analysis of Forest Plantations. Preliminary study: Analysis of individual trees

NASA Astrophysics Data System (ADS)

Mora, R.; Barahona, A.; Aguilar, H.

2015-04-01

This paper presents a method for using high detail volumetric information, captured with a land based photogrammetric survey, to obtain information from individual trees. Applying LIDAR analysis techniques it is possible to measure diameter at breast height, height at first branch (commercial height), basal area and volume of an individual tree. Given this information it is possible to calculate how much of that tree can be exploited as wood. The main objective is to develop a methodology for successfully surveying one individual tree, capturing every side of the stem a using high resolution digital camera and reference marks with GPS coordinates. The process is executed for several individuals of two species present in the metropolitan area in San Jose, Costa Rica, Delonix regia (Bojer) Raf. and Tabebuia rosea (Bertol.) DC., each one with different height, stem shape and crown area. Using a photogrammetry suite all the pictures are aligned, geo-referenced and a dense point cloud is generated with enough detail to perform the required measurements, as well as a solid tridimensional model for volume measurement. This research will open the way to develop a capture methodology with an airborne camera using close range UAVs. An airborne platform will make possible to capture every individual in a forest plantation, furthermore if the analysis techniques applied in this research are automated it will be possible to calculate with high precision the exploit potential of a forest plantation and improve its management.

Time-series analysis of delta13C from tree rings. I. Time trends and autocorrelation.

PubMed

Monserud, R A; Marshall, J D

2001-09-01

Univariate time-series analyses were conducted on stable carbon isotope ratios obtained from tree-ring cellulose. We looked for the presence and structure of autocorrelation. Significant autocorrelation violates the statistical independence assumption and biases hypothesis tests. Its presence would indicate the existence of lagged physiological effects that persist for longer than the current year. We analyzed data from 28 trees (60-85 years old; mean = 73 years) of western white pine (Pinus monticola Dougl.), ponderosa pine (Pinus ponderosa Laws.), and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. glauca) growing in northern Idaho. Material was obtained by the stem analysis method from rings laid down in the upper portion of the crown throughout each tree's life. The sampling protocol minimized variation caused by changing light regimes within each tree. Autoregressive moving average (ARMA) models were used to describe the autocorrelation structure over time. Three time series were analyzed for each tree: the stable carbon isotope ratio (delta(13)C); discrimination (delta); and the difference between ambient and internal CO(2) concentrations (c(a) - c(i)). The effect of converting from ring cellulose to whole-leaf tissue did not affect the analysis because it was almost completely removed by the detrending that precedes time-series analysis. A simple linear or quadratic model adequately described the time trend. The residuals from the trend had a constant mean and variance, thus ensuring stationarity, a requirement for autocorrelation analysis. The trend over time for c(a) - c(i) was particularly strong (R(2) = 0.29-0.84). Autoregressive moving average analyses of the residuals from these trends indicated that two-thirds of the individual tree series contained significant autocorrelation, whereas the remaining third were random (white noise) over time. We were unable to distinguish between individuals with and without significant autocorrelation beforehand. Significant ARMA models were all of low order, with either first- or second-order (i.e., lagged 1 or 2 years, respectively) models performing well. A simple autoregressive (AR(1)), model was the most common. The most useful generalization was that the same ARMA model holds for each of the three series (delta(13)C, delta, c(a) - c(i)) for an individual tree, if the time trend has been properly removed for each series. The mean series for the two pine species were described by first-order ARMA models (1-year lags), whereas the Douglas-fir mean series were described by second-order models (2-year lags) with negligible first-order effects. Apparently, the process of constructing a mean time series for a species preserves an underlying signal related to delta(13)C while canceling some of the random individual tree variation. Furthermore, the best model for the overall mean series (e.g., for a species) cannot be inferred from a consensus of the individual tree model forms, nor can its parameters be estimated reliably from the mean of the individual tree parameters. Because two-thirds of the individual tree time series contained significant autocorrelation, the normal assumption of a random structure over time is unwarranted, even after accounting for the time trend. The residuals of an appropriate ARMA model satisfy the independence assumption, and can be used to make hypothesis tests.

Forest Stand Segmentation Using Airborne LIDAR Data and Very High Resolution Multispectral Imagery

NASA Astrophysics Data System (ADS)

Dechesne, Clément; Mallet, Clément; Le Bris, Arnaud; Gouet, Valérie; Hervieu, Alexandre

2016-06-01

Forest stands are the basic units for forest inventory and mapping. Stands are large forested areas (e.g., ≥ 2 ha) of homogeneous tree species composition. The accurate delineation of forest stands is usually performed by visual analysis of human operators on very high resolution (VHR) optical images. This work is highly time consuming and should be automated for scalability purposes. In this paper, a method based on the fusion of airborne laser scanning data (or lidar) and very high resolution multispectral imagery for automatic forest stand delineation and forest land-cover database update is proposed. The multispectral images give access to the tree species whereas 3D lidar point clouds provide geometric information on the trees. Therefore, multi-modal features are computed, both at pixel and object levels. The objects are individual trees extracted from lidar data. A supervised classification is performed at the object level on the computed features in order to coarsely discriminate the existing tree species in the area of interest. The analysis at tree level is particularly relevant since it significantly improves the tree species classification. A probability map is generated through the tree species classification and inserted with the pixel-based features map in an energetical framework. The proposed energy is then minimized using a standard graph-cut method (namely QPBO with α-expansion) in order to produce a segmentation map with a controlled level of details. Comparison with an existing forest land cover database shows that our method provides satisfactory results both in terms of stand labelling and delineation (matching ranges between 94% and 99%).

Testing aggregation hypotheses among Neotropical trees and shrubs: results from a 50-ha plot over 20 years of sampling.

PubMed

Myster, Randall W; Malahy, Michael P

2012-09-01

Spatial patterns of tropical trees and shrubs are important to understanding their interaction and the resultant structure of tropical rainforests. To assess this issue, we took advantage of previously collected data, on Neotropical tree and shrub stem identified to species and mapped for spatial coordinates in a 50ha plot, with a frequency of every five years and over a 20 year period. These stems data were first placed into four groups, regardless of species, depending on their location in the vertical strata of the rainforest (shrubs, understory trees, mid-sized trees, tall trees) and then used to generate aggregation patterns for each sampling year. We found shrubs and understory trees clumped at small spatial scales of a few meters for several of the years sampled. Alternatively, mid-sized trees and tall trees did not clump, nor did they show uniform (regular) patterns, during any sampling period. In general (1) groups found higher in the canopy did not show aggregation on the ground and (2) the spatial patterns of all four groups showed similarity among different sampling years, thereby supporting a "shifting mosaic" view of plant communities over large areas. Spatial analysis, such as this one, are critical to understanding and predicting tree spaces, tree-tree replacements and the Neotropical forest patterns, such as biodiversity and those needed for sustainability efforts, they produce.

Exact solutions for species tree inference from discordant gene trees.

PubMed

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

2013-10-01

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

[Difference of water relationships of poplar trees in Zhangbei County, Hebei, China based on stable isotope and thermal dissipation method].

PubMed

Miao, Bo; Meng, Ping; Zhang, Jin Song; He, Fang Jie; Sun, Shou Jia

2017-07-18

The water sources and transpiration of poplar trees in Zhangbei County were measured using stable hydrogen isotope and thermal dissipation method. The differences in water relationships between dieback and non-dieback poplar trees were analyzed. The results showed that the dieback trees mainly used shallow water from 0-30 cm soil layer during growing season while the non-dieback trees mainly used water from 30-80 cm soil layer. There was a significant difference in water source between them. The non-dieback trees used more water from middle and deep soil layers than that of the dieback trees during the dry season. The percentage of poplar trees using water from 0-30 cm soil layer increased in wet season, and the increase of dieback trees was higher than that of non-dieback trees. The contributions of water from 30-180 cm soil layer of dieback and non-dieback trees both decreased in wet season. The sap flow rate of non-dieback trees was higher than that of dieback trees. There was a similar variation tend of sap flow rate between dieback and non-dieback trees in different weather conditions, but the start time of sap flow of non-dieback trees was earlier than that of dieback trees. Correlation analysis showed that the sap flow rate of either dieback or non-dieback poplar trees strongly related to soil temperature, wind speed, photosynthetically active radiation, relative humidity and air temperature. The sap flow rate of die-back poplar trees strongly negatively related to soil temperature and relative humidity, and strongly positively related to the other factors. The sap flow rate of non-dieback poplar trees only strongly negatively related to relative humidity but positively related to the other factors. The results revealed transpiration of both poplar trees was easily affected by environmental factors. The water consumption of dieback trees was less than non-dieback trees because the cumulative sap flow amount of dieback trees was lower. Reduced transpiration of dieback trees couldn't help to prevent poplar forest declining due to shallow water source.

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript

PubMed Central

2014-01-01

Background The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherited from the variety GT 1. Results We constructed the rubber tree mitochondrial genome of a cytoplasmic male sterile variety, BPM 24, using 454 sequencing, including 8 kb paired-end libraries, plus Illumina paired-end sequencing. We annotated this mitochondrial genome with the aid of Illumina RNA-seq data and performed comparative analysis. We then compared the sequence of BPM 24 to the contigs of the published rubber tree, variety RRIM 600, and identified a rearrangement that is unique to BPM 24 resulting in a novel transcript containing a portion of atp9. Conclusions The novel transcript is consistent with changes that cause cytoplasmic male sterility through a slight reduction to ATP production efficiency. The exhaustive nature of the search rules out alternative causes and supports previous findings of novel transcripts causing cytoplasmic male sterility. PMID:24512148

Industrial and occupational ergonomics in the petrochemical process industry: a regression trees approach.

PubMed

Bevilacqua, M; Ciarapica, F E; Giacchetta, G

2008-07-01

This work is an attempt to apply classification tree methods to data regarding accidents in a medium-sized refinery, so as to identify the important relationships between the variables, which can be considered as decision-making rules when adopting any measures for improvement. The results obtained using the CART (Classification And Regression Trees) method proved to be the most precise and, in general, they are encouraging concerning the use of tree diagrams as preliminary explorative techniques for the assessment of the ergonomic, management and operational parameters which influence high accident risk situations. The Occupational Injury analysis carried out in this paper was planned as a dynamic process and can be repeated systematically. The CART technique, which considers a very wide set of objective and predictive variables, shows new cause-effect correlations in occupational safety which had never been previously described, highlighting possible injury risk groups and supporting decision-making in these areas. The use of classification trees must not, however, be seen as an attempt to supplant other techniques, but as a complementary method which can be integrated into traditional types of analysis.

Decision-Tree Analysis for Predicting First-Time Pass/Fail Rates for the NCLEX-RN® in Associate Degree Nursing Students.

PubMed

Chen, Hsiu-Chin; Bennett, Sean

2016-08-01

Little evidence shows the use of decision-tree algorithms in identifying predictors and analyzing their associations with pass rates for the NCLEX-RN(®) in associate degree nursing students. This longitudinal and retrospective cohort study investigated whether a decision-tree algorithm could be used to develop an accurate prediction model for the students' passing or failing the NCLEX-RN. This study used archived data from 453 associate degree nursing students in a selected program. The chi-squared automatic interaction detection analysis of the decision trees module was used to examine the effect of the collected predictors on passing/failing the NCLEX-RN. The actual percentage scores of Assessment Technologies Institute®'s RN Comprehensive Predictor(®) accurately identified students at risk of failing. The classification model correctly classified 92.7% of the students for passing. This study applied the decision-tree model to analyze a sequence database for developing a prediction model for early remediation in preparation for the NCLEXRN. [J Nurs Educ. 2016;55(8):454-457.]. Copyright 2016, SLACK Incorporated.

Graphical fault tree analysis for fatal falls in the construction industry.

PubMed

Chi, Chia-Fen; Lin, Syuan-Zih; Dewi, Ratna Sari

2014-11-01

The current study applied a fault tree analysis to represent the causal relationships among events and causes that contributed to fatal falls in the construction industry. Four hundred and eleven work-related fatalities in the Taiwanese construction industry were analyzed in terms of age, gender, experience, falling site, falling height, company size, and the causes for each fatality. Given that most fatal accidents involve multiple events, the current study coded up to a maximum of three causes for each fall fatality. After the Boolean algebra and minimal cut set analyses, accident causes associated with each falling site can be presented as a fault tree to provide an overview of the basic causes, which could trigger fall fatalities in the construction industry. Graphical icons were designed for each falling site along with the associated accident causes to illustrate the fault tree in a graphical manner. A graphical fault tree can improve inter-disciplinary discussion of risk management and the communication of accident causation to first line supervisors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Radiocarbon Dating of an Olive Tree Cross-Section: New Insights on Growth Patterns and Implications for Age Estimation of Olive Trees.

PubMed

Ehrlich, Yael; Regev, Lior; Kerem, Zohar; Boaretto, Elisabetta

2017-01-01

The age of living massive olive trees is often assumed to be between hundreds and even thousands of years. These estimations are usually based on the girth of the trunk and an extrapolation based on a theoretical annual growth rate. It is difficult to objectively verify these claims, as a monumental tree may not be cut down for analysis of its cross-section. In addition, the inner and oldest part of the trunk in olive trees usually rots, precluding the possibility of carting out radiocarbon analysis of material from the first years of life of the tree. In this work we present a cross-section of an olive tree, previously estimated to be hundreds of years old, which was cut down post-mortem in 2013. The cross-section was radiocarbon dated at numerous points following the natural growth pattern, which was made possible to observe by viewing the entire cross-section. Annual growth rate values were calculated and compared between different radii. The cross-section also revealed a nearly independent segment of growth, which would clearly offset any estimations based solely on girth calculations. Multiple piths were identified, indicating the beginning of branching within the trunk. Different radii were found to have comparable growth rates, resulting in similar estimates dating the piths to the 19th century. The estimated age of the piths represent a terminus ante quem for the age of the tree, as these are piths of separate branches. However, the tree is likely not many years older than the dated piths, and certainly not centuries older. The oldest radiocarbon-datable material in this cross-section was less than 200 years old, which is in agreement with most other radiocarbon dates of internal wood from living olive trees, rarely older than 300 years.

Ectomycorrhizal fungal communities on seedlings and conspecific trees of Pinus mugo grown on the coastal dunes of the Curonian Spit in Lithuania.

PubMed

Aučina, Algis; Rudawska, Maria; Leski, Tomasz; Ryliškis, Darius; Pietras, Marcin; Riepšas, Edvardas

2011-04-01

Ectomycorrhizal (ECM) communities of mature trees and regenerating seedlings of a non-native tree species Pinus mugo grown in a harsh environment of the coastal region of the Curonian Spit National Park in Lithuania were assessed. We established three study sites (S1, S2, and S3) that were separated from each other by 15 km. The ECM species richness was rather low in particular for mature, 100-year-old trees: 12 ectomycorrhizal taxa were identified by molecular analysis from 11 distinguished morphotypes. All 12 taxa were present on seedlings and on mature trees, with between 8-11 and 9-11 taxa present on seedlings and mature trees, respectively. Cenococcum geophilum dominated all ECM communities, but the relative abundance of C. geophilum mycorrhizas was nearly two times higher on seedlings than on mature trees. Mycorrhizal associations formed by Wilcoxina sp., Lactarius rufus, and Russula paludosa were also abundant. Several fungal taxa were only occasionally detected, including Cortinarius sp., Cortinarius obtusus, Cortinarius croceus, and Meliniomyces sp. Shannon's diversity indices for the ECM assemblages of P. mugo ranged from 0.98 to 1.09 for seedling and from 1.05 to 1.31 for mature trees. According to analysis of similarity, the mycorrhizal communities were similar between the sites (R = 0.085; P = 0.06) and only slightly separated between seedlings and mature trees (R = 0.24; P < 0.0001). An incidental fruiting body survey that was conducted weakly reflected the below-ground assessment of the ECM fungal community and once again showed that ECM and fruiting body studies commonly supply different partial accounts of the true ECM fungal diversity. Our results show that P. mugo has moved into quite distinct habitats and is able to adapt a suite of ECM symbionts that sufficiently support growth and development of this tree and allow for natural seedling regeneration.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

PubMed

Chesters, Douglas

2017-05-01

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Climate Response of Tree Radial Growth at Different Timescales in the Qinling Mountains.

PubMed

Sun, Changfeng; Liu, Yu

2016-01-01

The analysis of the tree radial growth response to climate is crucial for dendroclimatological research. However, the response relationships between tree-ring indices and climatic factors at different timescales are not yet clear. In this study, the tree-ring width of Huashan pine (Pinus armandii) from Huashan in the Qinling Mountains, north-central China, was used to explore the response differences of tree growth to climatic factors at daily, pentad (5 days), dekad (10 days) and monthly timescales. Correlation function and linear regression analysis were applied in this paper. The tree-ring width showed a more sensitive response to daily and pentad climatic factors. With the timescale decreasing, the absolute value of the maximum correlation coefficient between the tree-ring data and precipitation increases as well as temperature (mean, minimum and maximum temperature). Compared to the other three timescales, pentad was more suitable for analysing the response of tree growth to climate. Relative to the monthly climate data, the association between the tree-ring data and the pentad climate data was more remarkable and accurate, and the reconstruction function based on the pentad climate was also more reliable and stable. We found that the major climatic factor limiting Huashan pine growth was the precipitation of pentads 20-35 (from April 6 to June 24) rather than the well-known April-June precipitation. The pentad was also proved to be a better timescale for analysing the climate and tree growth in the western and eastern Qinling Mountains. The formation of the earlywood density of Chinese pine (Pinus tabulaeformis) from Shimenshan in western Qinling was mainly affected by the maximum temperature of pentads 28-32 (from May 16 to June 9). The maximum temperature of pentads 28-33 (from May 16 to June 14) was the major factor affecting the ring width of Chinese pine from Shirenshan in eastern Qinling.

Use of Bayesian event trees in semi-quantitative volcano eruption forecasting and hazard analysis

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

Use of Bayesian event trees to forecast eruptive activity during volcano crises is an increasingly common practice for the USGS-USAID Volcano Disaster Assistance Program (VDAP) in collaboration with foreign counterparts. This semi-quantitative approach combines conceptual models of volcanic processes with current monitoring data and patterns of occurrence to reach consensus probabilities. This approach allows a response team to draw upon global datasets, local observations, and expert judgment, where the relative influence of these data depends upon the availability and quality of monitoring data and the degree to which the volcanic history is known. The construction of such event trees additionally relies upon existence and use of relevant global databases and documented past periods of unrest. Because relevant global databases may be underpopulated or nonexistent, uncertainty in probability estimations may be large. Our 'hybrid' approach of combining local and global monitoring data and expert judgment facilitates discussion and constructive debate between disciplines: including seismology, gas geochemistry, geodesy, petrology, physical volcanology and technology/engineering, where difference in opinion between response team members contributes to definition of the uncertainty in the probability estimations. In collaboration with foreign colleagues, we have created event trees for numerous areas experiencing volcanic unrest. Event trees are created for a specified time frame and are updated, revised, or replaced as the crisis proceeds. Creation of an initial tree is often prompted by a change in monitoring data, such that rapid assessment of probability is needed. These trees are intended as a vehicle for discussion and a way to document relevant data and models, where the target audience is the scientists themselves. However, the probabilities derived through the event-tree analysis can also be used to help inform communications with emergency managers and the public. VDAP trees evaluate probabilities of: magmatic intrusion, likelihood of eruption, magnitude of eruption, and types of associated hazardous events and their extents. In a few cases, trees have been extended to also assess and communicate vulnerability and relative risk.

Geometric Modelling of Tree Roots with Different Levels of Detail

NASA Astrophysics Data System (ADS)

Guerrero Iñiguez, J. I.

2017-09-01

This paper presents a geometric approach for modelling tree roots with different Levels of Detail, suitable for analysis of the tree anchoring, potentially occupied underground space, interaction with urban elements and damage produced and taken in the built-in environment. Three types of tree roots are considered to cover several species: tap root, heart shaped root and lateral roots. Shrubs and smaller plants are not considered, however, a similar approach can be considered if the information is available for individual species. The geometrical approach considers the difficulties of modelling the actual roots, which are dynamic and almost opaque to direct observation, proposing generalized versions. For each type of root, different geometric models are considered to capture the overall shape of the root, a simplified block model, and a planar or surface projected version. Lower detail versions are considered as compatibility version for 2D systems while higher detail models are suitable for 3D analysis and visualization. The proposed levels of detail are matched with CityGML Levels of Detail, enabling both analysis and aesthetic views for urban modelling.

The effect of trees on preferential flow and soil infiltrability in an agroforestry parkland in semiarid Burkina Faso.

PubMed

Bargués Tobella, A; Reese, H; Almaw, A; Bayala, J; Malmer, A; Laudon, H; Ilstedt, U

2014-04-01

Water scarcity constrains the livelihoods of millions of people in tropical drylands. Tree planting in these environments is generally discouraged due to the large water consumption by trees, but this view may neglect their potential positive impacts on water availability. The effect of trees on soil hydraulic properties linked to groundwater recharge is poorly understood. In this study, we performed 18 rainfall simulations and tracer experiments in an agroforestry parkland in Burkina Faso to investigate the effect of trees and associated termite mounds on soil infiltrability and preferential flow. The sampling points were distributed in transects each consisting of three positions: (i) under a single tree, (ii) in the middle of an open area, and (iii) under a tree associated with a termite mound. The degree of preferential flow was quantified through parameters based on the dye infiltration patterns, which were analyzed using image analysis of photographs. Our results show that the degree of preferential flow was highest under trees associated with termite mounds, intermediate under single trees, and minimal in the open areas. Tree density also had an influence on the degree of preferential flow, with small open areas having more preferential flow than large ones. Soil infiltrability was higher under single trees than in the open areas or under trees associated with a termite mound. The findings from this study demonstrate that trees have a positive impact on soil hydraulic properties influencing groundwater recharge, and thus such effects must be considered when evaluating the impact of trees on water resources in drylands. Trees in dryland landscapes increase soil infiltrability and preferential flow Termite mounds in association with trees further enhance preferential flow.

The effect of trees on preferential flow and soil infiltrability in an agroforestry parkland in semiarid Burkina Faso

PubMed Central

Bargués Tobella, A; Reese, H; Almaw, A; Bayala, J; Malmer, A; Laudon, H; Ilstedt, U

2014-01-01

Water scarcity constrains the livelihoods of millions of people in tropical drylands. Tree planting in these environments is generally discouraged due to the large water consumption by trees, but this view may neglect their potential positive impacts on water availability. The effect of trees on soil hydraulic properties linked to groundwater recharge is poorly understood. In this study, we performed 18 rainfall simulations and tracer experiments in an agroforestry parkland in Burkina Faso to investigate the effect of trees and associated termite mounds on soil infiltrability and preferential flow. The sampling points were distributed in transects each consisting of three positions: (i) under a single tree, (ii) in the middle of an open area, and (iii) under a tree associated with a termite mound. The degree of preferential flow was quantified through parameters based on the dye infiltration patterns, which were analyzed using image analysis of photographs. Our results show that the degree of preferential flow was highest under trees associated with termite mounds, intermediate under single trees, and minimal in the open areas. Tree density also had an influence on the degree of preferential flow, with small open areas having more preferential flow than large ones. Soil infiltrability was higher under single trees than in the open areas or under trees associated with a termite mound. The findings from this study demonstrate that trees have a positive impact on soil hydraulic properties influencing groundwater recharge, and thus such effects must be considered when evaluating the impact of trees on water resources in drylands. Key Points Trees in dryland landscapes increase soil infiltrability and preferential flow Termite mounds in association with trees further enhance preferential flow PMID:25641996

Rate of tree carbon accumulation increases continuously with tree size.

PubMed

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

2014-03-06

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.

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

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

2013-01-01

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

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

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

2013-01-01

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

An inventory of trees in Dublin city centre.

PubMed

Ningal, Tine; Mills, Gerald; Smithwick, Pamela

2010-01-01

While urban areas are often considered to be comprised chiefly of artificial surfaces, they can contain a substantial portion of green space and a great diversity of natural habitats. These spaces include public parks, private gardens and street trees, all of which can provide valuable environmental services, such as improved air quality. Trees play a particular role in cities as they are often placed along roadsides and in the median strip of busy streets. As such they regulate access to sunshine, restrict airflow, provide shelter, scavenge air pollutants and manage noise at the street level. A tree planting policy can be an important part of a broader environmental strategy aimed at improving the quality of life in urban areas but this requires up-to-date knowledge of the current tree stock, which does not exist for Dublin. This article presents an inventory of trees in Dublin's city centre, defined as the area between the Grand and Royal canals. The results show that there are over 10,000 trees in the study area representing a density of 684 trees km-2 or one tree to approximately every 50 residents of the city centre. The tree canopy extent when in full foliage was nearly 1 km2 in extent or 6% of the study area. A more detailed analysis of those trees planted along streets shows little species variation but clear distinction in the sizes of trees, which is indicative of the age of planting. These data are used to estimate the carbon stored in Dublin's trees.

Gaps in sampling and limitations to tree biomass estimation: a review of past sampling efforts over the past 50 years

Treesearch

Aaron Weiskittel; Jereme Frank; James Westfall; David Walker; Phil Radtke; David Affleck; David Macfarlane

2015-01-01

Tree biomass models are widely used but differ due to variation in the quality and quantity of data used in their development. We reviewed over 250 biomass studies and categorized them by species, location, sampled diameter distribution, and sample size. Overall, less than half of the tree species in Forest Inventory and Analysis database (FIADB) are without a...

Content of chemical elements in tree rings of lodgepole pine and whitebark pine from a subalpine Sierra Nevada forest

Treesearch

David L. Peterson; Darren R. Anderson

1990-01-01

The wood of lodgepole pines and whitebark pines from a high elevation site in the east central Sierra Nevada of California was analyzed for chemical content to determine whether there were any temporal patterns of chemical distribution in tree rings. Cores were taken from 10 trees of each species and divided into 5-year increments for chemical analysis. Correlation...

Economic analysis of the gypsy moth problem in the northeast: II. applied to residential property

Treesearch

Brian R. Payne; William B. White; Roger E. McCay; Robert R. McNichols

1973-01-01

Guidelines are presented for determining dollar losses in residential property values from tree mortality caused by the gypsy moth. The method is based on an earlier study in Amherst, Massachusetts, of the contribution of trees to property values. For each target area, the method requires data on property value, lot size, and number of trees 6 inches dbh and larger for...