Software For Fault-Tree Diagnosis Of A System

NASA Technical Reports Server (NTRS)

Iverson, Dave; Patterson-Hine, Ann; Liao, Jack

1993-01-01

Fault Tree Diagnosis System (FTDS) computer program is automated-diagnostic-system program identifying likely causes of specified failure on basis of information represented in system-reliability mathematical models known as fault trees. Is modified implementation of failure-cause-identification phase of Narayanan's and Viswanadham's methodology for acquisition of knowledge and reasoning in analyzing failures of systems. Knowledge base of if/then rules replaced with object-oriented fault-tree representation. Enhancement yields more-efficient identification of causes of failures and enables dynamic updating of knowledge base. Written in C language, C++, and Common LISP.

Methods in Symbolic Computation and p-Adic Valuations of Polynomials

NASA Astrophysics Data System (ADS)

Guan, Xiao

Symbolic computation has widely appear in many mathematical fields such as combinatorics, number theory and stochastic processes. The techniques created in the area of experimental mathematics provide us efficient ways of symbolic computing and verification of complicated relations. Part I consists of three problems. The first one focuses on a unimodal sequence derived from a quartic integral. Many of its properties are explored with the help of hypergeometric representations and automatic proofs. The second problem tackles the generating function of the reciprocal of Catalan number. It springs from the closed form given by Mathematica. Furthermore, three methods in special functions are used to justify this result. The third issue addresses the closed form solutions for the moments of products of generalized elliptic integrals , which combines the experimental mathematics and classical analysis. Part II concentrates on the p-adic valuations of polynomials from the perspective of trees. For a given polynomial f( n) indexed in positive integers, the package developed in Mathematica will create certain tree structure following a couple of rules. The evolution of such trees are studied both rigorously and experimentally from the view of field extension, nonparametric statistics and random matrix.

Project Learning Tree. A Program of the American Forest Foundation.

ERIC Educational Resources Information Center

American Forest Foundation, Washington, DC.

Project Learning Tree (PLT) is a supplementary environmental education program intended for use in and out of the classroom with young people, their leaders, and teachers in kindergarten through grade 12. The PLT curriculum provides supplementary activities in various subject areas, such as social studies, language arts, mathematics, science, and…

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.

About rats and jackfruit trees: modeling the carrying capacity of a Brazilian Atlantic Forest spiny-rat Trinomys dimidiatus (Günther, 1877) - Rodentia, Echimyidae - population with varying jackfruit tree (Artocarpus heterophyllus L.) abundances.

PubMed

Mello, J H F; Moulton, T P; Raíces, D S L; Bergallo, H G

2015-01-01

We carried out a six-year study aimed at evaluating if and how a Brazilian Atlantic Forest small mammal community responded to the presence of the invasive exotic species Artocarpus heterophyllus, the jackfruit tree. In the surroundings of Vila Dois Rios, Ilha Grande, RJ, 18 grids were established, 10 where the jackfruit tree was present and eight were it was absent. Previous results indicated that the composition and abundance of this small mammal community were altered by the presence and density of A. heterophyllus. One observed effect was the increased population size of the spiny-rat Trinomys dimidiatus within the grids where the jackfruit trees were present. Therefore we decided to create a mathematical model for this species, based on the Verhulst-Pearl logistic equation. Our objectives were i) to calculate the carrying capacity K based on real data of the involved species and the environment; ii) propose and evaluate a mathematical model to estimate the population size of T. dimidiatus based on the monthly seed production of jackfruit tree, Artocarpus heterophyllus and iii) determinate the minimum jackfruit tree seed production to maintain at least two T. dimidiatus individuals in one study grid. Our results indicated that the predicted values by the model for the carrying capacity K were significantly correlated with real data. The best fit was found considering 20~35% energy transfer efficiency between trophic levels. Within the scope of assumed premises, our model showed itself to be an adequate simulator for Trinomys dimidiatus populations where the invasive jackfruit tree is present.

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

Variations of anthropogenic CO2 in urban area deduced by radiocarbon concentration in modern tree rings.

PubMed

Rakowski, Andrzej Z; Nakamura, Toshio; Pazdur, Anna

2008-10-01

Radiocarbon concentration in the atmosphere is significantly lower in areas where man-made emissions of carbon dioxide occur. This phenomenon is known as Suess effect, and is caused by the contamination of clean air with non-radioactive carbon from fossil fuel combustion. The effect is more strongly observed in industrial and densely populated urban areas. Measurements of carbon isotope concentrations in a study area can be compared to those from areas of clear air in order to estimate the amount of carbon dioxide emission from fossil fuel combustion by using a simple mathematical model. This can be calculated using the simple mathematical model. The result of the mathematical model followed in this study suggests that the use of annual rings of trees to obtain the secular variations of 14C concentration of atmospheric CO2 can be useful and efficient for environmental monitoring and modeling of the carbon distribution in local scale.

Beyond Problem-Solving: Elementary Students' Mathematical Dispositions When Faced with the Challenge of Unsolved Problems

ERIC Educational Resources Information Center

O'Dell, Jenna R.

2017-01-01

The goal of this study was to document the characteristics of students' dispositions towards mathematics when they engaged in the exploration of parts of unsolved problems: Graceful Tree Conjecture and Collatz Conjecture. Ten students, Grades 4 and 5, from an after-school program in the Midwest participated in the study. I focused on the…

An automated approach to the design of decision tree classifiers

NASA Technical Reports Server (NTRS)

Argentiero, P.; Chin, R.; Beaudet, P.

1982-01-01

An automated technique is presented for designing effective decision tree classifiers predicated only on a priori class statistics. The procedure relies on linear feature extractions and Bayes table look-up decision rules. Associated error matrices are computed and utilized to provide an optimal design of the decision tree at each so-called 'node'. A by-product of this procedure is a simple algorithm for computing the global probability of correct classification assuming the statistical independence of the decision rules. Attention is given to a more precise definition of decision tree classification, the mathematical details on the technique for automated decision tree design, and an example of a simple application of the procedure using class statistics acquired from an actual Landsat scene.

Phylogenetic tree and community structure from a Tangled Nature model.

PubMed

Canko, Osman; Taşkın, Ferhat; Argın, Kamil

2015-10-07

In evolutionary biology, the taxonomy and origination of species are widely studied subjects. An estimation of the evolutionary tree can be done via available DNA sequence data. The calculation of the tree is made by well-known and frequently used methods such as maximum likelihood and neighbor-joining. In order to examine the results of these methods, an evolutionary tree is pursued computationally by a mathematical model, called Tangled Nature. A relatively small genome space is investigated due to computational burden and it is found that the actual and predicted trees are in reasonably good agreement in terms of shape. Moreover, the speciation and the resulting community structure of the food-web are investigated by modularity. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Fault Tree Compiler (FTC): Program and mathematics

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1989-01-01

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

Xylem anisotropy and water transport--a model for the double sawcut experiment

Treesearch

Paul J. Schulte; David G. Costa

2010-01-01

Early experiments with overlapping cuts to the stems of trees demonstrated that lateral flow within the stem must be possible to allow such trees to maintain water flow to their leaves. We present a mathematical approach to considering lateral flow in stems by treating the xylem as an anisotropic medium for flow and develop an expression of its conductivity in the form...

[Research advances in dendrochronology].

PubMed

Fang, Ke-Yan; Chen, Qiu-Yan; Liu, Chang-Zhi; Cao, Chun-Fu; Chen, Ya-Jun; Zhou, Fei-Fei

2014-07-01

Tree-ring studies in China have achieved great advances since the 1990s, particularly for the dendroclimatological studies which have made some influence around the world. However, because of the uneven development, limited attention has been currently paid on the other branches of dendrochronology. We herein briefly compared the advances of dendrochronology in China and of the world and presented suggestions on future dendrochronological studies. Large-scale tree-ring based climate reconstructions in China are highly needed by employing mathematical methods and a high quality tree-ring network of the ring-width, density, stable isotope and wood anatomy. Tree-ring based field climate reconstructions provide potentials on explorations of climate forcings during the reconstructed periods via climate diagnosis and process simulation.

Mathematical analysis of dynamic spread of Pine Wilt disease.

PubMed

Dimitrijevic, D D; Bacic, J

2013-01-01

Since its detection in Portugal in 1999, the pinewood nematode Bursaphelenchus xylophilus (Steiner and Buhrer), a causal agent of Pine Wilt Disease, represents a threat to European forestry. Significant amount of money has been spent on its monitoring and eradication. This paper presents mathematical analysis of spread of pine wilt disease using a set of partial differential equations with space (longitude and latitude) and time as parameters of estimated spread of disease. This methodology can be used to evaluate risk of various assumed entry points of disease and make defense plans in advance. In case of an already existing outbreak, it can be used to draw optimal line of defense and plan removal of trees. Optimization constraints are economic loss of removal of susceptible trees as well as budgetary constraints of workforce cost.

The NASA SCI Files[TM]: The Case of the Powerful Pulleys. A Lesson Guide with Activities in Mathematics, Science, and Technology.

ERIC Educational Resources Information Center

Ricles, Shannon

This teacher's guide, with accompanying videotape, presents an episode of the NASA SCI Files. In this episode, one of the tree house detectives has had an accident and cannot get into the tree house. Using problem-based learning, the rest of the gang investigates the world of simple machines and physical science and "pull" together to…

Method and system for dynamic probabilistic risk assessment

NASA Technical Reports Server (NTRS)

Dugan, Joanne Bechta (Inventor); Xu, Hong (Inventor)

2013-01-01

The DEFT methodology, system and computer readable medium extends the applicability of the PRA (Probabilistic Risk Assessment) methodology to computer-based systems, by allowing DFT (Dynamic Fault Tree) nodes as pivot nodes in the Event Tree (ET) model. DEFT includes a mathematical model and solution algorithm, supports all common PRA analysis functions and cutsets. Additional capabilities enabled by the DFT include modularization, phased mission analysis, sequence dependencies, and imperfect coverage.

Temporal Subtraction of Digital Breast Tomosynthesis Images for Improved Mass Detection

DTIC Science & Technology

2009-11-01

imaging using two distinct methods7-15: mathematically based models defined by geometric primitives and voxelized models derived from real human...trees to complete them. We also plan to add further detail by defining the Cooper’s ligaments using geometrical NURBS surfaces. Realistic...generated model for the coronary arterial tree based on multislice CT and morphometric data," Medical Imaging 2006: Physics of Medical Imaging 6142

Phylogenomics with paralogs

PubMed Central

Hellmuth, Marc; Wieseke, Nicolas; Lechner, Marcus; Lenhof, Hans-Peter; Middendorf, Martin; Stadler, Peter F.

2015-01-01

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer. PMID:25646426

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.

A Heuristic Bioinspired for 8-Piece Puzzle

NASA Astrophysics Data System (ADS)

Machado, M. O.; Fabres, P. A.; Melo, J. C. L.

2017-10-01

This paper investigates a mathematical model inspired by nature, and presents a Meta-Heuristic that is efficient in improving the performance of an informed search, when using strategy A * using a General Search Tree as data structure. The work hypothesis suggests that the investigated meta-heuristic is optimal in nature and may be promising in minimizing the computational resources required by an objective-based agent in solving high computational complexity problems (n-part puzzle) as well as In the optimization of objective functions for local search agents. The objective of this work is to describe qualitatively the characteristics and properties of the mathematical model investigated, correlating the main concepts of the A * function with the significant variables of the metaheuristic used. The article shows that the amount of memory required to perform this search when using the metaheuristic is less than using the A * function to evaluate the nodes of a general search tree for the eight-piece puzzle. It is concluded that the meta-heuristic must be parameterized according to the chosen heuristic and the level of the tree that contains the possible solutions to the chosen problem.

The probability of monophyly of a sample of gene lineages on a species tree

PubMed Central

Mehta, Rohan S.; Bryant, David; Rosenberg, Noah A.

2016-01-01

Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte. PMID:27432988

A Mathematical Framework for Image Analysis

DTIC Science & Technology

1991-08-01

The results reported here were derived from the research project ’A Mathematical Framework for Image Analysis ’ supported by the Office of Naval...Research, contract N00014-88-K-0289 to Brown University. A common theme for the work reported is the use of probabilistic methods for problems in image ... analysis and image reconstruction. Five areas of research are described: rigid body recognition using a decision tree/combinatorial approach; nonrigid

Rewrite Systems, Pattern Matching, and Code Generation

DTIC Science & Technology

1988-06-09

Transformations Quicn a bucn arbol se anima, buena sombra le cobija1 [Old Spanish Saying] 1 Trees arc hierarchical mathematical objects. Their...subtrees of a tree may m atch one or more rewrite rules. Traditional research in term rewrite systems is concerned with de termining if a given system...be simulated by sets of rewrite rules. Non-local condjtions are des cribed in an awkward way since the only way to transmit information is indirectly

A mathematical framework for modelling cambial surface evolution using a level set method

PubMed Central

Sellier, Damien; Plank, Michael J.; Harrington, Jonathan J.

2011-01-01

Background and Aims During their lifetime, tree stems take a series of successive nested shapes. Individual tree growth models traditionally focus on apical growth and architecture. However, cambial growth, which is distributed over a surface layer wrapping the whole organism, equally contributes to plant form and function. This study aims at providing a framework to simulate how organism shape evolves as a result of a secondary growth process that occurs at the cellular scale. Methods The development of the vascular cambium is modelled as an expanding surface using the level set method. The surface consists of multiple compartments following distinct expansion rules. Growth behaviour can be formulated as a mathematical function of surface state variables and independent variables to describe biological processes. Key Results The model was coupled to an architectural model and to a forest stand model to simulate cambium dynamics and wood formation at the scale of the organism. The model is able to simulate competition between cambia, surface irregularities and local features. Predicting the shapes associated with arbitrarily complex growth functions does not add complexity to the numerical method itself. Conclusions Despite their slenderness, it is sometimes useful to conceive of trees as expanding surfaces. The proposed mathematical framework provides a way to integrate through time and space the biological and physical mechanisms underlying cambium activity. It can be used either to test growth hypotheses or to generate detailed maps of wood internal structure. PMID:21470972

From statistics of regular tree-like graphs to distribution function and gyration radius of branched polymers

NASA Astrophysics Data System (ADS)

Grosberg, Alexander Y.; Nechaev, Sergei K.

2015-08-01

We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius R, at large R, obeys, in the scaling sense, Δ S˜ {R}2/({a}2L), with a bond length (or Kuhn segment) and L defined as an average spanning distance. We show that this estimate is valid up to at most the logarithmic correction for any tree. We do so by explicitly computing the largest eigenvalues of Kramers matrices for both regular and ‘sparse’ three-branched trees, uncovering on the way their peculiar mathematical properties.

Investigation of Fuel Oil/Lube Oil Spray Fires On Board Vessels. Volume 3.

DTIC Science & Technology

1998-11-01

U.S. Coast Guard Research and Development Center 1082 Shennecossett Road, Groton, CT 06340-6096 Report No. CG-D-01-99, III Investigation of Fuel ...refinery). Developed the technical and mathematical specifications for BRAVO™2.0, a state-of-the-art Windows program for performing event tree and fault...tree analyses. Also managed the development of and prepared the technical specifications for QRA ROOTS™, a Windows program for storing, searching K-4

How should leaf area, sapwood area and stomatal conductance vary with tree height to maximize growth?

PubMed

Buckley, Thomas N; Roberts, David W

2006-02-01

Conventional wisdom holds that the ratio of leaf area to sapwood area (L/S) should decline during height (H) growth to maintain hydraulic homeostasis and prevent stomatal conductance (g(s)) from declining. We contend that L/S should increase with H based on a numerical simulation, a mathematical analysis and a conceptual argument: (1) numerical simulation--a tree growth model, DESPOT (Deducing Emergent Structure and Physiology Of Trees), in which carbon (C) allocation is regulated to maximize C gain, predicts L/S should increase during most of H growth; (2) mathematical analysis--the formal criterion for optimal C allocation, applied to a simplified analytical model of whole tree carbon-water balance, predicts L/S should increase with H if leaf-level gas exchange parameters including g(s) are conserved; and (3) conceptual argument--photosynthesis is limited by several substitutable resources (chiefly nitrogen (N), water and light) and H growth increases the C cost of water transport but not necessarily of N and light capture, so if the goal is to maximize C gain or growth, allocation should shift in favor of increasing photosynthetic capacity and irradiance, rather than sustaining g(s). Although many data are consistent with the prediction that L/S should decline with H, many others are not, and we discuss possible reasons for these discrepancies.

Scattering measurements on natural and model trees

NASA Technical Reports Server (NTRS)

Rogers, James C.; Lee, Sung M.

1990-01-01

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

A simple mathematical model of society collapse applied to Easter Island

NASA Astrophysics Data System (ADS)

Bologna, M.; Flores, J. C.

2008-02-01

In this paper we consider a mathematical model for the evolution and collapse of the Easter Island society. Based on historical reports, the available primary resources consisted almost exclusively in the trees, then we describe the inhabitants and the resources as an isolated dynamical system. A mathematical, and numerical, analysis about the Easter Island community collapse is performed. In particular, we analyze the critical values of the fundamental parameters and a demographic curve is presented. The technological parameter, quantifying the exploitation of the resources, is calculated and applied to the case of another extinguished civilization (Copán Maya) confirming the consistency of the adopted model.

Structural modeling and analysis of an effluent treatment process for electroplating--a graph theoretic approach.

PubMed

Kumar, Abhishek; Clement, Shibu; Agrawal, V P

2010-07-15

An attempt is made to address a few ecological and environment issues by developing different structural models for effluent treatment system for electroplating. The effluent treatment system is defined with the help of different subsystems contributing to waste minimization. Hierarchical tree and block diagram showing all possible interactions among subsystems are proposed. These non-mathematical diagrams are converted into mathematical models for design improvement, analysis, comparison, storage retrieval and commercially off-the-shelf purchases of different subsystems. This is achieved by developing graph theoretic model, matrix models and variable permanent function model. Analysis is carried out by permanent function, hierarchical tree and block diagram methods. Storage and retrieval is done using matrix models. The methodology is illustrated with the help of an example. Benefits to the electroplaters/end user are identified. 2010 Elsevier B.V. All rights reserved.

Mathematics and evolutionary biology make bioinformatics education comprehensible.

PubMed

Jungck, John R; Weisstein, Anton E

2013-09-01

The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

Mathematics and evolutionary biology make bioinformatics education comprehensible

PubMed Central

Weisstein, Anton E.

2013-01-01

The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

Using Tree-Ring Data, Research, and Expeditions as an Accessible, Hands-on "Bridge" into Climate Studies for Diverse Audiences

NASA Astrophysics Data System (ADS)

Davi, N. K.; Wattenberg, F.; Pringle, P. T.; Tanenbaum, J.; O'Brien, A.; Greidanus, I.; Perry, M.

2012-12-01

Tree-ring research provides an engaging, intuitive, and relevant entryway into understanding both climate-change and environmental research, as well as the process of science from inspiration, to fieldwork, to analysis, to publishing and communicating. The basic premise of dendrochronology is that annual rings reflect environmental conditions year-by-year and that by studying long-lived trees we can learn about past environments and climates for hundreds-to-thousands of years in the past. 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. Scientist exciting stories and images from the field can be leveraged to connect students to the study and the data. Second, tree-rings can be more easily explained as a proxy for climate than other methods (ice cores, carbon-isotope ratios, etc.), and 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 will present several projects have been initiated for a range of audiences, including; elementary school, where 5th graders visited a local forest to collect samples and apply their samples and what they learned to math and science classes. 5th grade students also leaned how to use Climate Explorer (KNMI), an online tool that allows scientist and students the opportunity to access and visualize global climate data within a few clicks. Geared to 2 and 4 year colleges, we are also collaboratively developing new interdisciplinary science and mathematical curriculum, interactive game modules, and multi-media that focus on using tree-ring expeditions and research projects that have real-world applications related to societal concerns (drought, warming, or in some cases, finances) to support student-centered inquiry-based learning. We are also creating professional development guides for teachers.

Evolutionarily stable strategy of carbon and nitrogen investments in forest leaves and its application in vegetation dynamic modeling

NASA Astrophysics Data System (ADS)

Weng, E.; Farrior, C.; Dybzinski, R.; Pacala, S. W.

2015-12-01

Leaf mass per area (LMA) and leaf lifespan (LL) are two highly correlated plant traits that are key to plant physiological and ecological properties. Usually, low LMA means short LL, high nitrogen (N) content per unit mass, and fast turnover rates of nutrients; high LMA leads to long LL, low N content, and slow turnover rates. Deciduous trees with low LMA and short lifespan leaves have low carbon cost but high nitrogen demand; and evergreen trees, with high LMA and long lifespan leaves, have high carbon cost but low nitrogen demand. These relationships lead to: 1) evergreen trees have higher leaf area index than deciduous trees; 2) evergreen trees' carbon use efficiency is lower than the deciduous trees' because of their thick leaves and therefore high maintenance respiration; 3) the advantage of evergreens trees brought by their extra leaves over deciduous trees diminishes with increase N in ecosystem. These facts determine who will win when trees compete with each other in a N-limited ecosystem. In this study, we formulate a mathematical model according to the relationships between LMA, LL, leaf nitrogen, and leaf building and maintenance cost, where LMA is the fundamental variable determining the other three. We analyze the evolutionarily stable strategies (ESSs) of LMA with this mathematical model by examining the benefits of carbon and nitrogen investments to leaves in ecosystems with different N. The model shows the ESS converges to low LMA at high N and high LMA at low N. At intermediate N, there are two ESSs at low and high ends of LMA, respectively. The ESS also leads to low forest productivity by outcompeting the possible high productive strategies. We design a simulation scheme in an individual-based competition model (LM3-PPA) to simulate forest dynamics as results of the competition between deciduous and evergreen trees in three different biomes, which are temperate deciduous forest, deciduous-evergreen mixed forest, and boreal evergreen forest. The simulated results are consistent with the actual forests. Our model and simulated results indicate the distribution of evergreen and deciduous forests can be explained by one single leaf trait (i.e., LMA) and associated physiological and biogeochemical processes.

Self-aligning and compressed autosophy video databases

NASA Astrophysics Data System (ADS)

Holtz, Klaus E.

1993-04-01

Autosophy, an emerging new science, explains `self-assembling structures,' such as crystals or living trees, in mathematical terms. This research provides a new mathematical theory of `learning' and a new `information theory' which permits the growing of self-assembling data network in a computer memory similar to the growing of `data crystals' or `data trees' without data processing or programming. Autosophy databases are educated very much like a human child to organize their own internal data storage. Input patterns, such as written questions or images, are converted to points in a mathematical omni dimensional hyperspace. The input patterns are then associated with output patterns, such as written answers or images. Omni dimensional information storage will result in enormous data compression because each pattern fragment is only stored once. Pattern recognition in the text or image files is greatly simplified by the peculiar omni dimensional storage method. Video databases will absorb input images from a TV camera and associate them with textual information. The `black box' operations are totally self-aligning where the input data will determine their own hyperspace storage locations. Self-aligning autosophy databases may lead to a new generation of brain-like devices.

A method of building of decision trees based on data from wearable device during a rehabilitation of patients with tibia fractures

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

Kupriyanov, M. S., E-mail: mikhail.kupriyanov@gmail.com; Shukeilo, E. Y., E-mail: eyshukeylo@gmail.com; Shichkina, J. A., E-mail: strange.y@mail.ru

2015-11-17

Nowadays technologies which are used in traumatology are a combination of mechanical, electronic, calculating and programming tools. Relevance of development of mobile applications for an expeditious data processing which are received from medical devices (in particular, wearable devices), and formulation of management decisions increases. Using of a mathematical method of building of decision trees for an assessment of a patient’s health condition using data from a wearable device considers in this article.

A method of building of decision trees based on data from wearable device during a rehabilitation of patients with tibia fractures

NASA Astrophysics Data System (ADS)

Kupriyanov, M. S.; Shukeilo, E. Y.; Shichkina, J. A.

2015-11-01

Nowadays technologies which are used in traumatology are a combination of mechanical, electronic, calculating and programming tools. Relevance of development of mobile applications for an expeditious data processing which are received from medical devices (in particular, wearable devices), and formulation of management decisions increases. Using of a mathematical method of building of decision trees for an assessment of a patient's health condition using data from a wearable device considers in this article.

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.

A parallelized binary search tree

USDA-ARS?s Scientific Manuscript database

PTTRNFNDR is an unsupervised statistical learning algorithm that detects patterns in DNA sequences, protein sequences, or any natural language texts that can be decomposed into letters of a finite alphabet. PTTRNFNDR performs complex mathematical computations and its processing time increases when i...

7 CFR 3430.902 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., including agricultural crops and trees, wood and wood wastes and residues, plants (including aquatic plants... credit toward such a degree; or (B) Offers a 2-year program in engineering, mathematics, or the physical...-professional level in engineering, scientific, or other technological fields requiring the understanding and...

7 CFR 3430.902 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., including agricultural crops and trees, wood and wood wastes and residues, plants (including aquatic plants... credit toward such a degree; or (B) Offers a 2-year program in engineering, mathematics, or the physical...-professional level in engineering, scientific, or other technological fields requiring the understanding and...

7 CFR 3430.902 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., including agricultural crops and trees, wood and wood wastes and residues, plants (including aquatic plants... credit toward such a degree; or (B) Offers a 2-year program in engineering, mathematics, or the physical...-professional level in engineering, scientific, or other technological fields requiring the understanding and...

7 CFR 3430.902 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., including agricultural crops and trees, wood and wood wastes and residues, plants (including aquatic plants... credit toward such a degree; or (B) Offers a 2-year program in engineering, mathematics, or the physical...-professional level in engineering, scientific, or other technological fields requiring the understanding and...

Capturing spiral radial growth of conifers using the superellipse to model tree-ring geometric shape

PubMed Central

Shi, Pei-Jian; Huang, Jian-Guo; Hui, Cang; Grissino-Mayer, Henri D.; Tardif, Jacques C.; Zhai, Li-Hong; Wang, Fu-Sheng; Li, Bai-Lian

2015-01-01

Tree-rings are often assumed to approximate a circular shape when estimating forest productivity and carbon dynamics. However, tree rings are rarely, if ever, circular, thereby possibly resulting in under- or over-estimation in forest productivity and carbon sequestration. Given the crucial role played by tree ring data in assessing forest productivity and carbon storage within a context of global change, it is particularly important that mathematical models adequately render cross-sectional area increment derived from tree rings. We modeled the geometric shape of tree rings using the superellipse equation and checked its validation based on the theoretical simulation and six actual cross sections collected from three conifers. We found that the superellipse better describes the geometric shape of tree rings than the circle commonly used. We showed that a spiral growth trend exists on the radial section over time, which might be closely related to spiral grain along the longitudinal axis. The superellipse generally had higher accuracy than the circle in predicting the basal area increment, resulting in an improved estimate for the basal area. The superellipse may allow better assessing forest productivity and carbon storage in terrestrial forest ecosystems. PMID:26528316

Capturing spiral radial growth of conifers using the superellipse to model tree-ring geometric shape.

PubMed

Shi, Pei-Jian; Huang, Jian-Guo; Hui, Cang; Grissino-Mayer, Henri D; Tardif, Jacques C; Zhai, Li-Hong; Wang, Fu-Sheng; Li, Bai-Lian

2015-01-01

Tree-rings are often assumed to approximate a circular shape when estimating forest productivity and carbon dynamics. However, tree rings are rarely, if ever, circular, thereby possibly resulting in under- or over-estimation in forest productivity and carbon sequestration. Given the crucial role played by tree ring data in assessing forest productivity and carbon storage within a context of global change, it is particularly important that mathematical models adequately render cross-sectional area increment derived from tree rings. We modeled the geometric shape of tree rings using the superellipse equation and checked its validation based on the theoretical simulation and six actual cross sections collected from three conifers. We found that the superellipse better describes the geometric shape of tree rings than the circle commonly used. We showed that a spiral growth trend exists on the radial section over time, which might be closely related to spiral grain along the longitudinal axis. The superellipse generally had higher accuracy than the circle in predicting the basal area increment, resulting in an improved estimate for the basal area. The superellipse may allow better assessing forest productivity and carbon storage in terrestrial forest ecosystems.

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.

Group theoretic approach to the perturbative string S-matrix

NASA Astrophysics Data System (ADS)

Neveu, A.; West, P.

1987-07-01

A new approach to the computation of string scattering is given. From duality, unitarity and a generic overlap property, we determine entirely the N-string amplitude, including the integration measure, and its gauge properties. The techniques do not use any oscillator algebra, but the computation is reduced to a straightforward exercise in conformal group theory. This can be applied to fermionic trees and multiloop diagrams, but in this paper it is demonstrated on the open bosonic tree. Permanent address: Mathematics Department, King's College, Strand, London WC2R 2LS, UK.

SANDERLING Final Report: Parts A and B, A Research Study into KBS for Command and Control in Naval and TMD Applications

DTIC Science & Technology

1990-04-01

focus of attention ). The inherent local control in the FA/C model allows it to achieve just that, since it only requires a global goal to become...Computing Terms Agent Modelling : is concerned with modelling actor’s intentions and plans, and their modification in the light of information... model or program that is based on a mathematical system of logic. B-tree : or "binary-tree" is a self organising storage mechanism that works by taking

Glide performance and aerodynamics of non-equilibrium glides in northern flying squirrels (Glaucomys sabrinus)

PubMed Central

Bahlman, Joseph W.; Swartz, Sharon M.; Riskin, Daniel K.; Breuer, Kenneth S.

2013-01-01

Gliding is an efficient form of travel found in every major group of terrestrial vertebrates. Gliding is often modelled in equilibrium, where aerodynamic forces exactly balance body weight resulting in constant velocity. Although the equilibrium model is relevant for long-distance gliding, such as soaring by birds, it may not be realistic for shorter distances between trees. To understand the aerodynamics of inter-tree gliding, we used direct observation and mathematical modelling. We used videography (60–125 fps) to track and reconstruct the three-dimensional trajectories of northern flying squirrels (Glaucomys sabrinus) in nature. From their trajectories, we calculated velocities, aerodynamic forces and force coefficients. We determined that flying squirrels do not glide at equilibrium, and instead demonstrate continuously changing velocities, forces and force coefficients, and generate more lift than needed to balance body weight. We compared observed glide performance with mathematical simulations that use constant force coefficients, a characteristic of equilibrium glides. Simulations with varying force coefficients, such as those of live squirrels, demonstrated better whole-glide performance compared with the theoretical equilibrium state. Using results from both the observed glides and the simulation, we describe the mechanics and execution of inter-tree glides, and then discuss how gliding behaviour may relate to the evolution of flapping flight. PMID:23256188

Glide performance and aerodynamics of non-equilibrium glides in northern flying squirrels (Glaucomys sabrinus).

PubMed

Bahlman, Joseph W; Swartz, Sharon M; Riskin, Daniel K; Breuer, Kenneth S

2013-03-06

Gliding is an efficient form of travel found in every major group of terrestrial vertebrates. Gliding is often modelled in equilibrium, where aerodynamic forces exactly balance body weight resulting in constant velocity. Although the equilibrium model is relevant for long-distance gliding, such as soaring by birds, it may not be realistic for shorter distances between trees. To understand the aerodynamics of inter-tree gliding, we used direct observation and mathematical modelling. We used videography (60-125 fps) to track and reconstruct the three-dimensional trajectories of northern flying squirrels (Glaucomys sabrinus) in nature. From their trajectories, we calculated velocities, aerodynamic forces and force coefficients. We determined that flying squirrels do not glide at equilibrium, and instead demonstrate continuously changing velocities, forces and force coefficients, and generate more lift than needed to balance body weight. We compared observed glide performance with mathematical simulations that use constant force coefficients, a characteristic of equilibrium glides. Simulations with varying force coefficients, such as those of live squirrels, demonstrated better whole-glide performance compared with the theoretical equilibrium state. Using results from both the observed glides and the simulation, we describe the mechanics and execution of inter-tree glides, and then discuss how gliding behaviour may relate to the evolution of flapping flight.

System Analysis by Mapping a Fault-tree into a Bayesian-network

NASA Astrophysics Data System (ADS)

Sheng, B.; Deng, C.; Wang, Y. H.; Tang, L. H.

2018-05-01

In view of the limitations of fault tree analysis in reliability assessment, Bayesian Network (BN) has been studied as an alternative technology. After a brief introduction to the method for mapping a Fault Tree (FT) into an equivalent BN, equations used to calculate the structure importance degree, the probability importance degree and the critical importance degree are presented. Furthermore, the correctness of these equations is proved mathematically. Combining with an aircraft landing gear’s FT, an equivalent BN is developed and analysed. The results show that richer and more accurate information have been achieved through the BN method than the FT, which demonstrates that the BN is a superior technique in both reliability assessment and fault diagnosis.

Are There Infinite Irrigation Trees?

NASA Astrophysics Data System (ADS)

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

2006-08-01

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

Measuring Growth on a Museum Field Trip: Dinosaur Bones and Tree Cross Sections

ERIC Educational Resources Information Center

Sedzielarz, Maija; Robinson, Christopher

2007-01-01

The MathPacks program at the Science Museum of Minnesota provides students with in-depth understanding of real-world applications of mathematics and science. Students measure museum specimens and investigate ratios, patterns, and mapping while simulating the work of scientists.

Babbage, Charles (1792-1871)

NASA Astrophysics Data System (ADS)

Murdin, P.

2000-11-01

Polymath, eleventh Lucasian Professor at Cambridge. Known not only for work on astronomy but also in cryptanalysis, probability, geophysics, altimetry, ophthalmoscopy, statistical linguistics, meteorology, actuarial science, lighthouse technology, the use of tree rings as historic climatic records, magnetism, biology, geology, religion, submarines, politics, economics and mathematics. Most import...

Fitting a Structured Juvenile-Adult Model for Green Tree Frogs to Population Estimates from Capture-Mark-Recapture Field Data

USGS Publications Warehouse

Ackleh, A.S.; Carter, J.; Deng, K.; Huang, Q.; Pal, N.; Yang, X.

2012-01-01

We derive point and interval estimates for an urban population of green tree frogs (Hyla cinerea) from capture-mark-recapture field data obtained during the years 2006-2009. We present an infinite-dimensional least-squares approach which compares a mathematical population model to the statistical population estimates obtained from the field data. The model is composed of nonlinear first-order hyperbolic equations describing the dynamics of the amphibian population where individuals are divided into juveniles (tadpoles) and adults (frogs). To solve the least-squares problem, an explicit finite difference approximation is developed. Convergence results for the computed parameters are presented. Parameter estimates for the vital rates of juveniles and adults are obtained, and standard deviations for these estimates are computed. Numerical results for the model sensitivity with respect to these parameters are given. Finally, the above-mentioned parameter estimates are used to illustrate the long-time behavior of the population under investigation. ?? 2011 Society for Mathematical Biology.

Mathematical structure of unit systems

NASA Astrophysics Data System (ADS)

Kitano, Masao

2013-05-01

We investigate the mathematical structure of unit systems and the relations between them. Looking over the entire set of unit systems, we can find a mathematical structure that is called preorder (or quasi-order). For some pair of unit systems, there exists a relation of preorder such that one unit system is transferable to the other unit system. The transfer (or conversion) is possible only when all of the quantities distinguishable in the latter system are always distinguishable in the former system. By utilizing this structure, we can systematically compare the representations in different unit systems. Especially, the equivalence class of unit systems (EUS) plays an important role because the representations of physical quantities and equations are of the same form in unit systems belonging to an EUS. The dimension of quantities is uniquely defined in each EUS. The EUS's form a partially ordered set. Using these mathematical structures, unit systems and EUS's are systematically classified and organized as a hierarchical tree.

A Simulator for the Respiratory Tree in Healthy Subjects Derived from Continued Fractions Expansions

NASA Astrophysics Data System (ADS)

Muntean, Ionuţ; Ionescu, Clara; Naşcu, Ioan

2009-04-01

Taking into account the self-similar recurrent geometrical structure of the human respiratory tree, the total respiratory impedance can be represented using an electrical equivalent of a ladder network model. In this paper, the parameters of the respiratory tree are employed in simulation, based on clinical insight and morphology. Once the transfer function of the total input impedance model is calculated, it is further interpreted in its continued fraction expansion form. The purpose is to compare the ladder network structure with the continuous fraction expansion form of the impedance. The results are supporting the theory of fractional-order impedance appearance (also known as constant-phase behaviour) and help understanding the mathematical and morphological basis for constructing a physiology-based simulator of the human lungs.

Automatic extraction of tree crowns from aerial imagery in urban environment

NASA Astrophysics Data System (ADS)

Liu, Jiahang; Li, Deren; Qin, Xunwen; Yang, Jianfeng

2006-10-01

Traditionally, field-based investigation is the main method to investigate greenbelt in urban environment, which is costly and low updating frequency. In higher resolution image, the imagery structure and texture of tree canopy has great similarity in statistics despite the great difference in configurations of tree canopy, and their surface structures and textures of tree crown are very different from the other types. In this paper, we present an automatic method to detect tree crowns using high resolution image in urban environment without any apriori knowledge. Our method catches unique structure and texture of tree crown surface, use variance and mathematical expectation of defined image window to position the candidate canopy blocks coarsely, then analysis their inner structure and texture to refine these candidate blocks. The possible spans of all the feature parameters used in our method automatically generate from the small number of samples, and HOLE and its distribution as an important characteristics are introduced into refining processing. Also the isotropy of candidate image block and holes' distribution is integrated in our method. After introduction the theory of our method, aerial imageries were used ( with a resolution about 0.3m ) to test our method, and the results indicate that our method is an effective approach to automatically detect tree crown in urban environment.

Synchronizing Fireflies

ERIC Educational Resources Information Center

Zhou, Ying; Gall, Walter; Nabb, Karen Mayumi

2006-01-01

"Imagine a tenth of a mile of river front with an unbroken line of trees with fireflies on ever leaf flashing in synchronism. ... Then, if one's imagination is sufficiently vivid, he may form some conception of this amazing spectacle." So wrote the naturalist Hugh Smith. In this article we consider how one might model mathematically the…

How-to-Do-It: An Interdisciplinary Approach to Forestry Education.

ERIC Educational Resources Information Center

Zipko, Stephen J.

1983-01-01

Describes a four- to six-week minicourse featuring topics from language arts, law, history, sociology, mathematics, art, and woodworking in addition to botany, zoology, genetics, ecology, and evolution. Student study is divided into five phases: tree-ring analysis; forest history; seedling competition; genetic improvement and cloning; and a…

Activities in Mathematics and Science for Young Children Using the School Yard.

ERIC Educational Resources Information Center

Williams, Robert; Sherwood, Elizabeth

1982-01-01

Activity topics suggested were selected from the many areas of study which can be drawn from the outdoor school environment: See That Tree; Time Passing; Critters; and Digging in the Dirt. The ideas shared are intended as a beginning on which teachers and children can build. (MP)

Growing Together with the Treetures. Activity Guide. Series 1.

ERIC Educational Resources Information Center

Schnell, Bobbi; Blau, Judith H.; Hinrichs, Jennifer Judd

This activity guide is designed to be used with the Growing Together program. Tree-related activities are correlated to the Benchmarks for Scientific Literacy, the recommended standards for mathematics, science, and technology suggested by the American Association for the Advancement of Science (AAAS). The Treature Educational Program is dedicated…

Modeling bidirectional reflectance of forests and woodlands using Boolean models and geometric optics

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Jupp, David L. B.

1990-01-01

Geometric-optical discrete-element mathematical models for forest canopies have been developed using the Boolean logic and models of Serra. The geometric-optical approach is considered to be particularly well suited to describing the bidirectional reflectance of forest woodland canopies, where the concentration of leaf material within crowns and the resulting between-tree gaps make plane-parallel, radiative-transfer models inappropriate. The approach leads to invertible formulations, in which the spatial and directional variance provides the means for remote estimation of tree crown size, shape, and total cover from remotedly sensed imagery.

Transport through a network of capillaries from ultrametric diffusion equation with quadratic nonlinearity

NASA Astrophysics Data System (ADS)

Oleschko, K.; Khrennikov, A.

2017-10-01

This paper is about a novel mathematical framework to model transport (of, e.g., fluid or gas) through networks of capillaries. This framework takes into account the tree structure of the networks of capillaries. (Roughly speaking, we use the tree-like system of coordinates.) As is well known, tree-geometry can be topologically described as the geometry of an ultrametric space, i.e., a metric space in which the metric satisfies the strong triangle inequality: in each triangle, the third side is less than or equal to the maximum of two other sides. Thus transport (e.g., of oil or emulsion of oil and water in porous media, or blood and air in biological organisms) through networks of capillaries can be mathematically modelled as ultrametric diffusion. Such modelling was performed in a series of recently published papers of the authors. However, the process of transport through capillaries can be only approximately described by the linear diffusion, because the concentration of, e.g., oil droplets, in a capillary can essentially modify the dynamics. Therefore nonlinear dynamical equations provide a more adequate model of transport in a network of capillaries. We consider a nonlinear ultrametric diffusion equation with quadratic nonlinearity - to model transport in such a network. Here, as in the linear case, we apply the theory of ultrametric wavelets. The paper also contains a simple introduction to theory of ultrametric spaces and analysis on them.

Stemflow acid neutralization capacity in a broadleaved deciduous forest: the role of edge effects.

PubMed

Shiklomanov, Alexey N; Levia, Delphis F

2014-10-01

Atmospheric deposition is an important pathway for moisture, nutrient, and pollutant exchange among the atmosphere, forest, and soils. Previous work has shown the importance of proximity to the forest edge to chemical fluxes in throughfall, but far less research has considered stemflow. This study examined the difference in acid neutralization capacity (ANC) of stemflow of nineteen Liriodendron tulipifera L. (yellow poplar) trees between the forest edge and interior in a rural area of northeastern Maryland. We measured ANC directly via potentiometric titration. Stemflow from trees at the forest edge was found to have significantly higher and more variable pH and ANC than in the forest interior (p < 0.01). No mathematical trend between ANC and distance to the forest edge was observed, indicating the importance of individual tree characteristics in stemflow production and chemistry. These results reaffirm the importance of stemflow for acid neutralization by deciduous tree species. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Competitiveness of biomass-fueled electrical power plants.

Treesearch

Bruce A. McCarl; Darius M. Adams; Ralph J. Alig; John T. Chmelik

2000-01-01

One way countries like the United States can comply with suggested rollbacks in greenhouse gas emissions is by employing power plants fueled with biomass. We examine the competitiveness of biomass-based fuel for electrical power as opposed to coal using a mathematical programming structure. We consider fueling power plants from milling residues, whole trees, logging...

[Research advances in mathematical model of coniferous trees cold hardiness].

PubMed

Zhang, Gang; Wang, Ai-Fang

2007-07-01

Plant cold hardiness has complicated attributes. This paper introduced the research advances in establishing the dynamic models of coniferous trees cold hardiness, with the advantages and disadvantages of the models presented and the further studies suggested. In the models established initially, temperature was concerned as the only environmental factor affecting the cold hardiness, and the concept of stationary level of cold hardiness was introduced. Due to the obvious prediction errors of these models, the stationary level of cold hardiness was modeled later by assuming the existence of an additive effect of temperature and photoperiod on the increase of cold hardiness. Furthermore, the responses of the annual development phases for cold hardiness to environment were considered. The model researchers have paid more attention to the additive effect models, and run some experiments to test the additivity principle. However, the research results on Scots pine (Pinus sylvestris) indicated that its organs did not support the presumption of an additive response of cold hardiness by temperature and photoperiod, and the interaction between environmental factors should be taken into account. The mathematical models of cold hardiness need to be developed and improved.

Automatic Classification of Trees from Laser Scanning Point Clouds

NASA Astrophysics Data System (ADS)

Sirmacek, B.; Lindenbergh, R.

2015-08-01

Development of laser scanning technologies has promoted tree monitoring studies to a new level, as the laser scanning point clouds enable accurate 3D measurements in a fast and environmental friendly manner. In this paper, we introduce a probability matrix computation based algorithm for automatically classifying laser scanning point clouds into 'tree' and 'non-tree' classes. Our method uses the 3D coordinates of the laser scanning points as input and generates a new point cloud which holds a label for each point indicating if it belongs to the 'tree' or 'non-tree' class. To do so, a grid surface is assigned to the lowest height level of the point cloud. The grids are filled with probability values which are calculated by checking the point density above the grid. Since the tree trunk locations appear with very high values in the probability matrix, selecting the local maxima of the grid surface help to detect the tree trunks. Further points are assigned to tree trunks if they appear in the close proximity of trunks. Since heavy mathematical computations (such as point cloud organization, detailed shape 3D detection methods, graph network generation) are not required, the proposed algorithm works very fast compared to the existing methods. The tree classification results are found reliable even on point clouds of cities containing many different objects. As the most significant weakness, false detection of light poles, traffic signs and other objects close to trees cannot be prevented. Nevertheless, the experimental results on mobile and airborne laser scanning point clouds indicate the possible usage of the algorithm as an important step for tree growth observation, tree counting and similar applications. While the laser scanning point cloud is giving opportunity to classify even very small trees, accuracy of the results is reduced in the low point density areas further away than the scanning location. These advantages and disadvantages of two laser scanning point cloud sources are discussed in detail.

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

PubMed

Gambette, Philippe; van Iersel, Leo; Kelk, Steven; Pardi, Fabio; Scornavacca, Celine

2016-09-01

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with one copy in all species can be explained by a given network. In mathematical terms, this is often translated in the following way: is a given phylogenetic tree contained in a given phylogenetic network? Recently this tree containment problem has been widely investigated from a computational perspective, but most studies have only focused on the topology of the phylogenies, ignoring a piece of information that, in the case of phylogenetic trees, is routinely inferred by evolutionary analyses: branch lengths. These measure the amount of change (e.g., nucleotide substitutions) that has occurred along each branch of the phylogeny. Here, we study a number of versions of the tree containment problem that explicitly account for branch lengths. We show that, although length information has the potential to locate more precisely a tree within a network, the problem is computationally hard in its most general form. On a positive note, for a number of special cases of biological relevance, we provide algorithms that solve this problem efficiently. This includes the case of networks of limited complexity, for which it is possible to recover, among the trees contained by the network with the same topology as the input tree, the closest one in terms of branch lengths.

Modeling the temporal dynamics of nonstructural carbohydrate pools in forest trees

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

Richardson, Andrew D.

Trees store carbohydrates, in the form of sugars and starch, as reserves to be used to power both future growth as well as to support day-to-day metabolic functions. These reserves are particularly important in the context of how trees cope with disturbance and stress—for example, as related to pest outbreaks, wind or ice damage, and extreme climate events. In this project, we measured the size of carbon reserves in forest trees, and determined how quickly these reserves are used and replaced—i.e., their “turnover time”. Our work was conducted at Harvard Forest, a temperate deciduous forest in central Massachusetts. Through fieldmore » sampling, laboratory-based chemical analyses, and allometric modeling, we scaled these measurements up to whole-tree NSC budgets. We used these data to test and improve computer simulation models of carbon flow through forest ecosystems. Our modeling focused on the mathematical representation of these stored carbon reserves, and we examined the sensitivity of model performance to different model structures. This project contributes to DOE’s goal to improve next-generation models of the earth system, and to understand the impacts of climate change on terrestrial ecosystems.« less

A Middle-School Classroom Inquiry: Estimating the Height of a Tree

ERIC Educational Resources Information Center

Watson, Jane; Brown, Natalie; Wright, Suzie; Skalicky, Jane

2011-01-01

There is an old saying that "there is more than one way to skin a cat." Such is the case with finding the height of tall objects, a task that people have been approximating for centuries. Following an article in the "Australian Primary Mathematics Classroom" (APMC) with methods appropriate for primary students (Brown, Watson,…

Joined-Up Reflections: Part 1

ERIC Educational Resources Information Center

Mason, John

2008-01-01

Just as the tree bridges the worlds of earth and air-light, transforming energies so that there is a flow of nutrients between these two worlds, so too teachers can be seen as bridges or mediators between the world of learners and the world of mathematics. In this speech, the author suggests that one of the principal roles for mathematics…

Wave processes in the human cardiovascular system: The measuring complex, computing models, and diagnostic analysis

NASA Astrophysics Data System (ADS)

Ganiev, R. F.; Reviznikov, D. L.; Rogoza, A. N.; Slastushenskiy, Yu. V.; Ukrainskiy, L. E.

2017-03-01

A description of a complex approach to investigation of nonlinear wave processes in the human cardiovascular system based on a combination of high-precision methods of measuring a pulse wave, mathematical methods of processing the empirical data, and methods of direct numerical modeling of hemodynamic processes in an arterial tree is given.

E-Learning Technologies: Employing Matlab Web Server to Facilitate the Education of Mathematical Programming

ERIC Educational Resources Information Center

Karagiannis, P.; Markelis, I.; Paparrizos, K.; Samaras, N.; Sifaleras, A.

2006-01-01

This paper presents new web-based educational software (webNetPro) for "Linear Network Programming." It includes many algorithms for "Network Optimization" problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such…

The Origins of Interest in Science and Mathematics.

ERIC Educational Resources Information Center

Miller, Jon D.

Children in the United States and other industrialized countries grow to adulthood in an age of science and technology. Satellites, television sets, microprocessors, and microwave ovens are as common as the sun and trees. The context of socialization to adulthood in the last half of the 20th century is far different in kind than any previous…

The Older of Two Trees: Young Children's Development of Operational Time

ERIC Educational Resources Information Center

Kamii, Constance; Russell, Kelly A.

2010-01-01

Piaget (1971) made a distinction between intuitive (preoperational) time and operational (logico-mathematical) time. According to Piaget, operational time develops around 7-8 years of age and is characterized by children's ability to deduce, for example, that if A was born before B, A will always be older than B. When time is still intuitive,…

How Do the Different Types of Computer Use Affect Math Achievement?

ERIC Educational Resources Information Center

Flores, Raymond; Inan, Fethi; Lin, Zhangxi

2013-01-01

In this study, the National Educational Longitudinal Study (ELS:2002) dataset was used and a predictive data mining technique, decision tree analysis, was implemented in order to examine which factors, in conjunction to computer use, can be used to predict high or low probability of success in high school mathematics. Specifically, this study…

Not the Norm: The Potential of Tree Analysis of Performance Data from Students in a Foundation Mathematics Module

ERIC Educational Resources Information Center

Kirby, Nicola; Dempster, Edith

2015-01-01

Quantitative methods of data analysis usually involve inferential statistics, and are not well known for their ability to reflect the intricacies of a diverse student population. The South African tertiary education sector is characterised by extreme inequality and diversity. Foundation programmes address issues of inequality of access by…

The Two-By-Two Array: An Aid in Conceptualization and Problem Solving

ERIC Educational Resources Information Center

Eberhart, James

2004-01-01

The fields of mathematics, science, and engineering are replete with diagrams of many varieties. They range in nature from the Venn diagrams of symbolic logic to the Periodic Chart of the Elements; and from the fault trees of risk assessment to the flow charts used to describe laboratory procedures, industrial processes, and computer programs. All…

Hyperplane arrangements, interval orders, and trees.

PubMed Central

Stanley, R P

1996-01-01

A hyperplane arrangement is a finite set of hyperplanes in a real affine space. An especially important arrangement is the braid arrangement, which is the set of all hyperplanes xi - xj = 1, 1

Fourier transform inequalities for phylogenetic trees.

PubMed

Matsen, Frederick A

2009-01-01

Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

Concept Model on Topological Learning

NASA Astrophysics Data System (ADS)

Ae, Tadashi; Kioi, Kazumasa

2010-11-01

We discuss a new model for concept based on topological learning, where the learning process on the neural network is represented by mathematical topology. The topological learning of neural networks is summarized by a quotient of input space and the hierarchical step induces a tree where each node corresponds to a quotient. In general, the concept acquisition is a difficult problem, but the emotion for a subject is represented by providing the questions to a person. Therefore, a kind of concept is captured by such data and the answer sheet can be mapped into a topology consisting of trees. In this paper, we will discuss a way of mapping the emotional concept to a topological learning model.

Maximal tree size of few-qubit states

NASA Astrophysics Data System (ADS)

Le, Huy Nguyen; Cai, Yu; Wu, Xingyao; Rabelo, Rafael; Scarani, Valerio

2014-06-01

Tree size (TS) is an interesting measure of complexity for multiqubit states: not only is it in principle computable, but one can obtain lower bounds for it. In this way, it has been possible to identify families of states whose complexity scales superpolynomially in the number of qubits. With the goal of progressing in the systematic study of the mathematical property of TS, in this work we characterize the tree size of pure states for the case where the number of qubits is small, namely, 3 or 4. The study of three qubits does not hold great surprises, insofar as the structure of entanglement is rather simple; the maximal TS is found to be 8, reached for instance by the |W> state. The study of four qubits yields several insights: in particular, the most economic description of a state is found not to be recursive. The maximal TS is found to be 16, reached for instance by a state called |Ψ(4)> which was already discussed in the context of four-photon down-conversion experiments. We also find that the states with maximal tree size form a set of zero measure: a smoothed version of tree size over a neighborhood of a state (ɛ-TS) reduces the maximal values to 6 and 14, respectively. Finally, we introduce a notion of tree size for mixed states and discuss it for a one-parameter family of states.

DBH Prediction Using Allometry Described by Bivariate Copula Distribution

NASA Astrophysics Data System (ADS)

Xu, Q.; Hou, Z.; Li, B.; Greenberg, J. A.

2017-12-01

Forest biomass mapping based on single tree detection from the airborne laser scanning (ALS) usually depends on an allometric equation that relates diameter at breast height (DBH) with per-tree aboveground biomass. The incapability of the ALS technology in directly measuring DBH leads to the need to predict DBH with other ALS-measured tree-level structural parameters. A copula-based method is proposed in the study to predict DBH with the ALS-measured tree height and crown diameter using a dataset measured in the Lassen National Forest in California. Instead of exploring an explicit mathematical equation that explains the underlying relationship between DBH and other structural parameters, the copula-based prediction method utilizes the dependency between cumulative distributions of these variables, and solves the DBH based on an assumption that for a single tree, the cumulative probability of each structural parameter is identical. Results show that compared with the bench-marking least-square linear regression and the k-MSN imputation, the copula-based method obtains better accuracy in the DBH for the Lassen National Forest. To assess the generalization of the proposed method, prediction uncertainty is quantified using bootstrapping techniques that examine the variability of the RMSE of the predicted DBH. We find that the copula distribution is reliable in describing the allometric relationship between tree-level structural parameters, and it contributes to the reduction of prediction uncertainty.

Response of advance lodgepole pine regeneration to overstory removal in eastern Idaho

Treesearch

Tanya E. Lewis Murphy; David L. Adams; Dennis E. Ferguson

1999-01-01

Twenty-two stands of advance lodgepole pine released with overstory removal were sampled to determine height growth response. Tree and site characteristics correlated with release response were identified, and a mathematical model was developed to predict height growth in years 6 through 10 after release as a function of residual overstory basal area, height at release...

The Contribution of Human Factors in Military System Development: Methodological Considerations

DTIC Science & Technology

1980-07-01

Risk/Uncertainty Analysis - Project Scoring - Utility Scales - Relevance Tree Techniques (Reverse Factor Analysis) 2. Computer Simulation Simulation...effectiveness of mathematical models for R&D project selection. Management Science, April 1973, 18. 6-43 .1~ *.-. Souder, W.E. h scoring methodology for...per some interval PROFICIENCY test scores (written) RADIATION radiation effects aircrew performance on radiation environments REACTION TIME 1) (time

Complex compatible taper and volume estimation systems for red and loblolly pine

Treesearch

John C. Byrne; David D. Reed

1986-01-01

Five equation systems are described which can be used to estimate upper stem diameter, total individual tree cubic-foot volume, and merchantable cubic-foot volumes to any merchantability imit (expressed in terms of diameter or height), both inside and outside bark. The equations provide consistent results since they are mathematically related and are fit using stem...

Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

PubMed

Strohm, S; Tyson, R C; Powell, J A

2013-10-01

Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

Coupled 0D-1D CFD Modeling of Right Heart and Pulmonary Artery Morphometry Tree

NASA Astrophysics Data System (ADS)

Dong, Melody; Yang, Weiguang; Feinstein, Jeffrey A.; Marsden, Alison

2017-11-01

Pulmonary arterial hypertension (PAH) is characterized by elevated pulmonary artery (PA) pressure and remodeling of the distal PAs resulting in right ventricular (RV) dysfunction and failure. It is hypothesized that patients with untreated ventricular septal defects (VSD) may develop PAH due to elevated flows and pressures in the PAs. Wall shear stress (WSS), due to elevated flows, and circumferential stress, due to elevated pressures, are known to play a role in vascular mechanobiology. Thus, simulating VSD hemodynamics and wall mechanics may facilitate our understanding of mechanical stimuli leading to PAH initiation and progression. Although 3D CFD models can capture detailed hemodynamics in the proximal PAs, they cannot easily model hemodynamics and wave propagation in the distal PAs, where remodeling occurs. To improve current PA models, we will present a new method that couples distal PA hemodynamics with RV function. Our model couples a 0D lumped parameter model of the RV to a 1D model of the PA tree, based on human PA morphometry data, to characterize RV performance and WSS changes in the PA tree. We will compare a VSD 0D-1D model and a 0D-3D model coupled to a mathematical morphometry tree model to quantify WSS in the entire PA vascular tree.

Operational forest management planning methods: proceedings, meeting of steering systems project group, International Union of Forestry Research Organizations, Bucharest, Romania, June 18-24, 1978

Treesearch

Daniel Navon

1978-01-01

These 14 papers were submitted to a conference of Project Group P4.07 Division IV, International Union of Forestry Research Organizations. Topics discussed included the uses of simulations, analytical techniques, and mathematical programming techniques in land management planning, reforestation programs, intensive forestry, timber management and production, tree growth...

The sine method as a more accurate height predictor for hardwoods

Treesearch

Don C. Bragg

2007-01-01

Most hypsometers apply a mathematical technique that utilizes the tangent of angles and a horizontal distance to deliver the exact height of a tree under idealized circumstances. Unfortunately, these conditions are rarely met for hardwoods in the field. A “new” predictor based on sine and slope distance and discussed here does not require the same assumptions for...

The NASA SCI Files[TM]: The Case of the Shaky Quake. A Lesson Guide with Activities in Mathematics, Science, and Technology.

ERIC Educational Resources Information Center

Ricles, Shannon

The NASA SCI Files is a series of instructional programs consisting of broadcast, print, and online elements emphasizing standards-based instruction, problem-based learning, and science as inquiry. The series seeks to motivate students in grades 3-5 to become critical thinkers and active problem solvers. In this program, the tree house detectives…

Computer-based synthetic data to assess the tree delineation algorithm from airborne LiDAR survey

Treesearch

Lei Wang; Andrew G. Birt; Charles W. Lafon; David M. Cairns; Robert N. Coulson; Maria D. Tchakerian; Weimin Xi; Sorin C. Popescu; James M. Guldin

2013-01-01

Small Footprint LiDAR (Light Detection And Ranging) has been proposed as an effective tool for measuring detailed biophysical characteristics of forests over broad spatial scales. However, by itself LiDAR yields only a sample of the true 3D structure of a forest. In order to extract useful forestry relevant information, this data must be interpreted using mathematical...

Comparison of different tree sap flow up-scaling procedures using Monte-Carlo simulations

NASA Astrophysics Data System (ADS)

Tatarinov, Fyodor; Preisler, Yakir; Roahtyn, Shani; Yakir, Dan

2015-04-01

An important task in determining forest ecosystem water balance is the estimation of stand transpiration, allowing separating evapotranspiration into transpiration and soil evaporation. This can be based on up-scaling measurements of sap flow in representative trees (SF), which can be done by different mathematical algorithms. The aim of the present study was to evaluate the error associated with different up-scaling algorithms under different conditions. Other types of errors (such as, measurement error, within tree SF variability, choice of sample plot etc.) were not considered here. A set of simulation experiments using Monte-Carlo technique was carried out and three up-scaling procedures were tested. (1) Multiplying mean stand sap flux density based on unit sapwood cross-section area (SFD) by total sapwood area (Klein et al, 2014); (2) deriving of linear dependence of tree sap flow on tree DBH and calculating SFstand using predicted SF by DBH classes and stand DBH distribution (Cermak et al., 2004); (3) same as method 2 but using non-linear dependency. Simulations were performed under different SFD(DBH) slope (bs, positive, negative, zero); different DBH and SFD standard deviations (Δd and Δs, respectively) and DBH class size. It was assumed that all trees in a unit area are measured and the total SF of all trees in the experimental plot was taken as the reference SFstand value. Under negative bs all models tend to overestimate SFstand and the error increases exponentially with decreasing bs. Under bs >0 all models tend to underestimate SFstand, but the error is much smaller than for bs

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

PubMed Central

Xu, Bo; Yang, Ziheng

2016-01-01

The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods. PMID:27927902

Graph Theory Roots of Spatial Operators for Kinematics and Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2011-01-01

Spatial operators have been used to analyze the dynamics of robotic multibody systems and to develop novel computational dynamics algorithms. Mass matrix factorization, inversion, diagonalization, and linearization are among several new insights obtained using such operators. While initially developed for serial rigid body manipulators, the spatial operators and the related mathematical analysis have been shown to extend very broadly including to tree and closed topology systems, to systems with flexible joints, links, etc. This work uses concepts from graph theory to explore the mathematical foundations of spatial operators. The goal is to study and characterize the properties of the spatial operators at an abstract level so that they can be applied to a broader range of dynamics problems. The rich mathematical properties of the kinematics and dynamics of robotic multibody systems has been an area of strong research interest for several decades. These properties are important to understand the inherent physical behavior of systems, for stability and control analysis, for the development of computational algorithms, and for model development of faithful models. Recurring patterns in spatial operators leads one to ask the more abstract question about the properties and characteristics of spatial operators that make them so broadly applicable. The idea is to step back from the specific application systems, and understand more deeply the generic requirements and properties of spatial operators, so that the insights and techniques are readily available across different kinematics and dynamics problems. In this work, techniques from graph theory were used to explore the abstract basis for the spatial operators. The close relationship between the mathematical properties of adjacency matrices for graphs and those of spatial operators and their kernels were established. The connections hold across very basic requirements on the system topology, the nature of the component bodies, the indexing schemes, etc. The relationship of the underlying structure is intimately connected with efficient, recursive computational algorithms. The results provide the foundational groundwork for a much broader look at the key problems in kinematics and dynamics. The properties of general graphs and trees of nodes and edge were examined, as well as the properties of adjacency matrices that are used to describe graph connectivity. The nilpotency property of such matrices for directed trees was reviewed, and the adjacency matrices were generalized to the notion of block weighted adjacency matrices that support block matrix elements. This leads us to the development of the notion of Spatial Kernel Operator SKO kernels. These kernels provide the basis for the development of SKO resolvent operators.

Propensity score estimation: neural networks, support vector machines, decision trees (CART), and meta-classifiers as alternatives to logistic regression.

PubMed

Westreich, Daniel; Lessler, Justin; Funk, Michele Jonsson

2010-08-01

Propensity scores for the analysis of observational data are typically estimated using logistic regression. Our objective in this review was to assess machine learning alternatives to logistic regression, which may accomplish the same goals but with fewer assumptions or greater accuracy. We identified alternative methods for propensity score estimation and/or classification from the public health, biostatistics, discrete mathematics, and computer science literature, and evaluated these algorithms for applicability to the problem of propensity score estimation, potential advantages over logistic regression, and ease of use. We identified four techniques as alternatives to logistic regression: neural networks, support vector machines, decision trees (classification and regression trees [CART]), and meta-classifiers (in particular, boosting). Although the assumptions of logistic regression are well understood, those assumptions are frequently ignored. All four alternatives have advantages and disadvantages compared with logistic regression. Boosting (meta-classifiers) and, to a lesser extent, decision trees (particularly CART), appear to be most promising for use in the context of propensity score analysis, but extensive simulation studies are needed to establish their utility in practice. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Numerical study of propagation of forest fires in the presence of fire breaks using an averaged setting

NASA Astrophysics Data System (ADS)

Marzaeva, S. I.; Galtseva, O. V.

2018-05-01

The forest fires spread in the pine forests have been numerically simulated using a three-dimensional mathematical model. The model was integrated with respect to the vertical coordinate because horizontal sizes of forest are much greater than the heights of trees. In this paper, the assignment and theoretical investigations of the problems of crown forest fires spread pass the firebreaks were carried out. In this context, a study ( mathematical modeling) of the conditions of forest fire spreading that would make it possible to obtain a detailed picture of the change in the temperature and component concentration fields with time, and determine as well as the limiting condition of fire propagation in forest with these fire breaks.

Percolating Contact Subnetworks on the Edge of Isostaticity

DTIC Science & Technology

2011-01-01

pressure, and cyclic loading of photoelastic disks under constant vol- ume. D. M. Walker · A. Tordesillas (B) Department of Mathematics and Statistics ...Complex networks · Spanning trees · Force chains · Force cycles · Isostatic 1 Introduction Ioannis Vardoulakis and his collaborators brought soil ...57, 706–727 (2009) 2. Vardoulakis, I.: Shear-banding and liquefaction in granular mate- rials on the basis of a Cosserat continuum theory. Ingenieur

Cosmic clustering

DOE PAGES

Anninos, Dionysios; Denef, Frederik

2016-06-30

We show that the late time Hartle-Hawking wave function for a free massless scalar in a fixed de Sitter background encodes a sharp ultrametric structure for the standard Euclidean distance on the space of field configurations. This implies a hierarchical, tree-like organization of the state space, reflecting its genesis as a branched diffusion process. In conclusion, an equivalent mathematical structure organizes the state space of the Sherrington-Kirkpatrick model of a spin glass.

New Splitting Criteria for Decision Trees in Stationary Data Streams.

PubMed

Jaworski, Maciej; Duda, Piotr; Rutkowski, Leszek; Jaworski, Maciej; Duda, Piotr; Rutkowski, Leszek; Rutkowski, Leszek; Duda, Piotr; Jaworski, Maciej

2018-06-01

The most popular tools for stream data mining are based on decision trees. In previous 15 years, all designed methods, headed by the very fast decision tree algorithm, relayed on Hoeffding's inequality and hundreds of researchers followed this scheme. Recently, we have demonstrated that although the Hoeffding decision trees are an effective tool for dealing with stream data, they are a purely heuristic procedure; for example, classical decision trees such as ID3 or CART cannot be adopted to data stream mining using Hoeffding's inequality. Therefore, there is an urgent need to develop new algorithms, which are both mathematically justified and characterized by good performance. In this paper, we address this problem by developing a family of new splitting criteria for classification in stationary data streams and investigating their probabilistic properties. The new criteria, derived using appropriate statistical tools, are based on the misclassification error and the Gini index impurity measures. The general division of splitting criteria into two types is proposed. Attributes chosen based on type- splitting criteria guarantee, with high probability, the highest expected value of split measure. Type- criteria ensure that the chosen attribute is the same, with high probability, as it would be chosen based on the whole infinite data stream. Moreover, in this paper, two hybrid splitting criteria are proposed, which are the combinations of single criteria based on the misclassification error and Gini index.

The equivalence of two phylogenetic biodiversity measures: the Shapley value and Fair Proportion index.

PubMed

Hartmann, Klaas

2013-11-01

Most biodiversity conservation programs are forced to prioritise species in order to allocate their funding. This paper contains a mathematical proof that provides biological support for one common approach based on phylogenetic indices. Phylogenetic trees describe the evolutionary relationships between a group of taxa. Two indices for computing the distinctiveness of each taxon in a phylogenetic tree are considered here-the Shapley value and the Fair Proportion index. These indices provide a measure of the importance of each taxon for overall biodiversity and have been used to prioritise taxa for conservation. The Shapley value is the biodiversity contribution a taxon is expected to make if all taxa are equally likely to become extinct. This interpretation makes it appealing to use the Shapley value in biodiversity conservation applications. The Fair Proportion index lacks a convenient interpretation, however it is significantly easier to calculate and understand. It has been empirically observed that there is a high correlation between the two indices. This paper shows the mathematical basis for this correlation and proves that as the number of taxa increases, the indices become equivalent. Consequently in biodiversity prioritisation the simpler Fair Proportion index can be used whilst retaining the appealing interpretation of the Shapley value.

2HOT: An Improved Parallel Hashed Oct-Tree N-Body Algorithm for Cosmological Simulation

DOE PAGES

Warren, Michael S.

2014-01-01

We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up to 256k (2 18 ) processors. We present error analysis and scientific application results from a series of more than ten 69 billion (4096 3 ) particle cosmological simulations, accounting for 4×10 20 floating point operations. These results include the first simulations using the new constraints on the standard model of cosmology from the Planck satellite. Our simulations set a new standard for accuracy andmore » scientific throughput, while meeting or exceeding the computational efficiency of the latest generation of hybrid TreePM N-body methods.« less

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

Ghost vertices for the bosonic string using the group-theoretic approach to string theory

NASA Astrophysics Data System (ADS)

Freeman, M. D.; West, P.

1988-04-01

The N-string tree-level scattering vertices for the bosonic string are extended to include anticommuting (ghost) oscillators. These vertices behave correctly under the action of the BRST charge Q and reproduce the known results for the scattering of physical states. This work is an application of the group-theoretic approach to string theory. Permanent address: Mathematics Department, King's College, Strand, London WC2R 2LS, UK.

JPRS Report, East Europe

DTIC Science & Technology

1990-04-16

Life movement, today auton- believe that if in 1965 there was initiated a competition omous and standing next to the Youth Union as an equal in artistic ...words. Tree of Life is entering performances, exhibits of new artists . At the Mathematics- the third year of camps in the womb of the emerging Physics...a monthly organ, which has a costly layout, of half-truths. Continuously supported by hundreds of the executive committee of the German Gymnastics

Modeling the survival kinetics of Salmonella in tree nuts for use in risk assessment.

PubMed

Santillana Farakos, Sofia M; Pouillot, Régis; Anderson, Nathan; Johnson, Rhoma; Son, Insook; Van Doren, Jane

2016-06-16

Salmonella has been shown to survive in tree nuts over long periods of time. This survival capacity and its variability are key elements for risk assessment of Salmonella in tree nuts. The aim of this study was to develop a mathematical model to predict survival of Salmonella in tree nuts at ambient storage temperatures that considers variability and uncertainty separately and can easily be incorporated into a risk assessment model. Data on Salmonella survival on raw almonds, pecans, pistachios and walnuts were collected from the peer reviewed literature. The Weibull model was chosen as the baseline model and various fixed effect and mixed effect models were fit to the data. The best model identified through statistical analysis testing was then used to develop a hierarchical Bayesian model. Salmonella in tree nuts showed slow declines at temperatures ranging from 21°C to 24°C. A high degree of variability in survival was observed across tree nut studies reported in the literature. Statistical analysis results indicated that the best applicable model was a mixed effect model that included a fixed and random variation of δ per tree nut (which is the time it takes for the first log10 reduction) and a fixed variation of ρ per tree nut (parameter which defines the shape of the curve). Higher estimated survival rates (δ) were obtained for Salmonella on pistachios, followed in decreasing order by pecans, almonds and walnuts. The posterior distributions obtained from Bayesian inference were used to estimate the variability in the log10 decrease levels in survival for each tree nut, and the uncertainty of these estimates. These modeled uncertainty and variability distributions of the estimates can be used to obtain a complete exposure assessment of Salmonella in tree nuts when including time-temperature parameters for storage and consumption data. The statistical approach presented in this study may be applied to any studies that aim to develop predictive models to be implemented in a probabilistic exposure assessment or a quantitative microbial risk assessment. Published by Elsevier B.V.

Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity.

PubMed

King, Brian R; Aburdene, Maurice; Thompson, Alex; Warres, Zach

2014-01-01

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

PubMed Central

Vallat, Brinda Kizhakke; Pillardy, Jaroslaw; Elber, Ron

2010-01-01

The first step in homology modeling is to identify a template protein for the target sequence. The template structure is used in later phases of the calculation to construct an atomically detailed model for the target. We have built from the Protein Data Bank a large-scale learning set that includes tens of millions of pair matches that can be either a true template or a false one. Discriminatory learning (learning from positive and negative examples) is employed to train a decision tree. Each branch of the tree is a mathematical programming model. The decision tree is tested on an independent set from PDB entries and on the sequences of CASP7. It provides significant enrichment of true templates (between 50-100 percent) when compared to PSI-BLAST. The model is further verified by building atomically detailed structures for each of the tentative true templates with modeller. The probability that a true match does not yield an acceptable structural model (within 6Å RMSD from the native structure), decays linearly as a function of the TM structural-alignment score. PMID:18300226

The algebra of the general Markov model on phylogenetic trees and networks.

PubMed

Sumner, J G; Holland, B R; Jarvis, P D

2012-04-01

It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the “splitting” operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.

Theoretical and empirical evidence for the relationship between stem diameter variations and the water status of mature temperate trees

NASA Astrophysics Data System (ADS)

Dietrich, Lars; Zweifel, Roman; Kahmen, Ansgar

2017-04-01

Assessing a trees' water status is essential to evaluate its water status during drought. In particular for mature trees it is extremely difficult to monitor the water status throughout the growing season because of the difficulty of canopy access. Daily variations of stem diameter (SDV) are discussed to provide a powerful alternative in measuring a trees' water status. SDV have been shown to incorporate both radial growth and the diurnal shrinkage and swelling of bark tissue, which is caused by daytime transpiration and nighttime refilling, respectively. During dry periods, bark tissue that is depleted in water cannot entirely refill at night resulting in a progressive overall shrinkage of the tree's stem diameter often called tree water deficit (TWD). Comprehensive comparisons of SDV-based values for TWD and reliable values of stem water potential are yet missing for mature trees. As such, TWD has not yet been fully established as a simple and continuous proxy for a trees' water status. Using a canopy crane situated in Northern Switzerland, we calculated TWD based on SDV for six Central European forest tree species during one moist (2014) and one exceptionally dry (2015) growing season and compared these values to the trees' branch water potential. We found a tight relationship between branch water potential and TWD in all six species. We further employed four different mathematical approaches to calculate TWD and tested what approach yielded the best relationship with water potential. Most approaches resulted in significant relationships (p < 0.001) for the different species. However, one TWD variable showed the highest explanatory power (R2) across the six species and both years (up to 86 % explained variation). Intriguingly, this variable does not account for radial growth during periods of shrinkage in its calculation indicating that plastic growth is impeded in such times. The relationship between TWD and stem water potential can best be explained by logistic functions. We propose that, based on such a function, TWD can be employed to estimate stem water potential of trees for an entire growing season. We conclude from our data that TWD is tightly correlated to the stem water potential of mature tree species and can, thus, be used to describe continuous seasonal variations in a tree's water status. Because of its relatively easy application and deployment, there is high potential for this method to play a major role in future investigations of tree water relations.

The Case of the Great Space Exploration: An Educator Guide with Activities in Mathematics, Science, and Technology. The NASA SCI Files. EG-2004-09-12-LARC

ERIC Educational Resources Information Center

Ricles, Shannon; Jaramillo, Becky; Fargo, Michelle

2004-01-01

In this companion to the "NASA SCI Files" episode "The Case of the Great Space Exploration," the tree house detectives learn about NASA's new vision for exploring space. In four segments aimed at grades 3-5, students learn about a variety of aspects of space exploration. Each segment of the guide includes an overview, a set of objectives,…

The Computational Complexity of Two-Level Morphology,

DTIC Science & Technology

1985-11-01

nent of t, KIMM() system described ;L specified in Gajek rt al. (1983). Au actiml instance of KIMM() IIE(’O(NITI()N will be any possible instance (A...word features are being recovered in this mathematical reduction. The detailed format of the dictionary component is described in Gajek et al. (1083...forms for automata, a id letter trees for lexicons ( Gajek et al., 1983). Hence one question to address is whether the complexity implied by the

Temporal Subtraction of Digital Breast Tomosynthesis Images for Improved Mass Detection

DTIC Science & Technology

2008-10-01

K. Fishman and B. M. W. Tsui, "Development of a computer-generated model for the coronary arterial tree based on multislice CT and morphometric data...mathematical models based on geometric primitives8-22. Bakic et al created synthetic x-ray mammograms using a 3D simulated breast tissue model consisting of...utilized a combination of voxel matrices and geometric primitives to create a breast phantom that includes the breast surface, the duct system, and

Estimating babassu palm density using automatic palm tree detection with very high spatial resolution satellite images.

PubMed

Dos Santos, Alessio Moreira; Mitja, Danielle; Delaître, Eric; Demagistri, Laurent; de Souza Miranda, Izildinha; Libourel, Thérèse; Petit, Michel

2017-05-15

High spatial resolution images as well as image processing and object detection algorithms are recent technologies that aid the study of biodiversity and commercial plantations of forest species. This paper seeks to contribute knowledge regarding the use of these technologies by studying randomly dispersed native palm tree. Here, we analyze the automatic detection of large circular crown (LCC) palm tree using a high spatial resolution panchromatic GeoEye image (0.50 m) taken on the area of a community of small agricultural farms in the Brazilian Amazon. We also propose auxiliary methods to estimate the density of the LCC palm tree Attalea speciosa (babassu) based on the detection results. We used the "Compt-palm" algorithm based on the detection of palm tree shadows in open areas via mathematical morphology techniques and the spatial information was validated using field methods (i.e. structural census and georeferencing). The algorithm recognized individuals in life stages 5 and 6, and the extraction percentage, branching factor and quality percentage factors were used to evaluate its performance. A principal components analysis showed that the structure of the studied species differs from other species. Approximately 96% of the babassu individuals in stage 6 were detected. These individuals had significantly smaller stipes than the undetected ones. In turn, 60% of the stage 5 babassu individuals were detected, showing significantly a different total height and a different number of leaves from the undetected ones. Our calculations regarding resource availability indicate that 6870 ha contained 25,015 adult babassu palm tree, with an annual potential productivity of 27.4 t of almond oil. The detection of LCC palm tree and the implementation of auxiliary field methods to estimate babassu density is an important first step to monitor this industry resource that is extremely important to the Brazilian economy and thousands of families over a large scale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Software For Design Of Life-Support Systems

NASA Technical Reports Server (NTRS)

Rudokas, Mary R.; Cantwell, Elizabeth R.; Robinson, Peter I.; Shenk, Timothy W.

1991-01-01

Design Assistant Workstation (DAWN) computer program is prototype of expert software system for analysis and design of regenerative, physical/chemical life-support systems that revitalize air, reclaim water, produce food, and treat waste. Incorporates both conventional software for quantitative mathematical modeling of physical, chemical, and biological processes and expert system offering user stored knowledge about materials and processes. Constructs task tree as it leads user through simulated process, offers alternatives, and indicates where alternative not feasible. Also enables user to jump from one design level to another.

Theoretical foundations for a quantitative approach to paleogenetics. I, II.

NASA Technical Reports Server (NTRS)

Holmquist, R.

1972-01-01

It is shown that by neglecting the phenomena of multiple hits, back mutation, and chance coincidence errors larger than 100% can be introduced in the calculated value of the average number of nucleotide base differences to be expected between two homologous polynucleotides. Mathematical formulas are derived to correct quantitatively for these effects. It is pointed out that the effects change materially the quantitative aspects of phylogenics, such as the length of the legs of the trees. A number of problems are solved without approximation.-

Bridging the Gap Between Theory and Practice: Structure and Randomization in Large Scale Combinatorial Search

DTIC Science & Technology

2012-01-17

PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION...world problems. Our work brings together techniques from constraint programming, mathematical programming, and satisfiability in a symbiotic way to...power-­‐law  search  tree  model  for  complete  or  exact  methods     (See [9] for a detailed description of this work and

Multiscale model of a freeze–thaw process for tree sap exudation

PubMed Central

Graf, Isabell; Ceseri, Maurizio; Stockie, John M.

2015-01-01

Sap transport in trees has long fascinated scientists, and a vast literature exists on experimental and modelling studies of trees during the growing season when large negative stem pressures are generated by transpiration from leaves. Much less attention has been paid to winter months when trees are largely dormant but nonetheless continue to exhibit interesting flow behaviour. A prime example is sap exudation, which refers to the peculiar ability of sugar maple (Acer saccharum) and related species to generate positive stem pressure while in a leafless state. Experiments demonstrate that ambient temperatures must oscillate about the freezing point before significantly heightened stem pressures are observed, but the precise causes of exudation remain unresolved. The prevailing hypothesis attributes exudation to a physical process combining freeze–thaw and osmosis, which has some support from experimental studies but remains a subject of active debate. We address this knowledge gap by developing the first mathematical model for exudation, while also introducing several essential modifications to this hypothesis. We derive a multiscale model consisting of a nonlinear system of differential equations governing phase change and transport within wood cells, coupled to a suitably homogenized equation for temperature on the macroscale. Numerical simulations yield stem pressures that are consistent with experiments and provide convincing evidence that a purely physical mechanism is capable of capturing exudation. PMID:26400199

Automated method for the identification and analysis of vascular tree structures in retinal vessel network

NASA Astrophysics Data System (ADS)

Joshi, Vinayak S.; Garvin, Mona K.; Reinhardt, Joseph M.; Abramoff, Michael D.

2011-03-01

Structural analysis of retinal vessel network has so far served in the diagnosis of retinopathies and systemic diseases. The retinopathies are known to affect the morphologic properties of retinal vessels such as course, shape, caliber, and tortuosity. Whether the arteries and the veins respond to these changes together or in tandem has always been a topic of discussion. However the diseases such as diabetic retinopathy and retinopathy of prematurity have been diagnosed with the morphologic changes specific either to arteries or to veins. Thus a method describing the separation of retinal vessel trees imaged in a two dimensional color fundus image may assist in artery-vein classification and quantitative assessment of morphologic changes particular to arteries or veins. We propose a method based on mathematical morphology and graph search to identify and label the retinal vessel trees, which provides a structural mapping of vessel network in terms of each individual primary vessel, its branches and spatial positions of branching and cross-over points. The method was evaluated on a dataset of 15 fundus images resulting into an accuracy of 92.87 % correctly assigned vessel pixels when compared with the manual labeling of separated vessel trees. Accordingly, the structural mapping method performs well and we are currently investigating its potential in evaluating the characteristic properties specific to arteries or veins.

Multiscale model of a freeze-thaw process for tree sap exudation.

PubMed

Graf, Isabell; Ceseri, Maurizio; Stockie, John M

2015-10-06

Sap transport in trees has long fascinated scientists, and a vast literature exists on experimental and modelling studies of trees during the growing season when large negative stem pressures are generated by transpiration from leaves. Much less attention has been paid to winter months when trees are largely dormant but nonetheless continue to exhibit interesting flow behaviour. A prime example is sap exudation, which refers to the peculiar ability of sugar maple (Acer saccharum) and related species to generate positive stem pressure while in a leafless state. Experiments demonstrate that ambient temperatures must oscillate about the freezing point before significantly heightened stem pressures are observed, but the precise causes of exudation remain unresolved. The prevailing hypothesis attributes exudation to a physical process combining freeze-thaw and osmosis, which has some support from experimental studies but remains a subject of active debate. We address this knowledge gap by developing the first mathematical model for exudation, while also introducing several essential modifications to this hypothesis. We derive a multiscale model consisting of a nonlinear system of differential equations governing phase change and transport within wood cells, coupled to a suitably homogenized equation for temperature on the macroscale. Numerical simulations yield stem pressures that are consistent with experiments and provide convincing evidence that a purely physical mechanism is capable of capturing exudation. © 2015 The Author(s).

A flooding algorithm for multirobot exploration.

PubMed

Cabrera-Mora, Flavio; Xiao, Jizhong

2012-06-01

In this paper, we present a multirobot exploration algorithm that aims at reducing the exploration time and to minimize the overall traverse distance of the robots by coordinating the movement of the robots performing the exploration. Modeling the environment as a tree, we consider a coordination model that restricts the number of robots allowed to traverse an edge and to enter a vertex during each step. This coordination is achieved in a decentralized manner by the robots using a set of active landmarks that are dropped by them at explored vertices. We mathematically analyze the algorithm on trees, obtaining its main properties and specifying its bounds on the exploration time. We also define three metrics of performance for multirobot algorithms. We simulate and compare the performance of this new algorithm with those of our multirobot depth first search (MR-DFS) approach presented in our recent paper and classic single-robot DFS.

Extraction of decision rules via imprecise probabilities

NASA Astrophysics Data System (ADS)

Abellán, Joaquín; López, Griselda; Garach, Laura; Castellano, Javier G.

2017-05-01

Data analysis techniques can be applied to discover important relations among features. This is the main objective of the Information Root Node Variation (IRNV) technique, a new method to extract knowledge from data via decision trees. The decision trees used by the original method were built using classic split criteria. The performance of new split criteria based on imprecise probabilities and uncertainty measures, called credal split criteria, differs significantly from the performance obtained using the classic criteria. This paper extends the IRNV method using two credal split criteria: one based on a mathematical parametric model, and other one based on a non-parametric model. The performance of the method is analyzed using a case study of traffic accident data to identify patterns related to the severity of an accident. We found that a larger number of rules is generated, significantly supplementing the information obtained using the classic split criteria.

Logarithmic Compression of Sensory Signals within the Dendritic Tree of a Collision-Sensitive Neuron

PubMed Central

2012-01-01

Neurons in a variety of species, both vertebrate and invertebrate, encode the kinematics of objects approaching on a collision course through a time-varying firing rate profile that initially increases, then peaks, and eventually decays as collision becomes imminent. In this temporal profile, the peak firing rate signals when the approaching object's subtended size reaches an angular threshold, an event which has been related to the timing of escape behaviors. In a locust neuron called the lobula giant motion detector (LGMD), the biophysical basis of this angular threshold computation relies on a multiplicative combination of the object's angular size and speed, achieved through a logarithmic-exponential transform. To understand how this transform is implemented, we modeled the encoding of angular velocity along the pathway leading to the LGMD based on the experimentally determined activation pattern of its presynaptic neurons. These simulations show that the logarithmic transform of angular speed occurs between the synaptic conductances activated by the approaching object onto the LGMD's dendritic tree and its membrane potential at the spike initiation zone. Thus, we demonstrate an example of how a single neuron's dendritic tree implements a mathematical step in a neural computation important for natural behavior. PMID:22492048

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.

Establishment of the mathematical model for diagnosing the engine valve faults by genetic programming

NASA Astrophysics Data System (ADS)

Yang, Wen-Xian

2006-05-01

Available machine fault diagnostic methods show unsatisfactory performances on both on-line and intelligent analyses because their operations involve intensive calculations and are labour intensive. Aiming at improving this situation, this paper describes the development of an intelligent approach by using the Genetic Programming (abbreviated as GP) method. Attributed to the simple calculation of the mathematical model being constructed, different kinds of machine faults may be diagnosed correctly and quickly. Moreover, human input is significantly reduced in the process of fault diagnosis. The effectiveness of the proposed strategy is validated by an illustrative example, in which three kinds of valve states inherent in a six-cylinders/four-stroke cycle diesel engine, i.e. normal condition, valve-tappet clearance and gas leakage faults, are identified. In the example, 22 mathematical functions have been specially designed and 8 easily obtained signal features are used to construct the diagnostic model. Different from existing GPs, the diagnostic tree used in the algorithm is constructed in an intelligent way by applying a power-weight coefficient to each feature. The power-weight coefficients vary adaptively between 0 and 1 during the evolutionary process. Moreover, different evolutionary strategies are employed, respectively for selecting the diagnostic features and functions, so that the mathematical functions are sufficiently utilized and in the meantime, the repeated use of signal features may be fully avoided. The experimental results are illustrated diagrammatically in the following sections.

Quantitative and Qualitative Evaluation of The Structural Designing of Medical Informatics Dynamic Encyclopedia.

PubMed

Safdari, Reza; Shahmoradi, Leila; Hosseini-Beheshti, Molouk-Sadat; Nejad, Ahmadreza Farzaneh; Hosseiniravandi, Mohammad

2015-10-01

Encyclopedias and their compilation have become so prevalent as a valid cultural medium in the world. The daily development of computer industry and the expansion of various sciences have made indispensable the compilation of electronic, specialized encyclopedias, especially the web-based ones. This is an applied-developmental study conducted in 2014. First, the main terms in the field of medical informatics were gathered using MeSH Online 2014 and the supplementary terms of each were determined, and then the tree diagram of the terms was drawn based on their relationship in MeSH. Based on the studies done by the researchers, the tree diagram of the encyclopedia was drawn with respect to the existing areas in this field, and the terms gathered were put in related domains. In MeSH, 75 preferred terms together with 249 supplementary ones were indexed. One of the informatics' sub-branches is biomedical informatics and health which itself consists of three sub-divisions of bioinformatics, clinical informatics, and health informatics. Medical informatics which is a subdivision of clinical informatics has developed from the three fields of medical sciences, management and social sciences, and computational sciences and mathematics. Medical Informatics is created of confluence and fusion and applications of the three major scientific branches include health and biological sciences, social sciences and management sciences, computing and mathematical sciences, and according to that the structure of MeSH is weak for future development of Encyclopedia of Medical Informatics.

Segmentation of vessel-like patterns using mathematical morphology and curvature evaluation.

PubMed

Zana, F; Klein, J C

2001-01-01

This paper presents an algorithm based on mathematical morphology and curvature evaluation for the detection of vessel-like patterns in a noisy environment. Such patterns are very common in medical images. Vessel detection is interesting for the computation of parameters related to blood flow. Its tree-like geometry makes it a usable feature for registration between images that can be of a different nature. In order to define vessel-like patterns, segmentation is performed with respect to a precise model. We define a vessel as a bright pattern, piece-wise connected, and locally linear, mathematical morphology is very well adapted to this description, however other patterns fit such a morphological description. In order to differentiate vessels from analogous background patterns, a cross-curvature evaluation is performed. They are separated out as they have a specific Gaussian-like profile whose curvature varies smoothly along the vessel. The detection algorithm that derives directly from this modeling is based on four steps: (1) noise reduction; (2) linear pattern with Gaussian-like profile improvement; (3) cross-curvature evaluation; (4) linear filtering. We present its theoretical background and illustrate it on real images of various natures, then evaluate its robustness and its accuracy with respect to noise.

Pressure oscillation delivery to the lung: Computer simulation of neonatal breathing parameters.

PubMed

Al-Jumaily, Ahmed M; Reddy, Prasika I; Bold, Geoff T; Pillow, J Jane

2011-10-13

Preterm newborn infants may develop respiratory distress syndrome (RDS) due to functional and structural immaturity. A lack of surfactant promotes collapse of alveolar regions and airways such that newborns with RDS are subject to increased inspiratory effort and non-homogeneous ventilation. Pressure oscillation has been incorporated into one form of RDS treatment; however, how far it reaches various parts of the lung is still questionable. Since in-vivo measurement is very difficult if not impossible, mathematical modeling may be used as one way of assessment. Whereas many models of the respiratory system have been developed for adults, the neonatal lung remains essentially ill-described in mathematical models. A mathematical model is developed, which represents the first few generations of the tracheo-bronchial tree and the 5 lobes that make up the premature ovine lung. The elements of the model are derived using the lumped parameter approach and formulated in Simulink™ within the Matlab™ environment. The respiratory parameters at the airway opening compare well with those measured from experiments. The model demonstrates the ability to predict pressures, flows and volumes in the alveolar regions of a premature ovine lung. Copyright © 2011 Elsevier Ltd. All rights reserved.

Trees as environmental modifier to improve street canyon for pedestrian activities in Muscat

NASA Astrophysics Data System (ADS)

Khudhayer, Wael A.; Shaaban, Awni K.; Sukor, Nur Sabahiah Abdul

2017-10-01

Street shading efficiency is a function of orientation and profile proportion of its height to width. Under high sun altitude conditions, minimization of solar irradiance within the urban environment may often be a significant criterion in urban design. This reduction in solar irradiance achieved when the obstruction angle is large (high H/W ratio, H=height, W=width). High H/W values often lessen the solar access to streets. The horizontal sprawl of Muscat region is an example of low H/W ratio represented the remarkable challenge that causes the lack of shading rates in the urban street. This characteristic proliferates the negative impact on the pedestrian activities in the urban street. This research aims to improve the morphology of the street to promote the pedestrian behavior. The amendment based on suggesting different configurations of trees to increase effective shading of the urban street in Muscat. The street canyon abstracted into a virtual elongated channel formed of floor and walls of equal heights on both sides. Four street orientations (E/W, N/S, NE/SW, NW/SE) and three H/W ratio (0.5,1 and 2) are considered sufficient representative of street typologies. A mathematical model developed for calculation of shading efficiency of each street canyon. The trees assumed in this study as canyon's modifier to adjust the low H/W ratio of a street canyon to a higher one. Local trees and other plants in Muscat were studied concerning their morphology. The analysis selected two case study in Muscat to investigate the shading performance of their street canyons subsequently propose the modifications to improve it. The research concluded that the suggested changes of the street canyon by using a particular type of trees could increase the H/W ratio of street canyon significantly.

A recursive method for calculating the total number of spanning trees and its applications in self-similar small-world scale-free network models

NASA Astrophysics Data System (ADS)

Ma, Fei; Su, Jing; Yao, Bing

2018-05-01

The problem of determining and calculating the number of spanning trees of any finite graph (model) is a great challenge, and has been studied in various fields, such as discrete applied mathematics, theoretical computer science, physics, chemistry and the like. In this paper, firstly, thank to lots of real-life systems and artificial networks built by all kinds of functions and combinations among some simpler and smaller elements (components), we discuss some helpful network-operation, including link-operation and merge-operation, to design more realistic and complicated network models. Secondly, we present a method for computing the total number of spanning trees. As an accessible example, we apply this method to space of trees and cycles respectively, and our results suggest that it is indeed a better one for such models. In order to reflect more widely practical applications and potentially theoretical significance, we study the enumerating method in some existing scale-free network models. On the other hand, we set up a class of new models displaying scale-free feature, that is to say, following P(k) k-γ, where γ is the degree exponent. Based on detailed calculation, the degree exponent γ of our deterministic scale-free models satisfies γ > 3. In the rest of our discussions, we not only calculate analytically the solutions of average path length, which indicates our models have small-world property being prevailing in amounts of complex systems, but also derive the number of spanning trees by means of the recursive method described in this paper, which clarifies our method is convenient to research these models.

Multiscale topo-morphologic opening of arteries and veins: a validation study on phantoms and CT imaging of pulmonary vessel casting of pigs

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Holtze, Colin; Sonka, Milan; Hoffman, Eric; Saha, Punam K.

2010-03-01

Distinguishing pulmonary arterial and venous (A/V) trees via in vivo imaging is a critical first step in the quantification of vascular geometry for purposes of determining, for instance, pulmonary hypertension, detection of pulmonary emboli and more. A multi-scale topo-morphologic opening algorithm has recently been introduced by us separating A/V trees in pulmonary multiple-detector X-ray computed tomography (MDCT) images without contrast. The method starts with two sets of seeds - one for each of A/V trees and combines fuzzy distance transform, fuzzy connectivity, and morphologic reconstruction leading to multi-scale opening of two mutually fused structures while preserving their continuity. The method locally determines the optimum morphological scale separating the two structures. Here, a validation study is reported examining accuracy of the method using mathematically generated phantoms with different levels of fuzziness, overlap, scale, resolution, noise, and geometric coupling and MDCT images of pulmonary vessel casting of pigs. After exsanguinating the animal, a vessel cast was generated using rapid-hardening methyl methacrylate compound with additional contrast by 10cc of Ethiodol in the arterial side which was scanned in a MDCT scanner at 0.5mm slice thickness and 0.47mm in plane resolution. True segmentations of A/V trees were computed from these images by thresholding. Subsequently, effects of distinguishing A/V contrasts were eliminated and resulting images were used for A/V separation by our method. Experimental results show that 92% - 98% accuracy is achieved using only one seed for each object in phantoms while 94.4% accuracy is achieved in MDCT cast images using ten seeds for each of A/V trees.

Chronomics of tree rings for chronoastrobiology and beyond.

PubMed

Nintcheu-Fata, Sylvain; Katinas, George; Halberg, Franz; Cornélissen, Germaine; Tolstykh, Victor; Michael, Henry N; Otsuka, Kuniaki; Schwartzkopff, Othild; Bakken, Earl

2003-10-01

Gliding spectral windows illustrate the changes as a function of time in the relative prominence of signals in a given frequency range, viewed in 3D or as surface charts. As an example, the method is applied to a 2,189-year series of averages of ring measurements on 11 sequoia trees published by Douglass. Analyses of the original data and after filtering reveal, among others, components with periods of about 10.5 and 21 years similar to the Schwabe and Hale solar activity cycles. An alignment of gliding spectra with a global spectrum serves to define, by minima, the ranges of variability around the anticipated Schwabe and Hale cycles. This procedure may have more general applicability when dealing with ranges of only transiently synchronized, wobbly, and perhaps sometimes free-running periodicities. Solar activity is known to affect climate and changes in climate are reflected to some extent in tree growth. The spectral structure in tree rings could serve not only to check any relations of climate with sunspots, auroras and more modern measures of solar activity, but also to check any purely mathematical extrapolations from the much shorter available actual data on solar activity. With such extrapolated series and the data analyzed herein, the task remains to align physical and physiological variables to further study the influence of natural environmental factors near and far on biota, including international battles, which cover an even longer span of 2,556 years.

Master Logic Diagram: method for hazard and initiating event identification in process plants.

PubMed

Papazoglou, I A; Aneziris, O N

2003-02-28

Master Logic Diagram (MLD), a method for identifying events initiating accidents in chemical installations, is presented. MLD is a logic diagram that resembles a fault tree but without the formal mathematical properties of the latter. MLD starts with a Top Event "Loss of Containment" and decomposes it into simpler contributing events. A generic MLD has been developed which may be applied to all chemical installations storing toxic and/or flammable substances. The method is exemplified through its application to an ammonia storage facility.

Detecting long-term growth trends using tree rings: a critical evaluation of methods.

PubMed

Peters, Richard L; Groenendijk, Peter; Vlam, Mart; Zuidema, Pieter A

2015-05-01

Tree-ring analysis is often used to assess long-term trends in tree growth. A variety of growth-trend detection methods (GDMs) exist to disentangle age/size trends in growth from long-term growth changes. However, these detrending methods strongly differ in approach, with possible implications for their output. Here, we critically evaluate the consistency, sensitivity, reliability and accuracy of four most widely used GDMs: conservative detrending (CD) applies mathematical functions to correct for decreasing ring widths with age; basal area correction (BAC) transforms diameter into basal area growth; regional curve standardization (RCS) detrends individual tree-ring series using average age/size trends; and size class isolation (SCI) calculates growth trends within separate size classes. First, we evaluated whether these GDMs produce consistent results applied to an empirical tree-ring data set of Melia azedarach, a tropical tree species from Thailand. Three GDMs yielded similar results - a growth decline over time - but the widely used CD method did not detect any change. Second, we assessed the sensitivity (probability of correct growth-trend detection), reliability (100% minus probability of detecting false trends) and accuracy (whether the strength of imposed trends is correctly detected) of these GDMs, by applying them to simulated growth trajectories with different imposed trends: no trend, strong trends (-6% and +6% change per decade) and weak trends (-2%, +2%). All methods except CD, showed high sensitivity, reliability and accuracy to detect strong imposed trends. However, these were considerably lower in the weak or no-trend scenarios. BAC showed good sensitivity and accuracy, but low reliability, indicating uncertainty of trend detection using this method. Our study reveals that the choice of GDM influences results of growth-trend studies. We recommend applying multiple methods when analysing trends and encourage performing sensitivity and reliability analysis. Finally, we recommend SCI and RCS, as these methods showed highest reliability to detect long-term growth trends. © 2014 John Wiley & Sons Ltd.

Evolvable mathematical models: A new artificial Intelligence paradigm

NASA Astrophysics Data System (ADS)

Grouchy, Paul

We develop a novel Artificial Intelligence paradigm to generate autonomously artificial agents as mathematical models of behaviour. Agent/environment inputs are mapped to agent outputs via equation trees which are evolved in a manner similar to Symbolic Regression in Genetic Programming. Equations are comprised of only the four basic mathematical operators, addition, subtraction, multiplication and division, as well as input and output variables and constants. From these operations, equations can be constructed that approximate any analytic function. These Evolvable Mathematical Models (EMMs) are tested and compared to their Artificial Neural Network (ANN) counterparts on two benchmarking tasks: the double-pole balancing without velocity information benchmark and the challenging discrete Double-T Maze experiments with homing. The results from these experiments show that EMMs are capable of solving tasks typically solved by ANNs, and that they have the ability to produce agents that demonstrate learning behaviours. To further explore the capabilities of EMMs, as well as to investigate the evolutionary origins of communication, we develop NoiseWorld, an Artificial Life simulation in which interagent communication emerges and evolves from initially noncommunicating EMM-based agents. Agents develop the capability to transmit their x and y position information over a one-dimensional channel via a complex, dialogue-based communication scheme. These evolved communication schemes are analyzed and their evolutionary trajectories examined, yielding significant insight into the emergence and subsequent evolution of cooperative communication. Evolved agents from NoiseWorld are successfully transferred onto physical robots, demonstrating the transferability of EMM-based AIs from simulation into physical reality.

Metastability for discontinuous dynamical systems under Lévy noise: Case study on Amazonian Vegetation.

PubMed

Serdukova, Larissa; Zheng, Yayun; Duan, Jinqiao; Kurths, Jürgen

2017-08-24

For the tipping elements in the Earth's climate system, the most important issue to address is how stable is the desirable state against random perturbations. Extreme biotic and climatic events pose severe hazards to tropical rainforests. Their local effects are extremely stochastic and difficult to measure. Moreover, the direction and intensity of the response of forest trees to such perturbations are unknown, especially given the lack of efficient dynamical vegetation models to evaluate forest tree cover changes over time. In this study, we consider randomness in the mathematical modelling of forest trees by incorporating uncertainty through a stochastic differential equation. According to field-based evidence, the interactions between fires and droughts are a more direct mechanism that may describe sudden forest degradation in the south-eastern Amazon. In modeling the Amazonian vegetation system, we include symmetric α-stable Lévy perturbations. We report results of stability analysis of the metastable fertile forest state. We conclude that even a very slight threat to the forest state stability represents L´evy noise with large jumps of low intensity, that can be interpreted as a fire occurring in a non-drought year. During years of severe drought, high-intensity fires significantly accelerate the transition between a forest and savanna state.

3D Model of Surfactant Replacement Therapy

NASA Astrophysics Data System (ADS)

Grotberg, James; Tai, Cheng-Feng; Filoche, Marcel

2015-11-01

Surfactant Replacement Therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. Though successful in neonatal applications, its use in adults had early success followed by failure. We present the first mathematical model of 3D SRT where a liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug first deposits a coating film on the airway wall which subtracts from its volume, a ``coating cost''. Then the plug splits unevenly at the airway bifurcation due to gravity. The steps are repeated until a plug ruptures or reaches the tree endpoint alveoli/acinus. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published literature, the earlier successful adult SRT studies show comparatively good index values, while the later failed studies do not. Those unsuccessful studies used smaller dose volumes with higher concentration mixtures, apparently assuming a well mixed compartment. The model shows that adult lungs are not well mixed in SRT due to the coating cost and gravity effects. Returning to the higher dose volume protocols could save many thousands of lives annually in the US. Supported by NIH Grants HL85156, HL84370 and Agence Nationale de la Recherche, ANR no. 2010-BLAN-1119-05.

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation.

PubMed

Wang, Zhaocai; Huang, Dongmei; Meng, Huajun; Tang, Chengpei

2013-10-01

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m+n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Democratization in a passive dendritic tree: an analytical investigation.

PubMed

Timofeeva, Y; Cox, S J; Coombes, S; Josić, K

2008-10-01

One way to achieve amplification of distal synaptic inputs on a dendritic tree is to scale the amplitude and/or duration of the synaptic conductance with its distance from the soma. This is an example of what is often referred to as "dendritic democracy". Although well studied experimentally, to date this phenomenon has not been thoroughly explored from a mathematical perspective. In this paper we adopt a passive model of a dendritic tree with distributed excitatory synaptic conductances and analyze a number of key measures of democracy. In particular, via moment methods we derive laws for the transport, from synapse to soma, of strength, characteristic time, and dispersion. These laws lead immediately to synaptic scalings that overcome attenuation with distance. We follow this with a Neumann approximation of Green's representation that readily produces the synaptic scaling that democratizes the peak somatic voltage response. Results are obtained for both idealized geometries and for the more realistic geometry of a rat CA1 pyramidal cell. For each measure of democratization we produce and contrast the synaptic scaling associated with treating the synapse as either a conductance change or a current injection. We find that our respective scalings agree up to a critical distance from the soma and we reveal how this critical distance decreases with decreasing branch radius.

Construction and Maintenance of the Optimal Photosynthetic Systems of the Leaf, Herbaceous Plant and Tree: an Eco-developmental Treatise

PubMed Central

TERASHIMA, ICHIRO; ARAYA, TAKAO; MIYAZAWA, SHIN-ICHI; SONE, KOSEI; YANO, SATOSHI

2004-01-01

• Background and Aims The paper by Monsi and Saeki in 1953 (Japanese Journal of Botany 14: 22–52) was pioneering not only in mathematical modelling of canopy photosynthesis but also in eco-developmental studies of seasonal changes in leaf canopies. • Scope Construction and maintenance mechanisms of efficient photosynthetic systems at three different scaling levels—single leaves, herbaceous plants and trees—are reviewed mainly based on the nitrogen optimization theory. First, the nitrogen optimization theory with respect to the canopy and the single leaf is briefly introduced. Secondly, significance of leaf thickness in CO2 diffusion in the leaf and in leaf photosynthesis is discussed. Thirdly, mechanisms of adjustment of photosynthetic properties of the leaf within the herbaceous plant individual throughout its life are discussed. In particular, roles of sugar sensing, redox control and of cytokinin are highlighted. Finally, the development of a tree is considered. • Conclusions Various mechanisms contribute to construction and maintenance of efficient photosynthetic systems. Molecular backgrounds of these ecologically important mechanisms should be clarified. The construction mechanisms of the tree cannot be explained solely by the nitrogen optimization theory. It is proposed that the pipe model theory in its differential form could be a potential tool in future studies in this research area. PMID:15598701

Quantitative and Qualitative Evaluation of The Structural Designing of Medical Informatics Dynamic Encyclopedia

PubMed Central

Safdari, Reza; Shahmoradi, Leila; Hosseini-beheshti, Molouk-sadat; Nejad, Ahmadreza Farzaneh; Hosseiniravandi, Mohammad

2015-01-01

Introduction: Encyclopedias and their compilation have become so prevalent as a valid cultural medium in the world. The daily development of computer industry and the expansion of various sciences have made indispensable the compilation of electronic, specialized encyclopedias, especially the web-based ones. Materials and Methods: This is an applied-developmental study conducted in 2014. First, the main terms in the field of medical informatics were gathered using MeSH Online 2014 and the supplementary terms of each were determined, and then the tree diagram of the terms was drawn based on their relationship in MeSH. Based on the studies done by the researchers, the tree diagram of the encyclopedia was drawn with respect to the existing areas in this field, and the terms gathered were put in related domains. Findings: In MeSH, 75 preferred terms together with 249 supplementary ones were indexed. One of the informatics’ sub-branches is biomedical informatics and health which itself consists of three sub-divisions of bioinformatics, clinical informatics, and health informatics. Medical informatics which is a subdivision of clinical informatics has developed from the three fields of medical sciences, management and social sciences, and computational sciences and mathematics. Results and Discussion: Medical Informatics is created of confluence and fusion and applications of the three major scientific branches include health and biological sciences, social sciences and management sciences, computing and mathematical sciences, and according to that the structure of MeSH is weak for future development of Encyclopedia of Medical Informatics. PMID:26635440

The Urban Ecology Institute's field studies program: utilizing urban areas for experiential learning and ecological research

NASA Astrophysics Data System (ADS)

Starry, O.

2005-05-01

The Urban Ecology Institute (UEI) promotes the stewardship of healthy urban ecosystems by improving science and civic education for middle and high school youth and by working with urban communities to protect and transform natural resources. Established in 1999, UEI's field studies program engages over 1000 youth in the greater Boston area. A substantial component of this program involves water quality monitoring. We have recently adapted protocols from published leaf breakdown studies for incorporation into the UEI water quality curriculum. A 2004 pilot study of these leaf breakdown activities, conducted at four sites, compared rates of red maple breakdown to those of Norway maple, a potentially invasive urban street tree. Preliminary data from this successful pilot study suggest that leaf litter inputs from the two different tree species have varying effects on stream ecosystem function. We present this study as an example of how urban areas can be utilized for both ecological research and inclusive experiential learning through which science and mathematic knowledge can be effectively communicated.

Resolution of the 1D regularized Burgers equation using a spatial wavelet approximation

NASA Technical Reports Server (NTRS)

Liandrat, J.; Tchamitchian, PH.

1990-01-01

The Burgers equation with a small viscosity term, initial and periodic boundary conditions is resolved using a spatial approximation constructed from an orthonormal basis of wavelets. The algorithm is directly derived from the notions of multiresolution analysis and tree algorithms. Before the numerical algorithm is described these notions are first recalled. The method uses extensively the localization properties of the wavelets in the physical and Fourier spaces. Moreover, the authors take advantage of the fact that the involved linear operators have constant coefficients. Finally, the algorithm can be considered as a time marching version of the tree algorithm. The most important point is that an adaptive version of the algorithm exists: it allows one to reduce in a significant way the number of degrees of freedom required for a good computation of the solution. Numerical results and description of the different elements of the algorithm are provided in combination with different mathematical comments on the method and some comparison with more classical numerical algorithms.

Automation process for morphometric analysis of volumetric CT data from pulmonary vasculature in rats.

PubMed

Shingrani, Rahul; Krenz, Gary; Molthen, Robert

2010-01-01

With advances in medical imaging scanners, it has become commonplace to generate large multidimensional datasets. These datasets require tools for a rapid, thorough analysis. To address this need, we have developed an automated algorithm for morphometric analysis incorporating A Visualization Workshop computational and image processing libraries for three-dimensional segmentation, vascular tree generation and structural hierarchical ordering with a two-stage numeric optimization procedure for estimating vessel diameters. We combine this new technique with our mathematical models of pulmonary vascular morphology to quantify structural and functional attributes of lung arterial trees. Our physiological studies require repeated measurements of vascular structure to determine differences in vessel biomechanical properties between animal models of pulmonary disease. Automation provides many advantages including significantly improved speed and minimized operator interaction and biasing. The results are validated by comparison with previously published rat pulmonary arterial micro-CT data analysis techniques, in which vessels were manually mapped and measured using intense operator intervention. Published by Elsevier Ireland Ltd.

Calculated ventilation and effort distribution as a measure of respiratory disease and Heliox effectiveness.

PubMed

Pozin, N; Montesantos, S; Katz, I; Pichelin, M; Grandmont, C; Vignon-Clementel, I

2017-07-26

In spite of numerous clinical studies, there is no consensus on the benefit Heliox mixtures can bring to asthmatic patients in terms of work of breathing and ventilation distribution. In this article we use a 3D finite element mathematical model of the lung to study the impact of asthma on effort and ventilation distribution along with the effect of Heliox compared to air. Lung surface displacement fields extracted from computed tomography medical images are used to prescribe realistic boundary conditions to the model. Asthma is simulated by imposing bronchoconstrictions to some airways of the tracheo-bronchial tree based on statistical laws deduced from the literature. This study illuminates potential mechanisms for patient responsiveness to Heliox when affected by obstructive pulmonary diseases. Responsiveness appears to be function of the pathology severity, as well as its distal position in the tracheo-bronchial tree and geometrical position within the lung. Copyright © 2017 Elsevier Ltd. All rights reserved.

Predicting rates of interspecific interaction from phylogenetic trees.

PubMed

Nuismer, Scott L; Harmon, Luke J

2015-01-01

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

A general method for calculating the optimal leaf longevity from the viewpoint of carbon economy.

PubMed

Seki, Motohide; Yoshida, Tomohiko; Takada, Takenori

2015-09-01

According to the viewpoint of the optimal strategy theory, a tree is expected to shed its leaves when they no longer contribute to maximisation of net carbon gain. Several theoretical models have been proposed in which a tree was assumed to strategically shed an old deteriorated leaf to develop a new leaf. We mathematically refined an index used in a previous theoretical model [Kikuzawa (Am Nat 138:1250-1263, 1991)] so that the index is exactly proportional to a tree's lifelong net carbon gain. We also incorporated a tree's strategy that determines the timing of leaf expansion, and examined three kinds of strategies. Specifically, we assumed that a new leaf is expanded (1) immediately after shedding of an old leaf, (2) only at the beginning of spring, or (3) immediately after shedding of an old leaf if the shedding occurs during a non-winter season and at the beginning of spring otherwise. We derived a measure of optimal leaf longevity maximising the value of an appropriate index reflecting total net carbon gain and show that use of this index yielded results that are qualitatively consistent with empirical records. The model predicted that expanding a new leaf at the beginning of spring than immediately after shedding usually yields higher carbon gain, and combined strategy of the immediate replacement and the spring flushing earned the highest gain. In addition, our numerical analyses suggested that multiple flushing seen in a few species of subtropical zones can be explained in terms of carbon economy.

Optimisation of biomass productivity of black locust (Robinia pseudoacacia L.) on marginal lands - a case study in Lower Lusatia, NE Germany

NASA Astrophysics Data System (ADS)

Seserman, Diana-Maria; Veste, Maik; Freese, Dirk

2017-04-01

The profitability of reclaiming post-mining areas depends on the tree biomass productivity and the restoration of ecosystem functions, such as improving soil and water quality. Agroforestry systems, regarded as combined land-use systems of trees and crops, have the ability to facilitate soil development while reducing wind speed, soil erosion and evaporation. Achieving the maximum biomass productivity of the tree stands depends on the corresponding soil conditions and water availability, but is also influenced by stand structure and the competition between individual trees. For this purpose, black locust (Robinia pseudoacacia L.) trees were planted in a Nelder design in 2010, on a reclaimed post-mining site of the open-cast lignite mining in Welzow Süd (Brandenburg, Germany). Black locust is regarded as a drought-adapted tree species and commonly used for the reclamation of former lignite mining sites in Lower Lusatia, Germany. The Nelder design encompasses angles of arc of equal measure and with the same origin traversed by successive circumferences set at a predefined radial distance. Accordingly, a total of 1071 trees were planted in Welzow Süd at the intersection between 63 spokes and 17 circumferences and at densities ranging from 0.4 to 8.0 m2, with the aim of examining the influence of stand density on the tree growth in a timeframe of six years. In order to evaluate the biomass production of the trees and to determine an optimal planting density on a marginal land, various scenarios were assessed with the help of the Yield-SAFE model, a parameter-sparse process-based agroforestry model. The study revealed the consequences of choosing different tree densities on the tree biomass productivity and water use of trees in relation to the competition for light and water. References Keesman KJ, van der Werf W, van Keulen H, 2007. Production ecology of agroforestry systems: A minimal mechanistic model and analytical derivation of the land equivalent ratio. Mathematical Biosciences, vol. 209, pp. 608-623. Mantovani D, Veste M, Böhm C, Vignudelli M, Freese D, 2015. Drought impact on the spatial and temporal variation of growth performance and plant water status of black locust (Robinia pseudoacacia L.) in agroforestry systems in Lower Lusatia (Germany). iForest 8, 743-757. Mantovani D, Veste M, Freese D, 2014. Black locust (Robinia pseudoacacia L.) ecophysiological and morphological adaptations to drought and their consequence on biomass production and water use efficiency. New Zealand Journal of Forestry 44, 29. van der Werf W, Keesman K, Burgess PJ, Graves AR, Pilbeam D, Incoll LD, Metselaar K, Mayus M, Stappers R, van Keulen H, Palma JHN, Dupraz C, 2007. Yield-SAFE: a parameter-sparse process-based dynamic model for predicting resource capture, growth and production in agroforestry systems. Ecological Engineering, vol. 29, pp. 419-433.

Knowledge engineering in volcanology: Practical claims and general approach

NASA Astrophysics Data System (ADS)

Pshenichny, Cyril A.

2014-10-01

Knowledge engineering, being a branch of artificial intelligence, offers a variety of methods for elicitation and structuring of knowledge in a given domain. Only a few of them (ontologies and semantic nets, event/probability trees, Bayesian belief networks and event bushes) are known to volcanologists. Meanwhile, the tasks faced by volcanology and the solutions found so far favor a much wider application of knowledge engineering, especially tools for handling dynamic knowledge. This raises some fundamental logical and mathematical problems and requires an organizational effort, but may strongly improve panel discussions, enhance decision support, optimize physical modeling and support scientific collaboration.

Hierarchical classification in high dimensional numerous class cases

NASA Technical Reports Server (NTRS)

Kim, Byungyong; Landgrebe, D. A.

1990-01-01

As progress in new sensor technology continues, increasingly high resolution imaging sensors are being developed. These sensors give more detailed and complex data for each picture element and greatly increase the dimensionality of data over past systems. Three methods for designing a decision tree classifier are discussed: a top down approach, a bottom up approach, and a hybrid approach. Three feature extraction techniques are implemented. Canonical and extended canonical techniques are mainly dependent upon the mean difference between two classes. An autocorrelation technique is dependent upon the correlation differences. The mathematical relationship between sample size, dimensionality, and risk value is derived.

Rarefaction and blood pressure in systemic and pulmonary arteries

PubMed Central

OLUFSEN, METTE S.; HILL, N. A.; VAUGHAN, GARETH D. A.; SAINSBURY, CHRISTOPHER; JOHNSON, MARTIN

2012-01-01

The effects of vascular rarefaction (the loss of small arteries) on the circulation of blood are studied using a multiscale mathematical model that can predict blood flow and pressure in the systemic and pulmonary arteries. We augmented a model originally developed for the systemic arteries (Olufsen et al. 1998, 1999, 2000, 2004) to (a) predict flow and pressure in the pulmonary arteries, and (b) predict pressure propagation along the small arteries in the vascular beds. The systemic and pulmonary arteries are modelled as separate, bifurcating trees of compliant and tapering vessels. Each tree is divided into two parts representing the `large' and `small' arteries. Blood flow and pressure in the large arteries are predicted using a nonlinear cross-sectional area-averaged model for a Newtonian fluid in an elastic tube with inflow obtained from magnetic resonance measurements. Each terminal vessel within the network of the large arteries is coupled to a vascular bed of small `resistance' arteries, which are modelled as asymmetric structured trees with specified area and asymmetry ratios between the parent and daughter arteries. For the systemic circulation, each structured tree represents a specific vascular bed corresponding to major organs and limbs. For the pulmonary circulation, there are four vascular beds supplied by the interlobar arteries. This manuscript presents the first theoretical calculations of the propagation of the pressure and flow waves along systemic and pulmonary large and small arteries. Results for all networks were in agreement with published observations. Two studies were done with this model. First, we showed how rarefaction can be modelled by pruning the tree of arteries in the microvascular system. This was done by modulating parameters used for designing the structured trees. Results showed that rarefaction leads to increased mean and decreased pulse pressure in the large arteries. Second, we investigated the impact of decreasing vessel compliance in both large and small arteries. Results showed, that the effects of decreased compliance in the large arteries far outweigh the effects observed when decreasing the compliance of the small arteries. We further showed that a decrease of compliance in the large arteries results in pressure increases consistent with observations of isolated systolic hypertension, as occurs in ageing. PMID:22962497

The MeqTrees software system and its use for third-generation calibration of radio interferometers

NASA Astrophysics Data System (ADS)

Noordam, J. E.; Smirnov, O. M.

2010-12-01

Context. The formulation of the radio interferometer measurement equation (RIME) for a generic radio telescope by Hamaker et al. has provided us with an elegant mathematical apparatus for better understanding, simulation and calibration of existing and future instruments. The calibration of the new radio telescopes (LOFAR, SKA) would be unthinkable without the RIME formalism, and new software to exploit it. Aims: The MeqTrees software system is designed to implement numerical models, and to solve for arbitrary subsets of their parameters. It may be applied to many problems, but was originally geared towards implementing Measurement Equations in radio astronomy for the purposes of simulation and calibration. The technical goal of MeqTrees is to provide a tool for rapid implementation of such models, while offering performance comparable to hand-written code. We are also pursuing the wider goal of increasing the rate of evolution of radio astronomical software, by offering a tool that facilitates rapid experimentation, and exchange of ideas (and scripts). Methods: MeqTrees is implemented as a Python-based front-end called the meqbrowser, and an efficient (C++-based) computational back-end called the meqserver. Numerical models are defined on the front-end via a Python-based Tree Definition Language (TDL), then rapidly executed on the back-end. The use of TDL facilitates an extremely short turn-around time (hours rather than weeks or months) for experimentation with new ideas. This is also helped by unprecedented visualization capabilities for all final and intermediate results. A flexible data model and a number of important optimizations in the back-end ensures that the numerical performance is comparable to that of hand-written code. Results: MeqTrees is already widely used as the simulation tool for new instruments (LOFAR, SKA) and technologies (focal plane arrays). It has demonstrated that it can achieve a noise-limited dynamic range in excess of a million, on WSRT data. It is the only package that is specifically designed to handle what we propose to call third-generation calibration (3GC), which is needed for the new generation of giant radio telescopes, but can also improve the calibration of existing instruments.

Coalescent: an open-source and scalable framework for exact calculations in coalescent theory

PubMed Central

2012-01-01

Background Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. Results As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. Conclusions Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach. PMID:23033878

A novel model for DNA sequence similarity analysis based on graph theory.

PubMed

Qi, Xingqin; Wu, Qin; Zhang, Yusen; Fuller, Eddie; Zhang, Cun-Quan

2011-01-01

Determination of sequence similarity is one of the major steps in computational phylogenetic studies. As we know, during evolutionary history, not only DNA mutations for individual nucleotide but also subsequent rearrangements occurred. It has been one of major tasks of computational biologists to develop novel mathematical descriptors for similarity analysis such that various mutation phenomena information would be involved simultaneously. In this paper, different from traditional methods (eg, nucleotide frequency, geometric representations) as bases for construction of mathematical descriptors, we construct novel mathematical descriptors based on graph theory. In particular, for each DNA sequence, we will set up a weighted directed graph. The adjacency matrix of the directed graph will be used to induce a representative vector for DNA sequence. This new approach measures similarity based on both ordering and frequency of nucleotides so that much more information is involved. As an application, the method is tested on a set of 0.9-kb mtDNA sequences of twelve different primate species. All output phylogenetic trees with various distance estimations have the same topology, and are generally consistent with the reported results from early studies, which proves the new method's efficiency; we also test the new method on a simulated data set, which shows our new method performs better than traditional global alignment method when subsequent rearrangements happen frequently during evolutionary history.

When to Renew Software Licences at HPC Centres? A Mathematical Analysis

NASA Astrophysics Data System (ADS)

Baolai, Ge; MacIsaac, Allan B.

2010-11-01

In this paper we study a common problem faced by many high performance computing (HPC) centres: When and how to renew commercial software licences. Software vendors often sell perpetual licences along with forward update and support contracts at an additional, annual cost. Every year or so, software support personnel and the budget units of HPC centres are required to make the decision of whether or not to renew such support, and usually such decisions are made intuitively. The total cost for a continuing support contract can, however, be costly. One might therefore want a rational answer to the question of whether the option for a renewal should be exercised and when. In an attempt to study this problem within a market framework, we present the mathematical problem derived for the day to day operation of a hypothetical HPC centre that charges for the use of software packages. In the mathematical model, we assume that the uncertainty comes from the demand, number of users using the packages, as well as the price. Further we assume the availability of up to date software versions may also affect the demand. We develop a renewal strategy that aims to maximize the expected profit from the use the software under consideration. The derived problem involves a decision tree, which constitutes a numerical procedure that can be processed in parallel.

A Tree-Structured List in a Mathematical Series Text from Mesopotamia

NASA Astrophysics Data System (ADS)

Proust, Christine

The written culture of the Ancient Near East, whose history covers more than three millennia (from the beginning of the third millennium to the end of the first millennium BCE), underwent profound transformations over the centuries and showed many faces according to the region of the vast territory in which it developed. Yet despite the diversity of contexts in which they worked, the scholars of Mesopotamia and neighboring regions maintained and consistently cultivated a true `art of lists', in the fields of mathematics, lexicography, astrology, astronomy, medicine, law and accounting. The study of the writing techniques particular to lists represents therefore an important issue for the understanding of the intellectual history of the Ancient Near East. In this chapter, I consider extreme cases of list structures, and to do this I have chosen very long lists, most items of which are not semantically autonomous. More specifically, I shall study one of the most abstract and concise lists that have come down to us. It belongs to a series, of which one tablet is kept in the Oriental Institute in Chicago (no. A 24194). The study of this case will allow to set forth some of the writing techniques that were particularly developed in the series. Such a study of the structures of the mathematical texts could benefit other areas in Assyriology.

[Mathematic modeling and experimental validation of macrostate quality expression for multicomponent in Chinese materia medica].

PubMed

He, Fuyuan; Deng, Kaiwen; Shi, Jilian; Liu, Wenlong; Pi, Fengjuan

2011-11-01

To establish the unitive multicomponent quality system bridged macrostate mathematic model parameters of material quality and microstate component concentration for Chinese materia medica (CMM). According to law of biologic laws of thermodynamics, the state functions of macrostate qulity of the CMM were established. The validation test was carried out as modeling drug as alcohol extract of Radix Rhozome (AERR), their enthalpy of combustion was determined, and entropy and the capability of information by chromatographic fingerprint were assayed, and then the biologic apparent macrostate parameters were calculated. The biologic macrostate mathematic models, for the CMM quality controll, were established as parameters as the apparent equilibrium constant, biologic enthalpy, Gibbs free energy and biologic entropy etc. The total molarity for the 10 batchs of AERR were 0.153 4 mmol x g(-1) with 28.26% of RSD, with the average of apparent equilibrium constants, biologic enthalpy, Gibbs free energy and biologic entropy were 0.039 65, 8 005 J x mol(-1), -2.408 x 10(7) J x mol(-1) and - 8.078 x 10(4) J x K(-1) with RSD as 6.020%, 1.860%, 42.32% and 42.31%, respectively. The macrostate quality models for CMM can represent their intrinsic quality for multicomponent dynamic system such as the CMM, to manifest out as if the forest away from or tree near from to see it.

Analyzing linear spatial features in ecology.

PubMed

Buettel, Jessie C; Cole, Andrew; Dickey, John M; Brook, Barry W

2018-06-01

The spatial analysis of dimensionless points (e.g., tree locations on a plot map) is common in ecology, for instance using point-process statistics to detect and compare patterns. However, the treatment of one-dimensional linear features (fiber processes) is rarely attempted. Here we appropriate the methods of vector sums and dot products, used regularly in fields like astrophysics, to analyze a data set of mapped linear features (logs) measured in 12 × 1-ha forest plots. For this demonstrative case study, we ask two deceptively simple questions: do trees tend to fall downhill, and if so, does slope gradient matter? Despite noisy data and many potential confounders, we show clearly that topography (slope direction and steepness) of forest plots does matter to treefall. More generally, these results underscore the value of mathematical methods of physics to problems in the spatial analysis of linear features, and the opportunities that interdisciplinary collaboration provides. This work provides scope for a variety of future ecological analyzes of fiber processes in space. © 2018 by the Ecological Society of America.

Mathematical models application for mapping soils spatial distribution on the example of the farm from the North of Udmurt Republic of Russia

NASA Astrophysics Data System (ADS)

Dokuchaev, P. M.; Meshalkina, J. L.; Yaroslavtsev, A. M.

2018-01-01

Comparative analysis of soils geospatial modeling using multinomial logistic regression, decision trees, random forest, regression trees and support vector machines algorithms was conducted. The visual interpretation of the digital maps obtained and their comparison with the existing map, as well as the quantitative assessment of the individual soil groups detection overall accuracy and of the models kappa showed that multiple logistic regression, support vector method, and random forest models application with spatial prediction of the conditional soil groups distribution can be reliably used for mapping of the study area. It has shown the most accurate detection for sod-podzolics soils (Phaeozems Albic) lightly eroded and moderately eroded soils. In second place, according to the mean overall accuracy of the prediction, there are sod-podzolics soils - non-eroded and warp one, as well as sod-gley soils (Umbrisols Gleyic) and alluvial soils (Fluvisols Dystric, Umbric). Heavy eroded sod-podzolics and gray forest soils (Phaeozems Albic) were detected by methods of automatic classification worst of all.

Propensity score estimation: machine learning and classification methods as alternatives to logistic regression

PubMed Central

Westreich, Daniel; Lessler, Justin; Funk, Michele Jonsson

2010-01-01

Summary Objective Propensity scores for the analysis of observational data are typically estimated using logistic regression. Our objective in this Review was to assess machine learning alternatives to logistic regression which may accomplish the same goals but with fewer assumptions or greater accuracy. Study Design and Setting We identified alternative methods for propensity score estimation and/or classification from the public health, biostatistics, discrete mathematics, and computer science literature, and evaluated these algorithms for applicability to the problem of propensity score estimation, potential advantages over logistic regression, and ease of use. Results We identified four techniques as alternatives to logistic regression: neural networks, support vector machines, decision trees (CART), and meta-classifiers (in particular, boosting). Conclusion While the assumptions of logistic regression are well understood, those assumptions are frequently ignored. All four alternatives have advantages and disadvantages compared with logistic regression. Boosting (meta-classifiers) and to a lesser extent decision trees (particularly CART) appear to be most promising for use in the context of propensity score analysis, but extensive simulation studies are needed to establish their utility in practice. PMID:20630332

Toxic genes present a unique phylogenetic signature.

PubMed

Avni, Eliran; Snir, Sagi

2017-11-01

Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution. Copyright © 2017 Elsevier Inc. All rights reserved.

Tropical geometry of statistical models.

PubMed

Pachter, Lior; Sturmfels, Bernd

2004-11-16

This article presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient tool for evaluating specific coordinates. Here, we address the question of how the solutions to various inference problems depend on the model parameters. The proposed answer is expressed in terms of tropical algebraic geometry. The Newton polytope of a statistical model plays a key role. Our results are applied to the hidden Markov model and the general Markov model on a binary tree.

Mathematics make microbes beautiful, beneficial, and bountiful.

PubMed

Jungck, John R

2012-01-01

Microbiology is a rich area for visualizing the importance of mathematics in terms of designing experiments, data mining, testing hypotheses, and visualizing relationships. Historically, Nobel Prizes have acknowledged the close interplay between mathematics and microbiology in such examples as the fluctuation test and mutation rates using Poisson statistics by Luria and Delbrück and the use of graph theory of polyhedra by Caspar and Klug. More and more contemporary microbiology journals feature mathematical models, computational algorithms and heuristics, and multidimensional visualizations. While revolutions in research have driven these initiatives, a commensurate effort needs to be made to incorporate much more mathematics into the professional preparation of microbiologists. In order not to be daunting to many educators, a Bloom-like "Taxonomy of Quantitative Reasoning" is shared with explicit examples of microbiological activities for engaging students in (a) counting, measuring, calculating using image analysis of bacterial colonies and viral infections on variegated leaves, measurement of fractal dimensions of beautiful colony morphologies, and counting vertices, edges, and faces on viral capsids and using graph theory to understand self assembly; (b) graphing, mapping, ordering by applying linear, exponential, and logistic growth models of public health and sanitation problems, revisiting Snow's epidemiological map of cholera with computational geometry, and using interval graphs to do complementation mapping, deletion mapping, food webs, and microarray heatmaps; (c) problem solving by doing gene mapping and experimental design, and applying Boolean algebra to gene regulation of operons; (d) analysis of the "Bacterial Bonanza" of microbial sequence and genomic data using bioinformatics and phylogenetics; (e) hypothesis testing-again with phylogenetic trees and use of Poisson statistics and the Luria-Delbrück fluctuation test; and (f) modeling of biodiversity by using game theory, of epidemics with algebraic models, bacterial motion by using motion picture analysis and fluid mechanics of motility in multiple dimensions through the physics of "Life at Low Reynolds Numbers," and pattern formation of quorum sensing bacterial populations. Through a developmental model for preprofessional education that emphasizes the beauty, utility, and diversity of microbiological systems, we hope to foster creativity as well as mathematically rigorous reasoning. Copyright © 2012 Elsevier Inc. All rights reserved.

A conceptual approach to approximate tree root architecture in infinite slope models

NASA Astrophysics Data System (ADS)

Schmaltz, Elmar; Glade, Thomas

2016-04-01

Vegetation-related properties - particularly tree root distribution and coherent hydrologic and mechanical effects on the underlying soil mantle - are commonly not considered in infinite slope models. Indeed, from a geotechnical point of view, these effects appear to be difficult to be reproduced reliably in a physically-based modelling approach. The growth of a tree and the expansion of its root architecture are directly connected with both intrinsic properties such as species and age, and extrinsic factors like topography, availability of nutrients, climate and soil type. These parameters control four main issues of the tree root architecture: 1) Type of rooting; 2) maximum growing distance to the tree stem (radius r); 3) maximum growing depth (height h); and 4) potential deformation of the root system. Geometric solids are able to approximate the distribution of a tree root system. The objective of this paper is to investigate whether it is possible to implement root systems and the connected hydrological and mechanical attributes sufficiently in a 3-dimensional slope stability model. Hereby, a spatio-dynamic vegetation module should cope with the demands of performance, computation time and significance. However, in this presentation, we focus only on the distribution of roots. The assumption is that the horizontal root distribution around a tree stem on a 2-dimensional plane can be described by a circle with the stem located at the centroid and a distinct radius r that is dependent on age and species. We classified three main types of tree root systems and reproduced the species-age-related root distribution with three respective mathematical solids in a synthetic 3-dimensional hillslope ambience. Thus, two solids in an Euclidian space were distinguished to represent the three root systems: i) cylinders with radius r and height h, whilst the dimension of latter defines the shape of a taproot-system or a shallow-root-system respectively; ii) elliptic paraboloids represent a cordate-root-system with radius r, height h and a constant, species-independent curvature. This procedure simplifies the classification of tree species into the three defined geometric solids. In this study we introduce a conceptual approach to estimate the 2- and 3-dimensional distribution of different tree root systems, and to implement it in a raster environment, as it is used in infinite slope models. Hereto we used the PCRaster extension in a python framework. The results show that root distribution and root growth are spatially reproducible in a simple raster framework. The outputs exhibit significant effects for a synthetically generated slope on local scale for equal time-steps. The preliminary results depict an initial step to develop a vegetation module that can be coupled with hydro-mechanical slope stability models. This approach is expected to yield a valuable contribution to the implementation of vegetation-related properties, in particular effects of root-reinforcement, into physically-based approaches using infinite slope models.

Validation of the Gatortail method for accurate sizing of pulmonary vessels from 3D medical images.

PubMed

O'Dell, Walter G; Gormaley, Anne K; Prida, David A

2017-12-01

Detailed characterization of changes in vessel size is crucial for the diagnosis and management of a variety of vascular diseases. Because clinical measurement of vessel size is typically dependent on the radiologist's subjective interpretation of the vessel borders, it is often prone to high inter- and intra-user variability. Automatic methods of vessel sizing have been developed for two-dimensional images but a fully three-dimensional (3D) method suitable for vessel sizing from volumetric X-ray computed tomography (CT) or magnetic resonance imaging has heretofore not been demonstrated and validated robustly. In this paper, we refined and objectively validated Gatortail, a method that creates a mathematical geometric 3D model of each branch in a vascular tree, simulates the appearance of the virtual vascular tree in a 3D CT image, and uses the similarity of the simulated image to a patient's CT scan to drive the optimization of the model parameters, including vessel size, to match that of the patient. The method was validated with a 2-dimensional virtual tree structure under deformation, and with a realistic 3D-printed vascular phantom in which the diameter of 64 branches were manually measured 3 times each. The phantom was then scanned on a conventional clinical CT imaging system and the images processed with the in-house software to automatically segment and mathematically model the vascular tree, label each branch, and perform the Gatortail optimization of branch size and trajectory. Previously proposed methods of vessel sizing using matched Gaussian filters and tubularity metrics were also tested. The Gatortail method was then demonstrated on the pulmonary arterial tree segmented from a human volunteer's CT scan. The standard deviation of the difference between the manually measured and Gatortail-based radii in the 3D physical phantom was 0.074 mm (0.087 in-plane pixel units for image voxels of dimension 0.85 × 0.85 × 1.0 mm) over the 64 branches, representing vessel diameters ranging from 1.2 to 7 mm. The linear regression fit gave a slope of 1.056 and an R 2 value of 0.989. These three metrics reflect superior agreement of the radii estimates relative to previously published results over all sizes tested. Sizing via matched Gaussian filters resulted in size underestimates of >33% over all three test vessels, while the tubularity-metric matching exhibited a sizing uncertainty of >50%. In the human chest CT data set, the vessel voxel intensity profiles with and without branch model optimization showed excellent agreement and improvement in the objective measure of image similarity. Gatortail has been demonstrated to be an automated, objective, accurate and robust method for sizing of vessels in 3D non-invasively from chest CT scans. We anticipate that Gatortail, an image-based approach to automatically compute estimates of blood vessel radii and trajectories from 3D medical images, will facilitate future quantitative evaluation of vascular response to disease and environmental insult and improve understanding of the biological mechanisms underlying vascular disease processes. © 2017 American Association of Physicists in Medicine.

Mental Maps: A new instrument for teaching-learning-evaluation of engineering students

NASA Astrophysics Data System (ADS)

Oleschko, K.

2009-04-01

The use of interactive mind maps for teaching-learning-evaluation of postgraduate students is still not very common in Geosciences. Notwithstanding, these maps allow students to organize the huge volumes of information and data they are faced with (www.spinscape.com) for efficient research project elaboration and for understanding of basic anzatz and conjectures (Singer, 2009). The elaboration of mind maps is introduced as a principle teaching-learning-evaluation instrument (Cruza and Fierros, 2006) in my Research Methodology Seminar. Each student should to construct three types of multiscale mind maps before to write the formal proposal (Curiel and Radvansky, 2004; Zimmer, 2004). The main goal is to show how useful is to manage the physical, mathematical and linguistic information on the same structured way (Montibeller and Belton, 2009; Chu et al., 2009). The mental representation of the spatially and time organized physical world (physical map) is combined with the design of hierarchical tree of mathematical models used to describe it in mathematical terms (the map composed only by mathematical symbols), visualizing this tree branches by corresponding images inside the third map consisting on images. This three-faced representation of each research project helps the participant to perceive the complex nature of studied systems and visualize their features of universality and scale invariance. The maṕs elaboration is considered to be finished when any student of other specialties become able to present it in acceptable scientific way. Some examples of recent mental maps elaborated by the master degree students of Queretaro University, Mexico will be presented and discussed. Based on my experience I recommend this education technique in order to pass from sustainable engineer teaching to educate the engineers of Sustainability. References 1. Chu, H.-Ch., Chen, M.-Y., Chen, Y.-M., 2009. A semantic-based approach to content abstraction and annotation for content management. Expert Systems and Applications, 36: 2360-2376. 2. Cruza, N.S. and Fierros, L.E., 2006. Utility of conceptual schemes and mental maps on the teaching-learning process of residents in pediatrics. Gac. Med. Mex., 146 (6):457-465. 3. Curiel, J.M. and Radvansky, G.A., 2004. The accuracy of spatial information from temporally and spatially organized mental maps. Psychon. Bull. Rev., 11 (2):314-319. 4. Montibeller, G. and Belton, V. , 2009. Qualitative operators for reasoning maps: Evaluating multi-criteria options with networks of reasons. European J. of Operational Res., 195: 829-840. 5. Singer, F.M., 2009. The dynamic infrastructure of mind - A hypothesis and some of its applications. New ideas in Psychology, 27: 48-74. 6. http://www.spinscape.com 7. Zimmer, H.D. The construction of mental maps based on a fragmented view of physical maps. J. of Educational Psychology, 96 (3): 603-610.

Risk assessment techniques with applicability in marine engineering

NASA Astrophysics Data System (ADS)

Rudenko, E.; Panaitescu, F. V.; Panaitescu, M.

2015-11-01

Nowadays risk management is a carefully planned process. The task of risk management is organically woven into the general problem of increasing the efficiency of business. Passive attitude to risk and awareness of its existence are replaced by active management techniques. Risk assessment is one of the most important stages of risk management, since for risk management it is necessary first to analyze and evaluate risk. There are many definitions of this notion but in general case risk assessment refers to the systematic process of identifying the factors and types of risk and their quantitative assessment, i.e. risk analysis methodology combines mutually complementary quantitative and qualitative approaches. Purpose of the work: In this paper we will consider as risk assessment technique Fault Tree analysis (FTA). The objectives are: understand purpose of FTA, understand and apply rules of Boolean algebra, analyse a simple system using FTA, FTA advantages and disadvantages. Research and methodology: The main purpose is to help identify potential causes of system failures before the failures actually occur. We can evaluate the probability of the Top event.The steps of this analize are: the system's examination from Top to Down, the use of symbols to represent events, the use of mathematical tools for critical areas, the use of Fault tree logic diagrams to identify the cause of the Top event. Results: In the finally of study it will be obtained: critical areas, Fault tree logical diagrams and the probability of the Top event. These results can be used for the risk assessment analyses.

An endoscopic fluorescence imaging system for simultaneous visual examination and photodetection of cancers

NASA Astrophysics Data System (ADS)

Wagnières, Georges A.; Studzinski, André P.; van den Bergh, Hubert E.

1997-01-01

We describe the design and performance tested during six years of clinical trials of a fluorescence endoscope for the detection and delineation of cancers in several hollow organs. The apparatus is based on the imaging of the laser-induced fluorescence that differs between a tumor and its surrounding normal tissue. The tests are carried out in the upper aerodigestive tract, the tracheobronchial tree, the esophagus, and the colon. In the three former cases an exogenous dye is used (Photofrin II), whereas in the latter case fluorescein molecules conjugated with monoclonal antibodies directed against carcinoembryonic antigen are injected. The decrease of native tissue autofluorescence observed in early cancers is also used for detecting lesions in the tracheobronchial tree. The fluorescence contrast between the tumor and surrounding normal tissue is enhanced by real time image processing. This is done by simultaneously recording the fluorescence image in two spectral domains, after which these two images are digitized and manipulated with a mathematical operator (look-up table) at video frequency. Moreover, the device that is described below allows for an immediate observation of the endoscopic area under white light illumination during fluorescence detection in order to localize the origin of the "positive" fluorescence signals. Typical results obtained in the tracheobronchial tree and in the colon are presented and the sources of false positives and false negatives are evaluated in terms of the fluorescent dye, tissue optical properties, and illumination optics.

In Vitro Experimental Model for the Long-Term Analysis of Cellular Dynamics During Bronchial Tree Development from Lung Epithelial Cells

PubMed Central

Maruta, Naomichi; Marumoto, Moegi

2017-01-01

Lung branching morphogenesis has been studied for decades, but the underlying developmental mechanisms are still not fully understood. Cellular movements dynamically change during the branching process, but it is difficult to observe long-term cellular dynamics by in vivo or tissue culture experiments. Therefore, developing an in vitro experimental model of bronchial tree would provide an essential tool for developmental biology, pathology, and systems biology. In this study, we succeeded in reconstructing a bronchial tree in vitro by using primary human bronchial epithelial cells. A high concentration gradient of bronchial epithelial cells was required for branching initiation, whereas homogeneously distributed endothelial cells induced the formation of successive branches. Subsequently, the branches grew in size to the order of millimeter. The developed model contains only two types of cells and it facilitates the analysis of lung branching morphogenesis. By taking advantage of our experimental model, we carried out long-term time-lapse observations, which revealed self-assembly, collective migration with leader cells, rotational motion, and spiral motion of epithelial cells in each developmental event. Mathematical simulation was also carried out to analyze the self-assembly process and it revealed simple rules that govern cellular dynamics. Our experimental model has provided many new insights into lung development and it has the potential to accelerate the study of developmental mechanisms, pattern formation, left–right asymmetry, and disease pathogenesis of the human lung. PMID:28471293

FTC - THE FAULT-TREE COMPILER (SUN VERSION)

NASA Technical Reports Server (NTRS)

Butler, R. W.

1994-01-01

FTC, the Fault-Tree Compiler program, is a tool used to calculate the top-event probability for a fault-tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. The high-level input language is easy to understand and use. In addition, the program supports a hierarchical fault tree definition feature which simplifies the tree-description process and reduces execution time. A rigorous error bound is derived for the solution technique. This bound enables the program to supply an answer precisely (within the limits of double precision floating point arithmetic) at a user-specified number of digits accuracy. The program also facilitates sensitivity analysis with respect to any specified parameter of the fault tree such as a component failure rate or a specific event probability by allowing the user to vary one failure rate or the failure probability over a range of values and plot the results. The mathematical approach chosen to solve a reliability problem may vary with the size and nature of the problem. Although different solution techniques are utilized on different programs, it is possible to have a common input language. The Systems Validation Methods group at NASA Langley Research Center has created a set of programs that form the basis for a reliability analysis workstation. The set of programs are: SURE reliability analysis program (COSMIC program LAR-13789, LAR-14921); the ASSIST specification interface program (LAR-14193, LAR-14923), PAWS/STEM reliability analysis programs (LAR-14165, LAR-14920); and the FTC fault tree tool (LAR-14586, LAR-14922). FTC is used to calculate the top-event probability for a fault tree. PAWS/STEM and SURE are programs which interpret the same SURE language, but utilize different solution methods. ASSIST is a preprocessor that generates SURE language from a more abstract definition. SURE, ASSIST, and PAWS/STEM are also offered as a bundle. Please see the abstract for COS-10039/COS-10041, SARA - SURE/ASSIST Reliability Analysis Workstation, for pricing details. FTC was originally developed for DEC VAX series computers running VMS and was later ported for use on Sun computers running SunOS. The program is written in PASCAL, ANSI compliant C-language, and FORTRAN 77. The TEMPLATE graphics library is required to obtain graphical output. The standard distribution medium for the VMS version of FTC (LAR-14586) is a 9-track 1600 BPI magnetic tape in VMSINSTAL format. It is also available on a TK50 tape cartridge in VMSINSTAL format. Executables are included. The standard distribution medium for the Sun version of FTC (LAR-14922) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. Both Sun3 and Sun4 executables are included. FTC was developed in 1989 and last updated in 1992. DEC, VAX, VMS, and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories. SunOS is a trademark of Sun Microsystems, Inc.

FTC - THE FAULT-TREE COMPILER (VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

Butler, R. W.

1994-01-01

FTC, the Fault-Tree Compiler program, is a tool used to calculate the top-event probability for a fault-tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. The high-level input language is easy to understand and use. In addition, the program supports a hierarchical fault tree definition feature which simplifies the tree-description process and reduces execution time. A rigorous error bound is derived for the solution technique. This bound enables the program to supply an answer precisely (within the limits of double precision floating point arithmetic) at a user-specified number of digits accuracy. The program also facilitates sensitivity analysis with respect to any specified parameter of the fault tree such as a component failure rate or a specific event probability by allowing the user to vary one failure rate or the failure probability over a range of values and plot the results. The mathematical approach chosen to solve a reliability problem may vary with the size and nature of the problem. Although different solution techniques are utilized on different programs, it is possible to have a common input language. The Systems Validation Methods group at NASA Langley Research Center has created a set of programs that form the basis for a reliability analysis workstation. The set of programs are: SURE reliability analysis program (COSMIC program LAR-13789, LAR-14921); the ASSIST specification interface program (LAR-14193, LAR-14923), PAWS/STEM reliability analysis programs (LAR-14165, LAR-14920); and the FTC fault tree tool (LAR-14586, LAR-14922). FTC is used to calculate the top-event probability for a fault tree. PAWS/STEM and SURE are programs which interpret the same SURE language, but utilize different solution methods. ASSIST is a preprocessor that generates SURE language from a more abstract definition. SURE, ASSIST, and PAWS/STEM are also offered as a bundle. Please see the abstract for COS-10039/COS-10041, SARA - SURE/ASSIST Reliability Analysis Workstation, for pricing details. FTC was originally developed for DEC VAX series computers running VMS and was later ported for use on Sun computers running SunOS. The program is written in PASCAL, ANSI compliant C-language, and FORTRAN 77. The TEMPLATE graphics library is required to obtain graphical output. The standard distribution medium for the VMS version of FTC (LAR-14586) is a 9-track 1600 BPI magnetic tape in VMSINSTAL format. It is also available on a TK50 tape cartridge in VMSINSTAL format. Executables are included. The standard distribution medium for the Sun version of FTC (LAR-14922) is a .25 inch streaming magnetic tape cartridge in UNIX tar format. Both Sun3 and Sun4 executables are included. FTC was developed in 1989 and last updated in 1992. DEC, VAX, VMS, and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories. SunOS is a trademark of Sun Microsystems, Inc.

Homology groups for particles on one-connected graphs

NASA Astrophysics Data System (ADS)

MaciÄ Żek, Tomasz; Sawicki, Adam

2017-06-01

We present a mathematical framework for describing the topology of configuration spaces for particles on one-connected graphs. In particular, we compute the homology groups over integers for different classes of one-connected graphs. Our approach is based on some fundamental combinatorial properties of the configuration spaces, Mayer-Vietoris sequences for different parts of configuration spaces, and some limited use of discrete Morse theory. As one of the results, we derive the closed-form formulae for ranks of the homology groups for indistinguishable particles on tree graphs. We also give a detailed discussion of the second homology group of the configuration space of both distinguishable and indistinguishable particles. Our motivation is the search for new kinds of quantum statistics.

A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines

PubMed Central

Wang, Feng; Kang, Mengzhen; Lu, Qi; Letort, Véronique; Han, Hui; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2011-01-01

Background and Aims Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional–structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning. Methods In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source–sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions. Key Results The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees. Conclusions This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model. PMID:21062760

A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines.

PubMed

Wang, Feng; Kang, Mengzhen; Lu, Qi; Letort, Véronique; Han, Hui; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2011-04-01

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional-structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning. In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source-sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions. The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees. This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model.

Optimization of monitoring and inspections in the life-cycle of wind turbines

NASA Astrophysics Data System (ADS)

Hanish Nithin, Anu; Omenzetter, Piotr

2016-04-01

The past decade has witnessed a surge in the offshore wind farm developments across the world. Although this form of cleaner and greener energy is beneficial and eco-friendly, the production of wind energy entails high life-cycle costs. The costs associated with inspections, monitoring and repairs of wind turbines are primary contributors to the high costs of electricity produced in this way and are disadvantageous in today's competitive economic environment. There is limited research being done in the probabilistic optimization of life-cycle costs of offshore wind turbines structures and their components. This paper proposes a framework for assessing the life cycle cost of wind turbine structures subject to damage and deterioration. The objective of the paper is to develop a mathematical probabilistic cost assessment framework which considers deterioration, inspection, monitoring, repair and maintenance models and their uncertainties. The uncertainties are etched in the accuracy and precision of the monitoring and inspection methods and can be considered through the probability of damage detection of each method. Schedules for inspection, monitoring and repair actions are demonstrated using a decision tree. Examples of a generalised deterioration process integrated with the cost analysis using a decision tree are shown for a wind turbine foundation structure.

When does seed limitation matter for scaling up reforestation from patches to landscapes?

PubMed

Caughlin, T Trevor; Elliott, Stephen; Lichstein, Jeremy W

2016-12-01

Restoring forest to hundreds of millions of hectares of degraded land has become a centerpiece of international plans to sequester carbon and conserve biodiversity. Forest landscape restoration will require scaling up ecological knowledge of secondary succession from small-scale field studies to predict forest recovery rates in heterogeneous landscapes. However, ecological field studies reveal widely divergent times to forest recovery, in part due to landscape features that are difficult to replicate in empirical studies. Seed rain can determine reforestation rate and depends on landscape features that are beyond the scale of most field studies. We develop mathematical models to quantify how landscape configuration affects seed rain and forest regrowth in degraded patches. The models show how landscape features can alter the successional trajectories of otherwise identical patches, thus providing insight into why some empirical studies reveal a strong effect of seed rain on secondary succession, while others do not. We show that seed rain will strongly limit reforestation rate when patches are near a threshold for arrested succession, when positive feedbacks between tree canopy cover and seed rain occur during early succession, and when directed dispersal leads to between-patch interactions. In contrast, seed rain has weak effects on reforestation rate over a wide range of conditions, including when landscape-scale seed availability is either very high or very low. Our modeling framework incorporates growth and survival parameters that are commonly estimated in field studies of reforestation. We demonstrate how mathematical models can inform forest landscape restoration by allowing land managers to predict where natural regeneration will be sufficient to restore tree cover. Translating quantitative forecasts into spatially targeted interventions for forest landscape restoration could support target goals of restoring millions of hectares of degraded land and help mitigate global climate change. © 2016 by the Ecological Society of America.

Statistics, Computation, and Modeling in Cosmology

NASA Astrophysics Data System (ADS)

Jewell, Jeff; Guiness, Joe; SAMSI 2016 Working Group in Cosmology

2017-01-01

Current and future ground and space based missions are designed to not only detect, but map out with increasing precision, details of the universe in its infancy to the present-day. As a result we are faced with the challenge of analyzing and interpreting observations from a wide variety of instruments to form a coherent view of the universe. Finding solutions to a broad range of challenging inference problems in cosmology is one of the goals of the “Statistics, Computation, and Modeling in Cosmology” workings groups, formed as part of the year long program on ‘Statistical, Mathematical, and Computational Methods for Astronomy’, hosted by the Statistical and Applied Mathematical Sciences Institute (SAMSI), a National Science Foundation funded institute. Two application areas have emerged for focused development in the cosmology working group involving advanced algorithmic implementations of exact Bayesian inference for the Cosmic Microwave Background, and statistical modeling of galaxy formation. The former includes study and development of advanced Markov Chain Monte Carlo algorithms designed to confront challenging inference problems including inference for spatial Gaussian random fields in the presence of sources of galactic emission (an example of a source separation problem). Extending these methods to future redshift survey data probing the nonlinear regime of large scale structure formation is also included in the working group activities. In addition, the working group is also focused on the study of ‘Galacticus’, a galaxy formation model applied to dark matter-only cosmological N-body simulations operating on time-dependent halo merger trees. The working group is interested in calibrating the Galacticus model to match statistics of galaxy survey observations; specifically stellar mass functions, luminosity functions, and color-color diagrams. The group will use subsampling approaches and fractional factorial designs to statistically and computationally efficiently explore the Galacticus parameter space. The group will also use the Galacticus simulations to study the relationship between the topological and physical structure of the halo merger trees and the properties of the resulting galaxies.

Expressions Module for the Satellite Orbit Analysis Program

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

The Expressions Module is a software module that has been incorporated into the Satellite Orbit Analysis Program (SOAP). The module includes an expressions- parser submodule built on top of an analytical system, enabling the user to define logical and numerical variables and constants. The variables can capture output from SOAP orbital-prediction and geometric-engine computations. The module can combine variables and constants with built-in logical operators (such as Boolean AND, OR, and NOT), relational operators (such as >, <, or =), and mathematical operators (such as addition, subtraction, multiplication, division, modulus, exponentiation, differentiation, and integration). Parentheses can be used to specify precedence of operations. The module contains a library of mathematical functions and operations, including logarithms, trigonometric functions, Bessel functions, minimum/ maximum operations, and floating- point-to-integer conversions. The module supports combinations of time, distance, and angular units and has a dimensional- analysis component that checks for correct usage of units. A parser based on the Flex language and the Bison program looks for and indicates errors in syntax. SOAP expressions can be built using other expressions as arguments, thus enabling the user to build analytical trees. A graphical user interface facilitates use.

Three-dimensional model of surfactant replacement therapy

PubMed Central

Filoche, Marcel; Tai, Cheng-Feng; Grotberg, James B.

2015-01-01

Surfactant replacement therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. It is widely successful for treating surfactant deficiency in premature neonates who develop neonatal respiratory distress syndrome (NRDS). However, when applied to adults with acute respiratory distress syndrome (ARDS), early successes were followed by failures. This unexpected and puzzling situation is a vexing issue in the pulmonary community. A pressing question is whether the instilled surfactant mixture actually reaches the adult alveoli/acinus in therapeutic amounts. In this study, to our knowledge, we present the first mathematical model of SRT in a 3D lung structure to provide insight into answering this and other questions. The delivery is computed from fluid mechanical principals for 3D models of the lung airway tree for neonates and adults. A liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug deposits a coating film on the airway wall and then splits unevenly at the bifurcation due to gravity. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published procedural methods, we show the neonatal lung is a well-mixed compartment, whereas the adult lung is not. The earlier, successful adult SRT studies show comparatively good index values implying adequate delivery. The later, failed studies used different protocols resulting in very low values of both indexes, consistent with inadequate acinar delivery. Reasons for these differences and the evolution of failure from success are outlined and potential remedies discussed. PMID:26170310

An approach to localize the retinal blood vessels using bit planes and centerline detection.

PubMed

Fraz, M M; Barman, S A; Remagnino, P; Hoppe, A; Basit, A; Uyyanonvara, B; Rudnicka, A R; Owen, C G

2012-11-01

The change in morphology, diameter, branching pattern or tortuosity of retinal blood vessels is an important indicator of various clinical disorders of the eye and the body. This paper reports an automated method for segmentation of blood vessels in retinal images. A unique combination of techniques for vessel centerlines detection and morphological bit plane slicing is presented to extract the blood vessel tree from the retinal images. The centerlines are extracted by using the first order derivative of a Gaussian filter in four orientations and then evaluation of derivative signs and average derivative values is performed. Mathematical morphology has emerged as a proficient technique for quantifying the blood vessels in the retina. The shape and orientation map of blood vessels is obtained by applying a multidirectional morphological top-hat operator with a linear structuring element followed by bit plane slicing of the vessel enhanced grayscale image. The centerlines are combined with these maps to obtain the segmented vessel tree. The methodology is tested on three publicly available databases DRIVE, STARE and MESSIDOR. The results demonstrate that the performance of the proposed algorithm is comparable with state of the art techniques in terms of accuracy, sensitivity and specificity. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Optimal flow conditions of a tracheobronchial model to reengineer lung structures

NASA Astrophysics Data System (ADS)

Casarin, Stefano; Aletti, Federico; Baselli, Giuseppe; Garbey, Marc

2017-04-01

The high demand for lung transplants cannot be matched by an adequate number of lungs from donors. Since fully ex-novo lungs are far from being feasible, tissue engineering is actively considering implantation of engineered lungs where the devitalized structure of a donor is used as scaffold to be repopulated by stem cells of the receiving patient. A decellularized donated lung is treated inside a bioreactor where transport through the tracheobronchial tree (TBT) will allow for both deposition of stem cells and nourishment for their subsequent growth, thus developing new lung tissue. The key concern is to set optimally the boundary conditions to utilize in the bioreactor. We propose a predictive model of slow liquid ventilation, which combines a one-dimensional (1-D) mathematical model of the TBT and a solute deposition model strongly dependent on fluid velocity across the tree. With it, we were able to track and drive the concentration of a generic solute across the airways, looking for its optimal distribution. This was given by properly adjusting the pumps' regime serving the bioreactor. A feedback system, created by coupling the two models, allowed us to derive the optimal pattern. The TBT model can be easily invertible, thus yielding a straightforward flow/pressure law at the inlet to optimize the efficiency of the bioreactor.

Evaluation of Land Suitability and Potential Production of Gambir Uncaria gambir Roxb. L) at Salido Saribulan, Pesisir Selatan Regency

NASA Astrophysics Data System (ADS)

Yuni, Juniarti

2017-04-01

Gambir (Uncaria gambir Roxb. L) is a specific commodity of export in West Sumatra. Area of Gambir tree increases about 8 % per year in West Sumatera and until 1998 its production increased about 17% per year. However, in 1999 its area does not parallel with its production. In the last five years, the volume of export increases about 82.81%, while its value of export reaches US 2.5/kg. Therefore, this commodity has a strategic value for city's earnings. One of predicted causes is the use of unappropriated land. The aim of this research is to measure levels of land suitability in the buffer zone. TNKS (The National Park Kerinci-Seblat) in order to get the area, which is suitable for growing commodity of Gambir tree. To evaluate land suitability, quantitative model from FAO is used by combining environmental data, climate and condition of land (physical and chemical characteristic of the land). Estimation of Radiation Thermal Production Potential (RPP). Every data is measured (rating) individually and included in several mathematical formulas. After that, potential production of a land based on climate (Climate Production Potential) = CPP) is obtained quantitatively. By changing certain variant of this model program, it can predict the result of the plant in another area. By entering the real data of a land plant production, this model can predict the real plant production of land (Land Production Potential= LPP). Salido Saribulan area is included in class of land suitability S3f which is suitable for growing Gambir tree with a limitation factor of nutrient retention. Potential of actual gambir production at Salido Saribulan is 5 ton/ha, which is higher than actual gambir production.

Optimal Embedding for Shape Indexing in Medical Image Databases

PubMed Central

Qian, Xiaoning; Tagare, Hemant D.; Fulbright, Robert K.; Long, Rodney; Antani, Sameer

2010-01-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine x-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape-similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. PMID:20163981

Optimal embedding for shape indexing in medical image databases.

PubMed

Qian, Xiaoning; Tagare, Hemant D; Fulbright, Robert K; Long, Rodney; Antani, Sameer

2010-06-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine X-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. Copyright (c) 2010 Elsevier B.V. All rights reserved.

A new method of building footprints detection using airborne laser scanning data and multispectral image

NASA Astrophysics Data System (ADS)

Luo, Yiping; Jiang, Ting; Gao, Shengli; Wang, Xin

2010-10-01

It presents a new approach for detecting building footprints in a combination of registered aerial image with multispectral bands and airborne laser scanning data synchronously obtained by Leica-Geosystems ALS40 and Applanix DACS-301 on the same platform. A two-step method for building detection was presented consisting of selecting 'building' candidate points and then classifying candidate points. A digital surface model(DSM) derived from last pulse laser scanning data was first filtered and the laser points were classified into classes 'ground' and 'building or tree' based on mathematic morphological filter. Then, 'ground' points were resample into digital elevation model(DEM), and a Normalized DSM(nDSM) was generated from DEM and DSM. The candidate points were selected from 'building or tree' points by height value and area threshold in nDSM. The candidate points were further classified into building points and tree points by using the support vector machines(SVM) classification method. Two classification tests were carried out using features only from laser scanning data and associated features from two input data sources. The features included height, height finite difference, RGB bands value, and so on. The RGB value of points was acquired by matching laser scanning data and image using collinear equation. The features of training points were presented as input data for SVM classification method, and cross validation was used to select best classification parameters. The determinant function could be constructed by the classification parameters and the class of candidate points was determined by determinant function. The result showed that associated features from two input data sources were superior to features only from laser scanning data. The accuracy of more than 90% was achieved for buildings in first kind of features.

Travelling waves in a model of quasi-active dendrites with active spines

NASA Astrophysics Data System (ADS)

Timofeeva, Y.

2010-05-01

Dendrites, the major components of neurons, have many different types of branching structures and are involved in receiving and integrating thousands of synaptic inputs from other neurons. Dendritic spines with excitable channels can be present in large densities on the dendrites of many cells. The recently proposed Spike-Diffuse-Spike (SDS) model that is described by a system of point hot-spots (with an integrate-and-fire process) embedded throughout a passive tree has been shown to provide a reasonable caricature of a dendritic tree with supra-threshold dynamics. Interestingly, real dendrites equipped with voltage-gated ion channels can exhibit not only supra-threshold responses, but also sub-threshold dynamics. This sub-threshold resonant-like oscillatory behaviour has already been shown to be adequately described by a quasi-active membrane. In this paper we introduce a mathematical model of a branched dendritic tree based upon a generalisation of the SDS model where the active spines are assumed to be distributed along a quasi-active dendritic structure. We demonstrate how solitary and periodic travelling wave solutions can be constructed for both continuous and discrete spine distributions. In both cases the speed of such waves is calculated as a function of system parameters. We also illustrate that the model can be naturally generalised to an arbitrary branched dendritic geometry whilst remaining computationally simple. The spatio-temporal patterns of neuronal activity are shown to be significantly influenced by the properties of the quasi-active membrane. Active (sub- and supra-threshold) properties of dendrites are known to vary considerably among cell types and animal species, and this theoretical framework can be used in studying the combined role of complex dendritic morphologies and active conductances in rich neuronal dynamics.

A Simulation Approach to Assessing Sampling Strategies for Insect Pests: An Example with the Balsam Gall Midge

PubMed Central

Carleton, R. Drew; Heard, Stephen B.; Silk, Peter J.

2013-01-01

Estimation of pest density is a basic requirement for integrated pest management in agriculture and forestry, and efficiency in density estimation is a common goal. Sequential sampling techniques promise efficient sampling, but their application can involve cumbersome mathematics and/or intensive warm-up sampling when pests have complex within- or between-site distributions. We provide tools for assessing the efficiency of sequential sampling and of alternative, simpler sampling plans, using computer simulation with “pre-sampling” data. We illustrate our approach using data for balsam gall midge (Paradiplosis tumifex) attack in Christmas tree farms. Paradiplosis tumifex proved recalcitrant to sequential sampling techniques. Midge distributions could not be fit by a common negative binomial distribution across sites. Local parameterization, using warm-up samples to estimate the clumping parameter k for each site, performed poorly: k estimates were unreliable even for samples of n∼100 trees. These methods were further confounded by significant within-site spatial autocorrelation. Much simpler sampling schemes, involving random or belt-transect sampling to preset sample sizes, were effective and efficient for P. tumifex. Sampling via belt transects (through the longest dimension of a stand) was the most efficient, with sample means converging on true mean density for sample sizes of n∼25–40 trees. Pre-sampling and simulation techniques provide a simple method for assessing sampling strategies for estimating insect infestation. We suspect that many pests will resemble P. tumifex in challenging the assumptions of sequential sampling methods. Our software will allow practitioners to optimize sampling strategies before they are brought to real-world applications, while potentially avoiding the need for the cumbersome calculations required for sequential sampling methods. PMID:24376556

The use of phenological data to calculate chilling units in Olea europaea L. in relation to the onset of reproduction

NASA Astrophysics Data System (ADS)

Orlandi, F.; Fornaciari, M.; Romano, B.

2002-02-01

The aim of this study was to develop a practical method to evaluate the effective relationship between the amount of winter chilling and the response expressed as the spring reproductive re-starting dates in the olive ( Olea europaea L.). Two olive cultivars growing in a special olive orchard in Umbria (central Italy) were studied over a 3-year period (1998-2000): the cultivar Ascolana, typical of central Italy, and the cultivar Giarraffa, typical of southern Italy. The spring reproductive re-starts were assessed using data from detailed phenological observations made on 60 trees of each cultivar in an effort to establish the exact date of reproductive bud swelling. The chilling phenomenon was evaluated by using 341 functions derived from a formula developed by researchers at Utah State University to calculate chilling units. The mathematical functions are defined, and show the very close relationship between the amount of winter chilling and the spring reproductive response in the two cultivars in the orchard studied. The results can be used to define the relationship between local climate and plant development, and the mathematical approach can be used to draw maps that can show the suitability of different cultivars on the basis of local climatic conditions.

Method of optimum channel switching in equipment of infocommunication network in conditions of cyber attacks to their telecommunication infrastructure.

NASA Astrophysics Data System (ADS)

Kochedykov, S. S.; Noev, A. N.; Dushkin, A. V.; Gubin, I. A.

2018-05-01

On the basis of the mathematical graph theory, the method of optimum switching of infocommunication networks in the conditions of cyber attacks is developed. The idea of representation of a set of possible ways on the graph in the form of the multilevel tree ordered by rules of algebra of a logic theory is the cornerstone of a method. As a criterion of optimization, the maximum of network transmission capacity to which assessment Ford- Falkerson's theorem is applied is used. The method is realized in the form of a numerical algorithm, which can be used not only for design, but also for operational management of infocommunication networks in conditions of violation of the functioning of their switching centers.

Universality in the Evolution of Orientation Columns in the Visual Cortex

PubMed Central

Kaschube, Matthias; Schnabel, Michael; Löwel, Siegrid; Coppola, David M.; White, Leonard E.; Wolf, Fred

2011-01-01

The brain’s visual cortex processes information concerning form, pattern, and motion within functional maps that reflect the layout of neuronal circuits. We analyzed functional maps of orientation preference in the ferret, tree shrew, and galago—three species separated since the basal radiation of placental mammals more than 65 million years ago—and found a common organizing principle. A symmetry-based class of models for the self-organization of cortical networks predicts all essential features of the layout of these neuronal circuits, but only if suppressive long-range interactions dominate development. We show mathematically that orientation-selective long-range connectivity can mediate the required interactions. Our results suggest that self-organization has canalized the evolution of the neuronal circuitry underlying orientation preference maps into a single common design. PMID:21051599

The 1/ N Expansion of Tensor Models Beyond Perturbation Theory

NASA Astrophysics Data System (ADS)

Gurau, Razvan

2014-09-01

We analyze in full mathematical rigor the most general quartically perturbed invariant probability measure for a random tensor. Using a version of the Loop Vertex Expansion (which we call the mixed expansion) we show that the cumulants write as explicit series in 1/ N plus bounded rest terms. The mixed expansion recasts the problem of determining the subleading corrections in 1/ N into a simple combinatorial problem of counting trees decorated by a finite number of loop edges. As an aside, we use the mixed expansion to show that the (divergent) perturbative expansion of the tensor models is Borel summable and to prove that the cumulants respect an uniform scaling bound. In particular the quartically perturbed measures fall, in the N→ ∞ limit, in the universality class of Gaussian tensor models.

Monitoring the state of the human airways by analysis of respiratory sound

NASA Technical Reports Server (NTRS)

Hardin, J. C.; Patterson, J. L., Jr.

1978-01-01

A mechanism whereby sound is generated by the motion of vortices in the human lung is described. This mechanism is believed to be responsible for most of the sound which is generated both on inspiration and expiration in normal lungs. Mathematical expressions for the frequencies of sound generated, which depend only upon the axial flow velocity and diameters of the bronchi, are derived. This theory allows the location within the bronchial tree from which particular sounds emanate to be determined. Redistribution of pulmonary blood volume following transition from earth gravity to the weightless state probably alters the caliber of certain airways and doubtless alters sound transmission properties of the lung. We believe that these changes can be monitored effectively and non-invasively by spectral analysis of pulmonary sound.

Monitoring the state of the human airways by analysis of respiratory sound

NASA Technical Reports Server (NTRS)

Hardin, J. C.; Patterson, J. L. Jr

1979-01-01

A mechanism whereby sound is generated by the motion of vortices in the human lung is described. This mechanism is believed to be responsible for most of the sound which is generated both on inspiration and expiration in normal lungs. Mathematical expressions for the frequencies of sound generated, which depend only upon the axial flow velocity and diameters of the bronchi, are derived. This theory allows the location within the bronchial tree from which particular sounds emanate to be determined. Redistribution of pulmonary blood volume following transition from Earth gravity to the weightless state probably alters the caliber of certain airways and doubtless alters sound transmission properties of the lung. We believe that these changes can be monitored effectively and non-invasively by spectral analysis of pulmonary sound.

A constrained rasch model of trace redintegration in serial recall.

PubMed

Roodenrys, Steven; Miller, Leonie M

2008-04-01

The notion that verbal short-term memory tasks, such as serial recall, make use of information in long-term as well as in short-term memory is instantiated in many models of these tasks. Such models incorporate a process in which degraded traces retrieved from a short-term store are reconstructed, or redintegrated (Schweickert, 1993), through the use of information in long-term memory. This article presents a conceptual and mathematical model of this process based on a class of item-response theory models. It is demonstrated that this model provides a better fit to three sets of data than does the multinomial processing tree model of redintegration (Schweickert, 1993) and that a number of conceptual accounts of serial recall can be related to the parameters of the model.

Determining geographical spread pattern of MERS-CoV by distance method using Kimura model

NASA Astrophysics Data System (ADS)

Amiroch, Siti; Rohmatullah, Arif

2017-03-01

MERS-CoV or generally called as Middle East Respiratory Syndrome Coronavirus, a respiratory disease syndrome caused by a corona virus that attacks the respiratory tract ranging from mild to severe acute indication of fever, cough and shortness of breath. The cases happened relate to the countries in the Arabian Peninsula (Middle East) and there were 356 deaths have been reported due to the spread of the epidemic MERS. The data used in the case of MERS are the data DNA sequences taken from Genbank, the online database of the United States that stores the results of molecular biological experiments from all over the world (http://www.ncbi.nlm.nih.gov). In this case, bioinformatics plays an important role of reading sequences of DNA and genetic information by using the main device in the form of software that is supported by the availability of the Internet, while the analysis there in made and proven with mathematical methods. In similar research conducted by molecular biologists and physicians, the process of DNA sequencing is done with software that is already available like BLAST. In order to determine the MERS geographical distribution patterns in the Arabian Peninsula is done with program Clustal W, Bayesian, Phylip, etc. In this study, the writer use the Matlab simulation for all processes starting sequence alignment, counting the number of transitions and transversion substitutions for each sequence and its location up to the process of forming a phylogenetic tree that figures out the pattern of spread of the epidemic MERS. Mathematical analysis performed on a decline in the formula is to find Kimura evolutionary models and the process of forming a phylogenetic tree (the pattern of the epidemic MERS distribution) with neighbor joining algorithm. Finally it was obtained the pattern of geographical spread with 6 groups epidemic of MERS which ultimately turns out that all the MERS viruses that were spread in the Arabian Peninsula everything are almost the same as the virus sequence found in al-Hasa.

Attitude dynamics simulation subroutines for systems of hinge-connected rigid bodies with nonrigid appendages

NASA Technical Reports Server (NTRS)

Fleischer, G. E.; Likins, P. W.

1975-01-01

Three computer subroutines designed to solve the vector-dyadic differential equations of rotational motion for systems that may be idealized as a collection of hinge-connected rigid bodies assembled in a tree topology, with an optional flexible appendage attached to each body are reported. Deformations of the appendages are mathematically represented by modal coordinates and are assumed small. Within these constraints, the subroutines provide equation solutions for (1) the most general case of unrestricted hinge rotations, with appendage base bodies nominally rotating at a constant speed, (2) the case of unrestricted hinge rotations between rigid bodies, with the restriction that those rigid bodies carrying appendages are nominally nonspinning, and (3) the case of small hinge rotations and nominally nonrotating appendages. Sample problems and their solutions are presented to illustrate the utility of the computer programs.

Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input

PubMed Central

Segev, Idan; Shamma, Shihab

2014-01-01

An important task performed by a neuron is the selection of relevant inputs from among thousands of synapses impinging on the dendritic tree. Synaptic plasticity enables this by strenghtening a subset of synapses that are, presumably, functionally relevant to the neuron. A different selection mechanism exploits the resonance of the dendritic membranes to preferentially filter synaptic inputs based on their temporal rates. A widely held view is that a neuron has one resonant frequency and thus can pass through one rate. Here we demonstrate through mathematical analyses and numerical simulations that dendritic resonance is inevitably a spatially distributed property; and therefore the resonance frequency varies along the dendrites, and thus endows neurons with a powerful spatiotemporal selection mechanism that is sensitive both to the dendritic location and the temporal structure of the incoming synaptic inputs. PMID:25144440

Extraction of Children's Friendship Relation from Activity Level

NASA Astrophysics Data System (ADS)

Kono, Aki; Shintani, Kimio; Katsuki, Takuya; Kihara, Shin'ya; Ueda, Mari; Kaneda, Shigeo; Haga, Hirohide

Children learn to fit into society through living in a group, and it's greatly influenced by their friend relations. Although preschool teachers need to observe them to assist in the growth of children's social progress and support the development each child's personality, only experienced teachers can watch over children while providing high-quality guidance. To resolve the problem, this paper proposes a mathematical and objective method that assists teachers with observation. It uses numerical data of activity level recorded by pedometers, and we make tree diagram called dendrogram based on hierarchical clustering with recorded activity level. Also, we calculate children's ``breadth'' and ``depth'' of friend relations by using more than one dendrogram. When we record children's activity level in a certain kindergarten for two months and evaluated the proposed method, the results usually coincide with remarks of teachers about the children.

How mutation affects evolutionary games on graphs

PubMed Central

Allen, Benjamin; Traulsen, Arne; Tarnita, Corina E.; Nowak, Martin A.

2011-01-01

Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration. PMID:21473871

Branch Input Resistance and Steady Attenuation for Input to One Branch of a Dendritic Neuron Model

PubMed Central

Rall, Wilfrid; Rinzel, John

1973-01-01

Mathematical solutions and numerical illustrations are presented for the steady-state distribution of membrane potential in an extensively branched neuron model, when steady electric current is injected into only one dendritic branch. Explicit expressions are obtained for input resistance at the branch input site and for voltage attenuation from the input site to the soma; expressions for AC steady-state input impedance and attenuation are also presented. The theoretical model assumes passive membrane properties and the equivalent cylinder constraint on branch diameters. Numerical examples illustrate how branch input resistance and steady attenuation depend upon the following: the number of dendritic trees, the orders of dendritic branching, the electrotonic length of the dendritic trees, the location of the dendritic input site, and the input resistance at the soma. The application to cat spinal motoneurons, and to other neuron types, is discussed. The effect of a large dendritic input resistance upon the amount of local membrane depolarization at the synaptic site, and upon the amount of depolarization reaching the soma, is illustrated and discussed; simple proportionality with input resistance does not hold, in general. Also, branch input resistance is shown to exceed the input resistance at the soma by an amount that is always less than the sum of core resistances along the path from the input site to the soma. PMID:4715583

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo.

PubMed

Uhlirova, Hana; Tian, Peifang; Kılıç, Kıvılcım; Thunemann, Martin; Sridhar, Vishnu B; Chmelik, Radim; Bartsch, Hauke; Dale, Anders M; Devor, Anna; Saisan, Payam A

2018-05-04

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees. NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website 1 . The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.

Unravelling proximate cues of mass flowering in the tropical forests of South-East Asia from gene expression analyses.

PubMed

Yeoh, Suat Hui; Satake, Akiko; Numata, Shinya; Ichie, Tomoaki; Lee, Soon Leong; Basherudin, Norlia; Muhammad, Norwati; Kondo, Toshiaki; Otani, Tatsuya; Hashim, Mazlan; Tani, Naoki

2017-10-01

Elucidating the physiological mechanisms of the irregular yet concerted flowering rhythm of mass flowering tree species in the tropics requires long-term monitoring of flowering phenology, exogenous and endogenous environmental factors, as well as identifying interactions and dependencies among these factors. To investigate the proximate factors for floral initiation of mast seeding trees in the tropics, we monitored the expression dynamics of two key flowering genes, meteorological conditions and endogenous resources over two flowering events of Shorea curtisii and Shorea leprosula in the Malay Peninsula. Comparisons of expression dynamics of genes studied indicated functional conservation of FLOWERING LOCUS T (FT) and LEAFY (LFY) in Shorea. The genes were highly expressed at least 1 month before anthesis for both species. A mathematical model considering the synergistic effect of cool temperature and drought on activation of the flowering gene was successful in predicting the observed gene expression patterns. Requirement of both cool temperature and drought for floral transition suggested by the model implies that flowering phenologies of these species are sensitive to climate change. Our molecular phenology approach in the tropics sheds light on the conserved role of flowering genes in plants inhabiting different climate zones and can be widely applied to dissect the flowering processes in other plant species. © 2017 John Wiley & Sons Ltd.

Effect of spatial coherence of light on the photoregulation processes in cells

NASA Astrophysics Data System (ADS)

Budagovsky, A. V.; Solovykh, N. V.; Yankovskaya, M. B.; Maslova, M. V.; Budagovskaya, O. N.; Budagovsky, I. A.

2016-07-01

The effect of the statistical properties of light on the value of the photoinduced reaction of the biological objects, which differ in the morphological and physiological characteristics, the optical properties, and the size of cells, was studied. The fruit of apple trees, the pollen of cherries, the microcuttings of blackberries in vitro, and the spores and the mycelium of fungi were irradiated by quasimonochromatic light fluxes with identical energy parameters but different values of coherence length and radius of correlation. In all cases, the greatest stimulation effect occurred when the cells completely fit in the volume of the coherence of the field, while both temporal and spatial coherence have a significant and mathematically certain impact on the physiological activity of cells. It was concluded that not only the spectral, but also the statistical (coherent) properties of the acting light play an important role in the photoregulation process.

Amazonian forest-savanna bistability and human impact

NASA Astrophysics Data System (ADS)

Wuyts, Bert; Champneys, Alan R.; House, Joanna I.

2017-05-01

A bimodal distribution of tropical tree cover at intermediate precipitation levels has been presented as evidence of fire-induced bistability. Here we subdivide satellite vegetation data into those from human-unaffected areas and those from regions close to human-cultivated zones. Bimodality is found to be almost absent in the unaffected regions, whereas it is significantly enhanced close to cultivated zones. Assuming higher logging rates closer to cultivated zones and spatial diffusion of fire, our spatiotemporal mathematical model reproduces these patterns. Given a gradient of climatic and edaphic factors, rather than bistability there is a predictable spatial boundary, a Maxwell point, that separates regions where forest and savanna states are naturally selected. While bimodality can hence be explained by anthropogenic edge effects and natural spatial heterogeneity, a narrow range of bimodality remaining in the human-unaffected data indicates that there is still bistability, although on smaller scales than claimed previously.

Detection of forest decline in Monchegorsk area

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

Hagner, O.; Rigina, O.

1998-01-01

Forests on the Kola Peninsula in Northern Russia are growing close to the limits of the northern tree line. They are subjected to both natural (low temperatures and a short period of biochemical activity) and anthropogenic stress factors. The metallurgic industry complex Severo-nickel close to the city of Monchegorsk in the central Russian Kola Peninsula is one of the major sources of sulfur dioxide (SO{sub 2}), nickel, and copper emissions in the region. The environmental impact on the surrounding area is dramatic. In this study multispectral changes observed in Landsat-MSS satellite image data from 1978, 1986, and 1992 are usedmore » to evaluate the relevance of a mathematical model of SO{sub 2} concentration in ambient air as a component for assessment of forest decline. The multispectral changes detected were found to have a statistically significant correspondence to the modeled (SO{sub 2}) concentration levels in ambient air.« less

Dendritic trafficking faces physiologically critical speed-precision tradeoffs

DOE PAGES

Williams, Alex H.; O'Donnell, Cian; Sejnowski, Terrence J.; ...

2016-12-30

Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the ‘sushi-belt model’. Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, and show that it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimatesmore » of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. In conclusion, these findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons.« less

Collaborative eHealth Meets Security: Privacy-Enhancing Patient Profile Management.

PubMed

Sanchez-Guerrero, Rosa; Mendoza, Florina Almenarez; Diaz-Sanchez, Daniel; Cabarcos, Patricia Arias; Lopez, Andres Marin

2017-11-01

Collaborative healthcare environments offer potential benefits, including enhancing the healthcare quality delivered to patients and reducing costs. As a direct consequence, sharing of electronic health records (EHRs) among healthcare providers has experienced a noteworthy growth in the last years, since it enables physicians to remotely monitor patients' health and enables individuals to manage their own health data more easily. However, these scenarios face significant challenges regarding security and privacy of the extremely sensitive information contained in EHRs. Thus, a flexible, efficient, and standards-based solution is indispensable to guarantee selective identity information disclosure and preserve patient's privacy. We propose a privacy-aware profile management approach that empowers the patient role, enabling him to bring together various healthcare providers as well as user-generated claims into an unique credential. User profiles are represented through an adaptive Merkle Tree, for which we formalize the underlying mathematical model. Furthermore, performance of the proposed solution is empirically validated through simulation experiments.

Dendritic trafficking faces physiologically critical speed-precision tradeoffs

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

Williams, Alex H.; O'Donnell, Cian; Sejnowski, Terrence J.

Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the ‘sushi-belt model’. Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, and show that it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimatesmore » of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. In conclusion, these findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons.« less

Study on Failure of Third-Party Damage for Urban Gas Pipeline Based on Fuzzy Comprehensive Evaluation.

PubMed

Li, Jun; Zhang, Hong; Han, Yinshan; Wang, Baodong

2016-01-01

Focusing on the diversity, complexity and uncertainty of the third-party damage accident, the failure probability of third-party damage to urban gas pipeline was evaluated on the theory of analytic hierarchy process and fuzzy mathematics. The fault tree of third-party damage containing 56 basic events was built by hazard identification of third-party damage. The fuzzy evaluation of basic event probabilities were conducted by the expert judgment method and using membership function of fuzzy set. The determination of the weight of each expert and the modification of the evaluation opinions were accomplished using the improved analytic hierarchy process, and the failure possibility of the third-party to urban gas pipeline was calculated. Taking gas pipelines of a certain large provincial capital city as an example, the risk assessment structure of the method was proved to conform to the actual situation, which provides the basis for the safety risk prevention.

Physical principle of airway design in human lungs

NASA Astrophysics Data System (ADS)

Park, Keunhwan; Son, Taeho; Kim, Wonjung; Kim, Ho-Young

2014-11-01

From an engineering perspective, lungs are natural microfluidic devices that extract oxygen from air. In the bronchial tree, airways branch by dichotomy with a systematic reduction of their diameters. It is generally accepted that in conducting airways, which air passes on the way to the acinar airways from the atmosphere, the reduction ratio of diameter is closely related to the minimization of viscous dissipation. Such a principle is formulated as the Hess-Murray law. However, in acinar airways, where oxygen transfer to alveolae occurs, the diameter reduction with progressive generations is more moderate than in conducting airways. Noting that the dominant transfer mechanism in acinar airways is diffusion rather than advection, unlike conducting airways, we construct a mathematical model for oxygen transfer through a series of acinar airways. Our model allows us to predict the optimal airway reduction ratio that maximizes the oxygen transfer in a finite airway volume, thereby rationalizing the observed airway reduction ratio in acinar airways.

Model of two infectious diseases in nettle caterpillar population

NASA Astrophysics Data System (ADS)

Firdausi, F. Z.; Nuraini, N.

2016-04-01

Palm oil is a vital commodity to the economy of Indonesia. The area of oil palm plantations in Indonesia has increased from year to year. However, the effectiveness of palm oil production is reduced by pest infestation. One of the pest which often infests oil palm plantations is nettle caterpillar. The pest control used in this study is biological control, viz. biological agents given to oil palm trees. This paper describes a mathematical model of two infectious diseases in nettle caterpillar population. The two infectious diseases arise due to two biological agents, namely Bacillus thuringiensis bacterium and parasite which usually attack nettle caterpillars. The derivation of the model constructed in this paper is obtained from ordinary differential equations without time delay. The equilibrium points are analyzed. Two of three equilibrium points are stable if the Routh-Hurwitz criteria are fulfilled. In addition, this paper also presents the numerical simulation of the model which has been constructed.

Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago.

PubMed

Welch, Lonnie; Gaeta, Bruno; Kovats, Diane E; Frenkel Morgenstern, Milana

2018-01-01

The International Society of Computational Biology and Bioinformatics (ISCB) brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. Practitioners in these fields are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, structural formulae and protein models to flow diagrams, visual aids for problem-solving are omnipresent. The ISCB Art in Science Competition 2017 at the ISCB/ECCB 2017 conference in Prague offered a way to show the beauty of science in art form. Past artworks in this annual exhibition at ISMB combined outstanding beauty and aesthetics with deep insight that perfectly validated the exhibit's approach or went beyond the problem's solution. Others were surprising and inspiring through the transition from science to art, opening eyes and minds to reflect on the work being undertaken.

Non-Archimedean reaction-ultradiffusion equations and complex hierarchic systems

NASA Astrophysics Data System (ADS)

Zúñiga-Galindo, W. A.

2018-06-01

We initiate the study of non-Archimedean reaction-ultradiffusion equations and their connections with models of complex hierarchic systems. From a mathematical perspective, the equations studied here are the p-adic counterpart of the integro-differential models for phase separation introduced by Bates and Chmaj. Our equations are also generalizations of the ultradiffusion equations on trees studied in the 1980s by Ogielski, Stein, Bachas, Huberman, among others, and also generalizations of the master equations of the Avetisov et al models, which describe certain complex hierarchic systems. From a physical perspective, our equations are gradient flows of non-Archimedean free energy functionals and their solutions describe the macroscopic density profile of a bistable material whose space of states has an ultrametric structure. Some of our results are p-adic analogs of some well-known results in the Archimedean setting, however, the mechanism of diffusion is completely different due to the fact that it occurs in an ultrametric space.

Valiant load-balanced robust routing under hose model for WDM mesh networks

NASA Astrophysics Data System (ADS)

Zhang, Xiaoning; Li, Lemin; Wang, Sheng

2006-09-01

In this paper, we propose Valiant Load-Balanced robust routing scheme for WDM mesh networks under the model of polyhedral uncertainty (i.e., hose model), and the proposed routing scheme is implemented with traffic grooming approach. Our Objective is to maximize the hose model throughput. A mathematic formulation of Valiant Load-Balanced robust routing is presented and three fast heuristic algorithms are also proposed. When implementing Valiant Load-Balanced robust routing scheme to WDM mesh networks, a novel traffic-grooming algorithm called MHF (minimizing hop first) is proposed. We compare the three heuristic algorithms with the VPN tree under the hose model. Finally we demonstrate in the simulation results that MHF with Valiant Load-Balanced robust routing scheme outperforms the traditional traffic-grooming algorithm in terms of the throughput for the uniform/non-uniform traffic matrix under the hose model.

Flight dynamics simulation modeling and control of a large flexible tiltrotor aircraft

NASA Astrophysics Data System (ADS)

Juhasz, Ondrej

A high order rotorcraft mathematical model is developed and validated against the XV-15 and a Large Civil Tiltrotor (LCTR) concept. The mathematical model is generic and allows for any rotorcraft configuration, from single main rotor helicopters to coaxial and tiltrotor aircraft. Rigid-body and inflow states, as well as flexible wing and blade states are used in the analysis. The separate modeling of each rotorcraft component allows for structural flexibility to be included, which is important when modeling large aircraft where structural modes affect the flight dynamics frequency ranges of interest, generally 1 to 20 rad/sec. Details of the formulation of the mathematical model are given, including derivations of structural, aerodynamic, and inertial loads. The linking of the components of the aircraft is developed using an approach similar to multibody analyses by exploiting a tree topology, but without equations of constraints. Assessments of the effects of wing flexibility are given. Flexibility effects are evaluated by looking at the nature of the couplings between rigid-body modes and wing structural modes and vice versa. The effects of various different forms of structural feedback on aircraft dynamics are analyzed. A proportional-integral feedback on the structural acceleration is deemed to be most effective at both improving the damping and reducing the overall excitation of a structural mode. A model following control architecture is then implemented on full order flexible LCTR models. For this aircraft, the four lowest frequency structural modes are below 20 rad/sec, and are thus needed for control law development and analysis. The impact of structural feedback on both Attitude-Command, Attitude-Hold (ACAH) and Translational Rate Command (TRC) response types are investigated. A rigid aircraft model has optimistic performance characteristics, and a control system designed for a rigid aircraft could potentially destabilize a flexible one. The various control systems are flown in a fixed-base simulator. Pilot inputs and aircraft performance are recorded and analyzed.

Combined Effects of Pesticides and Trematode Infections on Hourglass Tree Frog Polypedates cruciger

PubMed Central

Jayawardena, Uthpala A.; Rohr, Jason R.; Navaratne, Ayanthi N.; Amerasinghe, Priyanie H.; Rajakaruna, Rupika S.

2016-01-01

The impact of widespread and common environmental factors, such as chemical contaminants, on infectious disease risk in amphibians is particularly important because both chemical contaminants and infectious disease have been implicated in worldwide amphibian declines. Here we report on the lone and combined effects of exposure to parasitic cercariae (larval stage) of the digenetic trematode, Acanthostomum burminis, and four commonly used pesticides (insecticides: chlorpyrifos, dimethoate; herbicides: glyphosate, propanil) at ecologically relevant concentrations on the survival, growth, and development of the common hourglass tree frog, Polypedates cruciger Blyth 1852. There was no evidence of any pesticide-induced mortality on cercariae because all the cercariae successfully penetrated each tadpole host regardless of pesticide treatment. In isolation, both cercarial and pesticide exposure significantly decreased frog survival, development, and growth, and increased developmental malformations, such as scoliosis, kyphosis, and also edema and skin ulcers. The combination of cercariae and pesticides generally posed greater risk to frogs than either factor alone by decreasing survival or growth or increasing time to metamorphosis or malformations. The exception was that lone exposure to chlorpyrifos had higher mortality without than with cercariae. Consistent with mathematical models that suggest that stress should increase the impact of generalist parasites, the weight of the evidence from the field and laboratory suggests that ecologically relevant concentrations of agrochemicals generally increase the threat that trematodes pose to amphibians, highlighting the importance of elucidating interactions between anthropogenic activities and infectious disease in taxa of conservation concern. PMID:26911919

Combined Effects of Pesticides and Trematode Infections on Hourglass Tree Frog Polypedates cruciger.

PubMed

Jayawardena, Uthpala A; Rohr, Jason R; Navaratne, Ayanthi N; Amerasinghe, Priyanie H; Rajakaruna, Rupika S

2016-03-01

The impact of widespread and common environmental factors, such as chemical contaminants, on infectious disease risk in amphibians is particularly important because both chemical contaminants and infectious disease have been implicated in worldwide amphibian declines. Here we report on the lone and combined effects of exposure to parasitic cercariae (larval stage) of the digenetic trematode, Acanthostomum burminis, and four commonly used pesticides (insecticides: chlorpyrifos, dimethoate; herbicides: glyphosate, propanil) at ecologically relevant concentrations on the survival, growth, and development of the common hourglass tree frog, Polypedates cruciger Blyth 1852. There was no evidence of any pesticide-induced mortality on cercariae because all the cercariae successfully penetrated each tadpole host regardless of pesticide treatment. In isolation, both cercarial and pesticide exposure significantly decreased frog survival, development, and growth, and increased developmental malformations, such as scoliosis, kyphosis, and also edema and skin ulcers. The combination of cercariae and pesticides generally posed greater risk to frogs than either factor alone by decreasing survival or growth or increasing time to metamorphosis or malformations. The exception was that lone exposure to chlorpyrifos had higher mortality without than with cercariae. Consistent with mathematical models that suggest that stress should increase the impact of generalist parasites, the weight of the evidence from the field and laboratory suggests that ecologically relevant concentrations of agrochemicals generally increase the threat that trematodes pose to amphibians, highlighting the importance of elucidating interactions between anthropogenic activities and infectious disease in taxa of conservation concern.

Spatial heterogeneity in the timing of birch budburst in response to future climate warming in Ireland

NASA Astrophysics Data System (ADS)

Caffarra, Amelia; Zottele, Fabio; Gleeson, Emily; Donnelly, Alison

2014-05-01

In order to predict the impact of future climate warming on trees it is important to quantify the effect climate has on their development. Our understanding of the phenological response to environmental drivers has given rise to various mathematical models of the annual growth cycle of plants. These models simulate the timing of phenophases by quantifying the relationship between development and its triggers, typically temperature. In addition, other environmental variables have an important role in determining the timing of budburst. For example, photoperiod has been shown to have a strong influence on phenological events of a number of tree species, including Betula pubescens (birch). A recently developed model for birch (DORMPHOT), which integrates the effects of temperature and photoperiod on budburst, was applied to future temperature projections from a 19-member ensemble of regional climate simulations (on a 25 km grid) generated as part of the ENSEMBLES project, to simulate the timing of birch budburst in Ireland each year up to the end of the present century. Gridded temperature time series data from the climate simulations were used as input to the DORMPHOT model to simulate future budburst timing. The results showed an advancing trend in the timing of birch budburst over most regions in Ireland up to 2100. Interestingly, this trend appeared greater in the northeast of the country than in the southwest, where budburst is currently relatively early. These results could have implications for future forest planning, species distribution modeling, and the birch allergy season.

A Hybrid Windkessel Model of Blood Flow in Arterial Tree Using Velocity Profile Method

NASA Astrophysics Data System (ADS)

Aboelkassem, Yasser; Virag, Zdravko

2016-11-01

For the study of pulsatile blood flow in the arterial system, we derived a coupled Windkessel-Womersley mathematical model. Initially, a 6-elements Windkessel model is proposed to describe the hemodynamics transport in terms of constant resistance, inductance and capacitance. This model can be seen as a two compartment model, in which the compartments are connected by a rigid pipe, modeled by one inductor and resistor. The first viscoelastic compartment models proximal part of the aorta, the second elastic compartment represents the rest of the arterial tree and aorta can be seen as the connection pipe. Although the proposed 6-elements lumped model was able to accurately reconstruct the aortic pressure, it can't be used to predict the axial velocity distribution in the aorta and the wall shear stress and consequently, proper time varying pressure drop. We then modified this lumped model by replacing the connection pipe circuit elements with a vessel having a radius R and a length L. The pulsatile flow motions in the vessel are resolved instantaneously along with the Windkessel like model enable not only accurate prediction of the aortic pressure but also wall shear stress and frictional pressure drop. The proposed hybrid model has been validated using several in-vivo aortic pressure and flow rate data acquired from different species such as, humans, dogs and pigs. The method accurately predicts the time variation of wall shear stress and frictional pressure drop. Institute for Computational Medicine, Dept. Biomedical Engineering.

Regression trees modeling and forecasting of PM10 air pollution in urban areas

NASA Astrophysics Data System (ADS)

Stoimenova, M.; Voynikova, D.; Ivanov, A.; Gocheva-Ilieva, S.; Iliev, I.

2017-10-01

Fine particulate matter (PM10) air pollution is a serious problem affecting the health of the population in many Bulgarian cities. As an example, the object of this study is the pollution with PM10 of the town of Pleven, Northern Bulgaria. The measured concentrations of this air pollutant for this city consistently exceeded the permissible limits set by European and national legislation. Based on data for the last 6 years (2011-2016), the analysis shows that this applies both to the daily limit of 50 micrograms per cubic meter and the allowable number of daily concentration exceedances to 35 per year. Also, the average annual concentration of PM10 exceeded the prescribed norm of no more than 40 micrograms per cubic meter. The aim of this work is to build high performance mathematical models for effective prediction and forecasting the level of PM10 pollution. The study was conducted with the powerful flexible data mining technique Classification and Regression Trees (CART). The values of PM10 were fitted with respect to meteorological data such as maximum and minimum air temperature, relative humidity, wind speed and direction and others, as well as with time and autoregressive variables. As a result the obtained CART models demonstrate high predictive ability and fit the actual data with up to 80%. The best models were applied for forecasting the level pollution for 3 to 7 days ahead. An interpretation of the modeling results is presented.

Coalgebraic structure of genetic inheritance.

PubMed

Tian, Jianjun; Li, Bai-Lian

2004-09-01

Although in the broadly defined genetic algebra, multiplication suggests a forward direction of from parents to progeny, when looking from the reverse direction, it also suggests to us a new algebraic structure-coalge- braic structure, which we call genetic coalgebras. It is not the dual coalgebraic structure and can be used in the construction of phylogenetic trees. Math- ematically, to construct phylogenetic trees means we need to solve equations x([n]) = a, or x([n]) = b. It is generally impossible to solve these equations inalgebras. However, we can solve them in coalgebras in the sense of tracing back for their ancestors. A thorough exploration of coalgebraic structure in genetics is apparently necessary. Here, we develop a theoretical framework of the coalgebraic structure of genetics. From biological viewpoint, we defined various fundamental concepts and examined their elementary properties that contain genetic significance. Mathematically, by genetic coalgebra, we mean any coalgebra that occurs in genetics. They are generally noncoassociative and without counit; and in the case of non-sex-linked inheritance, they are cocommutative. Each coalgebra with genetic realization has a baric property. We have also discussed the methods to construct new genetic coalgebras, including cocommutative duplication, the tensor product, linear combinations and the skew linear map, which allow us to describe complex genetic traits. We also put forward certain theorems that state the relationship between gametic coalgebra and gametic algebra. By Brower's theorem in topology, we prove the existence of equilibrium state for the in-evolution operator.

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.

PubMed

Bezemer, Daniela; Cori, Anne; Ratmann, Oliver; van Sighem, Ard; Hermanides, Hillegonda S; Dutilh, Bas E; Gras, Luuk; Rodrigues Faria, Nuno; van den Hengel, Rob; Duits, Ashley J; Reiss, Peter; de Wolf, Frank; Fraser, Christophe

2015-11-01

The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains. As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters. The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added.

Chang'E-3 data pre-processing system based on scientific workflow

NASA Astrophysics Data System (ADS)

tan, xu; liu, jianjun; wang, yuanyuan; yan, wei; zhang, xiaoxia; li, chunlai

2016-04-01

The Chang'E-3(CE3) mission have obtained a huge amount of lunar scientific data. Data pre-processing is an important segment of CE3 ground research and application system. With a dramatic increase in the demand of data research and application, Chang'E-3 data pre-processing system(CEDPS) based on scientific workflow is proposed for the purpose of making scientists more flexible and productive by automating data-driven. The system should allow the planning, conduct and control of the data processing procedure with the following possibilities: • describe a data processing task, include:1)define input data/output data, 2)define the data relationship, 3)define the sequence of tasks,4)define the communication between tasks,5)define mathematical formula, 6)define the relationship between task and data. • automatic processing of tasks. Accordingly, Describing a task is the key point whether the system is flexible. We design a workflow designer which is a visual environment for capturing processes as workflows, the three-level model for the workflow designer is discussed:1) The data relationship is established through product tree.2)The process model is constructed based on directed acyclic graph(DAG). Especially, a set of process workflow constructs, including Sequence, Loop, Merge, Fork are compositional one with another.3)To reduce the modeling complexity of the mathematical formulas using DAG, semantic modeling based on MathML is approached. On top of that, we will present how processed the CE3 data with CEDPS.

Multi-criteria manufacturability indices for ranking high-concentration monoclonal antibody formulations.

PubMed

Yang, Yang; Velayudhan, Ajoy; Thornhill, Nina F; Farid, Suzanne S

2017-09-01

The need for high-concentration formulations for subcutaneous delivery of therapeutic monoclonal antibodies (mAbs) can present manufacturability challenges for the final ultrafiltration/diafiltration (UF/DF) step. Viscosity levels and the propensity to aggregate are key considerations for high-concentration formulations. This work presents novel frameworks for deriving a set of manufacturability indices related to viscosity and thermostability to rank high-concentration mAb formulation conditions in terms of their ease of manufacture. This is illustrated by analyzing published high-throughput biophysical screening data that explores the influence of different formulation conditions (pH, ions, and excipients) on the solution viscosity and product thermostability. A decision tree classification method, CART (Classification and Regression Tree) is used to identify the critical formulation conditions that influence the viscosity and thermostability. In this work, three different multi-criteria data analysis frameworks were investigated to derive manufacturability indices from analysis of the stress maps and the process conditions experienced in the final UF/DF step. Polynomial regression techniques were used to transform the experimental data into a set of stress maps that show viscosity and thermostability as functions of the formulation conditions. A mathematical filtrate flux model was used to capture the time profiles of protein concentration and flux decay behavior during UF/DF. Multi-criteria decision-making analysis was used to identify the optimal formulation conditions that minimize the potential for both viscosity and aggregation issues during UF/DF. Biotechnol. Bioeng. 2017;114: 2043-2056. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Perodicals, Inc. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Perodicals, Inc.

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

PubMed Central

Kolaczkowski, Bryan; Thornton, Joseph W.

2009-01-01

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias—which is apparent under both controlled simulation conditions and in analyses of empirical sequence data—also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages—that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis. PMID:20011052

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

PubMed

Kolaczkowski, Bryan; Thornton, Joseph W

2009-12-09

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

Transient Response in a Dendritic Neuron Model for Current Injected at One Branch

PubMed Central

Rinzel, John; Rall, Wilfrid

1974-01-01

Mathematical expressions are obtained for the response function corresponding to an instantaneous pulse of current injected to a single dendritic branch in a branched dendritic neuron model. The theoretical model assumes passive membrane properties and the equivalent cylinder constraint on branch diameters. The response function when used in a convolution formula enables one to compute the voltage transient at any specified point in the dendritic tree for an arbitrary current injection at a given input location. A particular numerical example, for a brief current injection at a branch terminal, illustrates the attenuation and delay characteristics of the depolarization peak as it spreads throughout the neuron model. In contrast to the severe attenuation of voltage transients from branch input sites to the soma, the fraction of total input charge actually delivered to the soma and other trees is calculated to be about one-half. This fraction is independent of the input time course. Other numerical examples, which compare a branch terminal input site with a soma input site, demonstrate that, for a given transient current injection, the peak depolarization is not proportional to the input resistance at the injection site and, for a given synaptic conductance transient, the effective synaptic driving potential can be significantly reduced, resulting in less synaptic current flow and charge, for a branch input site. Also, for the synaptic case, the two inputs are compared on the basis of the excitatory post-synaptic potential (EPSP) seen at the soma and the total charge delivered to the soma. PMID:4424185

Multi‐criteria manufacturability indices for ranking high‐concentration monoclonal antibody formulations

PubMed Central

Velayudhan, Ajoy; Thornhill, Nina F.

2017-01-01

ABSTRACT The need for high‐concentration formulations for subcutaneous delivery of therapeutic monoclonal antibodies (mAbs) can present manufacturability challenges for the final ultrafiltration/diafiltration (UF/DF) step. Viscosity levels and the propensity to aggregate are key considerations for high‐concentration formulations. This work presents novel frameworks for deriving a set of manufacturability indices related to viscosity and thermostability to rank high‐concentration mAb formulation conditions in terms of their ease of manufacture. This is illustrated by analyzing published high‐throughput biophysical screening data that explores the influence of different formulation conditions (pH, ions, and excipients) on the solution viscosity and product thermostability. A decision tree classification method, CART (Classification and Regression Tree) is used to identify the critical formulation conditions that influence the viscosity and thermostability. In this work, three different multi‐criteria data analysis frameworks were investigated to derive manufacturability indices from analysis of the stress maps and the process conditions experienced in the final UF/DF step. Polynomial regression techniques were used to transform the experimental data into a set of stress maps that show viscosity and thermostability as functions of the formulation conditions. A mathematical filtrate flux model was used to capture the time profiles of protein concentration and flux decay behavior during UF/DF. Multi‐criteria decision‐making analysis was used to identify the optimal formulation conditions that minimize the potential for both viscosity and aggregation issues during UF/DF. Biotechnol. Bioeng. 2017;114: 2043–2056. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Perodicals, Inc. PMID:28464235

Comparing the performance of two CBIRS indexing schemes

NASA Astrophysics Data System (ADS)

Mueller, Wolfgang; Robbert, Guenter; Henrich, Andreas

2003-01-01

Content based image retrieval (CBIR) as it is known today has to deal with a number of challenges. Quickly summarized, the main challenges are firstly, to bridge the semantic gap between high-level concepts and low-level features using feedback, secondly to provide performance under adverse conditions. High-dimensional spaces, as well as a demanding machine learning task make the right way of indexing an important issue. When indexing multimedia data, most groups opt for extraction of high-dimensional feature vectors from the data, followed by dimensionality reduction like PCA (Principal Components Analysis) or LSI (Latent Semantic Indexing). The resulting vectors are indexed using spatial indexing structures such as kd-trees or R-trees, for example. Other projects, such as MARS and Viper propose the adaptation of text indexing techniques, notably the inverted file. Here, the Viper system is the most direct adaptation of text retrieval techniques to quantized vectors. However, while the Viper query engine provides decent performance together with impressive user-feedback behavior, as well as the possibility for easy integration of long-term learning algorithms, and support for potentially infinite feature vectors, there has been no comparison of vector-based methods and inverted-file-based methods under similar conditions. In this publication, we compare a CBIR query engine that uses inverted files (Bothrops, a rewrite of the Viper query engine based on a relational database), and a CBIR query engine based on LSD (Local Split Decision) trees for spatial indexing using the same feature sets. The Benchathlon initiative works on providing a set of images and ground truth for simulating image queries by example and corresponding user feedback. When performing the Benchathlon benchmark on a CBIR system (the System Under Test, SUT), a benchmarking harness connects over internet to the SUT, performing a number of queries using an agreed-upon protocol, the multimedia retrieval markup language (MRML). Using this benchmark one can measure the quality of retrieval, as well as the overall (speed) performance of the benchmarked system. Our Benchmarks will draw on the Benchathlon"s work for documenting the retrieval performance of both inverted file-based and LSD tree based techniques. However in addition to these results, we will present statistics, that can be obtained only inside the system under test. These statistics will include the number of complex mathematical operations, as well as the amount of data that has to be read from disk during operation of a query.

Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.

PubMed

Sumner, Jeremy G; Taylor, Amelia; Holland, Barbara R; Jarvis, Peter D

2017-12-01

Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site patterns that, in expectation value, either vanish for particular evolutionary trees (in the case of phylogenetic invariants) or have well understood transformation properties (in the case of Markov invariants). While both approaches have been valued for their intrinsic mathematical interest, it is not clear how they relate to each other, and to what extent they can be used as practical tools for inference of phylogenetic trees. In this paper, by focusing on the special case of binary sequence data and quartets of taxa, we are able to view these two different polynomial-based approaches within a common framework. To motivate the discussion, we present three desirable statistical properties that we argue any invariant-based phylogenetic method should satisfy: (1) sensible behaviour under reordering of input sequences; (2) stability as the taxa evolve independently according to a Markov process; and (3) explicit dependence on the assumption of a continuous-time process. Motivated by these statistical properties, we develop and explore several new phylogenetic inference methods. In particular, we develop a statistically bias-corrected version of the Markov invariants approach which satisfies all three properties. We also extend previous work by showing that the phylogenetic invariants can be implemented in such a way as to satisfy property (3). A simulation study shows that, in comparison to other methods, our new proposed approach based on bias-corrected Markov invariants is extremely powerful for phylogenetic inference. The binary case is of particular theoretical interest as-in this case only-the Markov invariants can be expressed as linear combinations of the phylogenetic invariants. A wider implication of this is that, for models with more than two states-for example DNA sequence alignments with four-state models-we find that methods which rely on phylogenetic invariants are incapable of satisfying all three of the stated statistical properties. This is because in these cases the relevant Markov invariants belong to a class of polynomials independent from the phylogenetic invariants.

Fast Marching Tree: a Fast Marching Sampling-Based Method for Optimal Motion Planning in Many Dimensions*

PubMed Central

Janson, Lucas; Schmerling, Edward; Clark, Ashley; Pavone, Marco

2015-01-01

In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional configuration spaces. This algorithm is proven to be asymptotically optimal and is shown to converge to an optimal solution faster than its state-of-the-art counterparts, chiefly PRM* and RRT*. The FMT* algorithm performs a “lazy” dynamic programming recursion on a predetermined number of probabilistically-drawn samples to grow a tree of paths, which moves steadily outward in cost-to-arrive space. As such, this algorithm combines features of both single-query algorithms (chiefly RRT) and multiple-query algorithms (chiefly PRM), and is reminiscent of the Fast Marching Method for the solution of Eikonal equations. As a departure from previous analysis approaches that are based on the notion of almost sure convergence, the FMT* algorithm is analyzed under the notion of convergence in probability: the extra mathematical flexibility of this approach allows for convergence rate bounds—the first in the field of optimal sampling-based motion planning. Specifically, for a certain selection of tuning parameters and configuration spaces, we obtain a convergence rate bound of order O(n−1/d+ρ), where n is the number of sampled points, d is the dimension of the configuration space, and ρ is an arbitrarily small constant. We go on to demonstrate asymptotic optimality for a number of variations on FMT*, namely when the configuration space is sampled non-uniformly, when the cost is not arc length, and when connections are made based on the number of nearest neighbors instead of a fixed connection radius. Numerical experiments over a range of dimensions and obstacle configurations confirm our the-oretical and heuristic arguments by showing that FMT*, for a given execution time, returns substantially better solutions than either PRM* or RRT*, especially in high-dimensional configuration spaces and in scenarios where collision-checking is expensive. PMID:27003958

[Effects of crop tree release on stand growth and stand structure of Cunninghamia lanceolata plantation].

PubMed

Wu, Jian-qiang; Wang, Yi-xiang; Yang, Yi; Zhu, Ting-ting; Zhu, Xu-dan

2015-02-01

Crop trees were selected in a 26-year-old even-aged Cunninghamia lanceolata plantation in Lin' an, and compared in plots that were released and unreleased to examine growth and structure responses for 3 years after thinning. Crop tree release significantly increased the mean increments of diameter and volume of individual tree by 1.30 and 1.25 times relative to trees in control stands, respectively. The increments of diameter and volume of crop trees were significantly higher than those of general trees in thinning plots, crop trees and general trees in control plots, which suggested that the responses from different tree types to crop tree release treatment were different. Crop tree release increased the average distances of crop trees to the nearest neighboring trees, reducing competition among crop trees by about 68.2%. 3-year stand volume increment for thinning stands had no significant difference with that of control stands although the number of trees was only 81.5% of the control. Crop trees in thinned plots with diameters over than 14 cm reached 18.0% over 3 years, compared with 12.0% for trees without thinning, suggesting that crop tree release benefited the larger individual trees. The pattern of tree locations in thinning plots tended to be random, complying with the rule that tree distribution pattern changes with growth. Crop tree release in C. lanceolata plantation not only promoted the stand growth, but also optimized the stand structure, benefiting crop trees sustained rapid growth and larger diameter trees production.

MATLAB for laser speckle contrast analysis (LASCA): a practice-based approach

NASA Astrophysics Data System (ADS)

Postnikov, Eugene B.; Tsoy, Maria O.; Postnov, Dmitry E.

2018-04-01

Laser Speckle Contrast Analysis (LASCA) is one of the most powerful modern methods for revealing blood dynamics. The experimental design and theory for this method are well established, and the computational recipie is often regarded to be trivial. However, the achieved performance and spatial resolution may considerable differ for different implementations. We comprise a minireview of known approaches to the spatial laser speckle contrast data processing and their realization in MATLAB code providing an explicit correspondence to the mathematical representation, a discussion of available implementations. We also present the algorithm based on the 2D Haar wavelet transform, also supplied with the program code. This new method provides an opportunity to introduce horizontal, vertical and diagonal speckle contrasts; it may be used for processing highly anisotropic images of vascular trees. We provide the comparative analysis of the accuracy of vascular pattern detection and the processing times with a special attention to details of the used MATLAB procedures.

A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

PubMed Central

Faure, Emmanuel; Savy, Thierry; Rizzi, Barbara; Melani, Camilo; Stašová, Olga; Fabrèges, Dimitri; Špir, Róbert; Hammons, Mark; Čúnderlík, Róbert; Recher, Gaëlle; Lombardot, Benoît; Duloquin, Louise; Colin, Ingrid; Kollár, Jozef; Desnoulez, Sophie; Affaticati, Pierre; Maury, Benoît; Boyreau, Adeline; Nief, Jean-Yves; Calvat, Pascal; Vernier, Philippe; Frain, Monique; Lutfalla, Georges; Kergosien, Yannick; Suret, Pierre; Remešíková, Mariana; Doursat, René; Sarti, Alessandro; Mikula, Karol; Peyriéras, Nadine; Bourgine, Paul

2016-01-01

The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology. PMID:26912388

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

PubMed Central

Tamura, Koichiro; Tao, Qiqing; Kumar, Sudhir

2018-01-01

Abstract RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits. PMID:29893954

Study on Failure of Third-Party Damage for Urban Gas Pipeline Based on Fuzzy Comprehensive Evaluation

PubMed Central

Li, Jun; Zhang, Hong; Han, Yinshan; Wang, Baodong

2016-01-01

Focusing on the diversity, complexity and uncertainty of the third-party damage accident, the failure probability of third-party damage to urban gas pipeline was evaluated on the theory of analytic hierarchy process and fuzzy mathematics. The fault tree of third-party damage containing 56 basic events was built by hazard identification of third-party damage. The fuzzy evaluation of basic event probabilities were conducted by the expert judgment method and using membership function of fuzzy set. The determination of the weight of each expert and the modification of the evaluation opinions were accomplished using the improved analytic hierarchy process, and the failure possibility of the third-party to urban gas pipeline was calculated. Taking gas pipelines of a certain large provincial capital city as an example, the risk assessment structure of the method was proved to conform to the actual situation, which provides the basis for the safety risk prevention. PMID:27875545

Accumulation of K{sup +} and Cs{sup +} in Tropical Plant Species

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

Velasco, H.; Rizzotto, M.; Lacerda, T.

2010-08-04

Concentrations of K{sup +} and {sup 137}Cs{sup +} in tissues of the Citrus aurantifolia were measured both by gamma spectrometry and neutron activation analysis, aiming to understand the behavior of monovalent inorganic cations in plants as well as its capability to store these elements. In contrast to K{sup +},Cs{sup +} ions are not essential elements to plants, what might explain the difference in bioavailability. However, our results have shown that {sup 137}Cs{sup +} is positively correlated to {sup 40}K{sup +} concentration within tropical plant species, suggesting that these elements might be assimilated in a similar way, and that they passmore » through the biological cycle together. A simple mathematical model was also proposed to describe the temporal evolution of {sup 40}K activity concentration in such tropical woody fruit species. This model exhibited close agreement with the {sup 40}K experimental results in the fruit ripening processes of lemon trees.« less

Dendritic trafficking faces physiologically critical speed-precision tradeoffs

PubMed Central

Williams, Alex H; O'Donnell, Cian; Sejnowski, Terrence J; O'Leary, Timothy

2016-01-01

Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the ‘sushi-belt model’ (Doyle and Kiebler, 2011). Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, and show that it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimates of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. These findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons. DOI: http://dx.doi.org/10.7554/eLife.20556.001 PMID:28034367

Quantification of intravoxel velocity standard deviation and turbulence intensity by generalizing phase-contrast MRI.

PubMed

Dyverfeldt, Petter; Sigfridsson, Andreas; Kvitting, John-Peder Escobar; Ebbers, Tino

2006-10-01

Turbulent flow, characterized by velocity fluctuations, is a contributing factor to the pathogenesis of several cardiovascular diseases. A clinical noninvasive tool for assessing turbulence is lacking, however. It is well known that the occurrence of multiple spin velocities within a voxel during the influence of a magnetic gradient moment causes signal loss in phase-contrast magnetic resonance imaging (PC-MRI). In this paper a mathematical derivation of an expression for computing the standard deviation (SD) of the blood flow velocity distribution within a voxel is presented. The SD is obtained from the magnitude of PC-MRI signals acquired with different first gradient moments. By exploiting the relation between the SD and turbulence intensity (TI), this method allows for quantitative studies of turbulence. For validation, the TI in an in vitro flow phantom was quantified, and the results compared favorably with previously published laser Doppler anemometry (LDA) results. This method has the potential to become an important tool for the noninvasive assessment of turbulence in the arterial tree.

Genomic region operation kit for flexible processing of deep sequencing data.

PubMed

Ovaska, Kristian; Lyly, Lauri; Sahu, Biswajyoti; Jänne, Olli A; Hautaniemi, Sampsa

2013-01-01

Computational analysis of data produced in deep sequencing (DS) experiments is challenging due to large data volumes and requirements for flexible analysis approaches. Here, we present a mathematical formalism based on set algebra for frequently performed operations in DS data analysis to facilitate translation of biomedical research questions to language amenable for computational analysis. With the help of this formalism, we implemented the Genomic Region Operation Kit (GROK), which supports various DS-related operations such as preprocessing, filtering, file conversion, and sample comparison. GROK provides high-level interfaces for R, Python, Lua, and command line, as well as an extension C++ API. It supports major genomic file formats and allows storing custom genomic regions in efficient data structures such as red-black trees and SQL databases. To demonstrate the utility of GROK, we have characterized the roles of two major transcription factors (TFs) in prostate cancer using data from 10 DS experiments. GROK is freely available with a user guide from >http://csbi.ltdk.helsinki.fi/grok/.

Requirements for plant coexistence through pollination niche partitioning

PubMed Central

Benadi, Gita

2015-01-01

Plant–pollinator interactions are often thought to have been a decisive factor in the diversification of flowering plants, but to be of little or no importance for the maintenance of existing plant diversity. In a recent opinion paper, Pauw (2013 Trends Ecol. Evol. 28, 30–37. (doi:10.1016/j.tree.2012.07.019)) challenged this view by proposing a mechanism of diversity maintenance based on pollination niche partitioning. In this article, I investigate under which conditions the mechanism suggested by Pauw can promote plant coexistence, using a mathematical model of plant and pollinator population dynamics. Numerical simulations show that this mechanism is most effective when the costs of searching for flowers are low, pollinator populations are strongly limited by resources other than pollen and nectar, and plant–pollinator interactions are sufficiently specialized. I review the empirical literature on these three requirements, discuss additional factors that may be important for diversity maintenance through pollination niche partitioning, and provide recommendations on how to detect this coexistence mechanism in natural plant communities. PMID:26108627

Anticipatory systems using a probabilistic-possibilistic formalism

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

Tsoukalas, L.H.

1989-01-01

A methodology for the realization of the Anticipatory Paradigm in the diagnosis and control of complex systems, such as power plants, is developed. The objective is to synthesize engineering systems as analogs of certain biological systems which are capable of modifying their present states on the basis of anticipated future states. These future states are construed to be the output of predictive, numerical, stochastic or symbolic models. The mathematical basis of the implementation is developed on the basis of a formulation coupling probabilistic (random) and possibilistic(fuzzy) data in the form of an Information Granule. Random data are generated from observationsmore » and sensors input from the environment. Fuzzy data consists of eqistemic information, such as criteria or constraints qualifying the environmental inputs. The approach generates mathematical performance measures upon which diagnostic inferences and control functions are based. Anticipated performance is generated using a fuzzified Bayes formula. Triplex arithmetic is used in the numerical estimation of the performance measures. Representation of the system is based upon a goal-tree within the rule-based paradigm from the field of Applied Artificial Intelligence. The ensuing construction incorporates a coupling of Symbolic and Procedural programming methods. As a demonstration of the possibility of constructing such systems, a model-based system of a nuclear reactor is constructed. A numerical model of the reactor as a damped simple harmonic oscillator is used. The neutronic behavior is described by a point kinetics model with temperature feedback. The resulting system is programmed in OPS5 for the symbolic component and in FORTRAN for the procedural part.« less

Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari)

PubMed Central

Gil, Zulma Nancy; Benavides, Pablo; Souza, Og De; Acevedo, Flor Edith; Lima, Eraldo

2015-01-01

The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was Y^=αβXi, being Y^ the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. PMID:26078300

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

PubMed Central

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

2016-01-01

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

Tree Nut Allergies

MedlinePlus

... Blog Vision Awards Common Allergens Tree Nut Allergy Tree Nut Allergy Learn about tree nut allergy, how ... a Tree Nut Label card . Allergic Reactions to Tree Nuts Tree nuts can cause a severe and ...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... agricultural products. Owner means one who had legal ownership of the trees, bushes, vines, or livestock for... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

TreePOD: Sensitivity-Aware Selection of Pareto-Optimal Decision Trees.

PubMed

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

2018-01-01

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

MASTtreedist: visualization of tree space based on maximum agreement subtree.

PubMed

Huang, Hong; Li, Yongji

2013-01-01

Phylogenetic tree construction process might produce many candidate trees as the "best estimates." As the number of constructed phylogenetic trees grows, the need to efficiently compare their topological or physical structures arises. One of the tree comparison's software tools, the Mesquite's Tree Set Viz module, allows the rapid and efficient visualization of the tree comparison distances using multidimensional scaling (MDS). Tree-distance measures, such as Robinson-Foulds (RF), for the topological distance among different trees have been implemented in Tree Set Viz. New and sophisticated measures such as Maximum Agreement Subtree (MAST) can be continuously built upon Tree Set Viz. MAST can detect the common substructures among trees and provide more precise information on the similarity of the trees, but it is NP-hard and difficult to implement. In this article, we present a practical tree-distance metric: MASTtreedist, a MAST-based comparison metric in Mesquite's Tree Set Viz module. In this metric, the efficient optimizations for the maximum weight clique problem are applied. The results suggest that the proposed method can efficiently compute the MAST distances among trees, and such tree topological differences can be translated as a scatter of points in two-dimensional (2D) space. We also provide statistical evaluation of provided measures with respect to RF-using experimental data sets. This new comparison module provides a new tree-tree pairwise comparison metric based on the differences of the number of MAST leaves among constructed phylogenetic trees. Such a new phylogenetic tree comparison metric improves the visualization of taxa differences by discriminating small divergences of subtree structures for phylogenetic tree reconstruction.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

2011-01-01

Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. PMID:22165819

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

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

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

PubMed Central

2013-01-01

Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

Thresholds of Disturbance: Land Management Effects on Vegetation and Nitrogen Dynamics

DTIC Science & Technology

2005-03-31

Legume 3 18 0.0435 Rhus aromatica Shrub 2 35 0.0002 Aesculus pavia Tree 0 10 0.0198 Celtis sp. Tree 1 30 0.0002 Crataegus sp. Tree 13 62 0.0001...Shrub 37 63 0.0001 Aesculus pavia Tree 0 12 0.0043 Cercis canadensis Tree 0 13 0.0021 Crataegus sp. Tree 22 49 0.0222 Fraxinus americana Tree 0 11... Aesculus pavia Tree 0 15 0.0126 Ilex opaca Tree 0 27 0.0003 Liquidambar styraciflua Tree 18 75 0.0001 Quercus falcata Tree 9 79 0.0001 Quercus

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

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

2008-07-01

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

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

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

2008-04-01

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

TreeCmp: Comparison of Trees in Polynomial Time

PubMed Central

Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

2012-01-01

When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees.

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

There's Life in Hazard Trees

Treesearch

Mary Torsello; Toni McLellan

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

Audubon Tree Study Program.

ERIC Educational Resources Information Center

National Audubon Society, New York, NY.

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

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.

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

Code of Federal Regulations, 2011 CFR

2011-07-01

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

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

Code of Federal Regulations, 2012 CFR

2012-07-01

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

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

Code of Federal Regulations, 2014 CFR

2014-07-01

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

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

Code of Federal Regulations, 2013 CFR

2013-07-01

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

7 CFR 1416.701 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 2005 Hurricane Tree Assistance Program § 1416.701 Definitions. Application means the “2005 Hurricane Tree Assistance Program” Application form. Fruit tree means a woody perennial plant having a single... acreage of the same crop of trees (including Christmas trees, ornamental trees, nursery trees, and potted...

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

PubMed

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

2011-06-01

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

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

PubMed

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

2015-01-01

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

ColorTree: a batch customization tool for phylogenic trees

PubMed Central

Chen, Wei-Hua; Lercher, Martin J

2009-01-01

Background Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. Findings In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. Conclusion ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files. PMID:19646243

ColorTree: a batch customization tool for phylogenic trees.

PubMed

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

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

Semiautomated landscape feature extraction and modeling

NASA Astrophysics Data System (ADS)

Wasilewski, Anthony A.; Faust, Nickolas L.; Ribarsky, William

2001-08-01

We have developed a semi-automated procedure for generating correctly located 3D tree objects form overhead imagery. Cross-platform software partitions arbitrarily large, geocorrected and geolocated imagery into management sub- images. The user manually selected tree areas from one or more of these sub-images. Tree group blobs are then narrowed to lines using a special thinning algorithm which retains the topology of the blobs, and also stores the thickness of the parent blob. Maxima along these thinned tree grous are found, and used as individual tree locations within the tree group. Magnitudes of the local maxima are used to scale the radii of the tree objects. Grossly overlapping trees are culled based on a comparison of tree-tree distance to combined radii. Tree color is randomly selected based on the distribution of sample tree pixels, and height is estimated form tree radius. The final tree objects are then inserted into a terrain database which can be navigated by VGIS, a high-resolution global terrain visualization system developed at Georgia Tech.

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

Technical Tree Climbing.

ERIC Educational Resources Information Center

Jenkins, Peter

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

The potential of the tree water potential.

PubMed

Steppe, Kathy

2018-06-12

Non-invasive quantification of tree water potential is one of the grand challenges for assessing the fate of trees and forests in the coming decades. Tree water potential is a robust and direct indicator of tree water status and is preferably used to track how trees, forests and vegetation in general respond to changes in climate and drought. In this issue of Tree Physiology, Dietrich et al. (2018) predict the daily canopy water potential of mature temperate trees from tree water deficit derived from stem diameter variation measurements.

[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.

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).

Tree Rings: Timekeepers of the Past.

ERIC Educational Resources Information Center

Phipps, R. L.; McGowan, J.

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

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.

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

PubMed Central

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

2014-01-01

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

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

USGS Publications Warehouse

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

2007-01-01

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

Current and potential tree locations in tree line ecotone of Changbai Mountains, Northeast China: the controlling effects of topography.

PubMed

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

2014-01-01

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

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.

Trees are good, but…

Treesearch

E.G. McPherson; F. Ferrini

2010-01-01

We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

Coalescent histories for caterpillar-like families.

PubMed

Rosenberg, Noah A

2013-01-01

A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree topology is important in gene tree probability computations, and more generally, in studying evolutionary possibilities for gene trees on species trees. Defining the Tr-caterpillar-like family as a sequence of n-taxon trees constructed by replacing the r-taxon subtree of n-taxon caterpillars by a specific r-taxon labeled topology Tr, we examine the number of coalescent histories for caterpillar-like families with matching gene tree and species tree labeled topologies. For each Tr with size r≤8, we compute the number of coalescent histories for n-taxon trees in the Tr-caterpillar-like family. Next, as n→∞, we find that the limiting ratio of the numbers of coalescent histories for the Tr family and caterpillars themselves is correlated with the number of labeled histories for Tr. The results support a view that large numbers of coalescent histories occur when a tree has both a relatively balanced subtree and a high tree depth, contributing to deeper understanding of the combinatorics of gene trees and species trees.

[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.

Growth of a Pine Tree

ERIC Educational Resources Information Center

Rollinson, Susan Wells

2012-01-01

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

A Metric on Phylogenetic Tree Shapes.

PubMed

Colijn, C; Plazzotta, G

2018-01-01

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

Predicting vegetation type through physiological and environmental interactions with leaf traits: evergreen and deciduous forests in an earth system modeling framework.

PubMed

Weng, Ensheng; Farrior, Caroline E; Dybzinski, Ray; Pacala, Stephen W

2017-06-01

Earth system models are incorporating plant trait diversity into their land components to better predict vegetation dynamics in a changing climate. However, extant plant trait distributions will not allow extrapolations to novel community assemblages in future climates, which will require a mechanistic understanding of the trade-offs that determine trait diversity. In this study, we show how physiological trade-offs involving leaf mass per unit area (LMA), leaf lifespan, leaf nitrogen, and leaf respiration may explain the distribution patterns of evergreen and deciduous trees in the temperate and boreal zones based on (1) an evolutionary analysis of a simple mathematical model and (2) simulation experiments of an individual-based dynamic vegetation model (i.e., LM3-PPA). The evolutionary analysis shows that these leaf traits set up a trade-off between carbon- and nitrogen-use efficiency at the scale of individual trees and therefore determine competitively dominant leaf strategies. As soil nitrogen availability increases, the dominant leaf strategy switches from one that is high in nitrogen-use efficiency to one that is high in carbon-use efficiency or, equivalently, from high-LMA/long-lived leaves (i.e., evergreen) to low-LMA/short-lived leaves (i.e., deciduous). In a region of intermediate soil nitrogen availability, the dominant leaf strategy may be either deciduous or evergreen depending on the initial conditions of plant trait abundance (i.e., founder controlled) due to feedbacks of leaf traits on soil nitrogen mineralization through litter quality. Simulated successional patterns by LM3-PPA from the leaf physiological trade-offs are consistent with observed successional dynamics of evergreen and deciduous forests at three sites spanning the temperate to boreal zones. © 2016 John Wiley & Sons Ltd.

Numerical simulation of blood flow and pressure drop in the pulmonary arterial and venous circulation

PubMed Central

Qureshi, M. Umar; Vaughan, Gareth D.A.; Sainsbury, Christopher; Johnson, Martin; Peskin, Charles S.; Olufsen, Mette S.; Hill, N.A.

2014-01-01

A novel multiscale mathematical and computational model of the pulmonary circulation is presented and used to analyse both arterial and venous pressure and flow. This work is a major advance over previous studies by Olufsen and coworkers (Ottesen et al., 2003; Olufsen et al., 2012) which only considered the arterial circulation. For the first three generations of vessels within the pulmonary circulation, geometry is specified from patient-specific measurements obtained using magnetic resonance imaging (MRI). Blood flow and pressure in the larger arteries and veins are predicted using a nonlinear, cross-sectional-area-averaged system of equations for a Newtonian fluid in an elastic tube. Inflow into the main pulmonary artery is obtained from MRI measurements, while pressure entering the left atrium from the main pulmonary vein is kept constant at the normal mean value of 2 mmHg. Each terminal vessel in the network of ‘large’ arteries is connected to its corresponding terminal vein via a network of vessels representing the vascular bed of smaller arteries and veins. We develop and implement an algorithm to calculate the admittance of each vascular bed, using bifurcating structured trees and recursion. The structured-tree models take into account the geometry and material properties of the ‘smaller’ arteries and veins of radii ≥ 50µm. We study the effects on flow and pressure associated with three classes of pulmonary hypertension expressed via stiffening of larger and smaller vessels, and vascular rarefaction. The results of simulating these pathological conditions are in agreement with clinical observations, showing that the model has potential for assisting with diagnosis and treatment of circulatory diseases within the lung. PMID:24610385

Predictions of the pathological response to neoadjuvant chemotherapy in patients with primary breast cancer using a data mining technique.

PubMed

Takada, M; Sugimoto, M; Ohno, S; Kuroi, K; Sato, N; Bando, H; Masuda, N; Iwata, H; Kondo, M; Sasano, H; Chow, L W C; Inamoto, T; Naito, Y; Tomita, M; Toi, M

2012-07-01

Nomogram, a standard technique that utilizes multiple characteristics to predict efficacy of treatment and likelihood of a specific status of an individual patient, has been used for prediction of response to neoadjuvant chemotherapy (NAC) in breast cancer patients. The aim of this study was to develop a novel computational technique to predict the pathological complete response (pCR) to NAC in primary breast cancer patients. A mathematical model using alternating decision trees, an epigone of decision tree, was developed using 28 clinicopathological variables that were retrospectively collected from patients treated with NAC (n = 150), and validated using an independent dataset from a randomized controlled trial (n = 173). The model selected 15 variables to predict the pCR with yielding area under the receiver operating characteristics curve (AUC) values of 0.766 [95 % confidence interval (CI)], 0.671-0.861, P value < 0.0001) in cross-validation using training dataset and 0.787 (95 % CI 0.716-0.858, P value < 0.0001) in the validation dataset. Among three subtypes of breast cancer, the luminal subgroup showed the best discrimination (AUC = 0.779, 95 % CI 0.641-0.917, P value = 0.0059). The developed model (AUC = 0.805, 95 % CI 0.716-0.894, P value < 0.0001) outperformed multivariate logistic regression (AUC = 0.754, 95 % CI 0.651-0.858, P value = 0.00019) of validation datasets without missing values (n = 127). Several analyses, e.g. bootstrap analysis, revealed that the developed model was insensitive to missing values and also tolerant to distribution bias among the datasets. Our model based on clinicopathological variables showed high predictive ability for pCR. This model might improve the prediction of the response to NAC in primary breast cancer patients.

Parameter estimation in tree graph metabolic networks.

PubMed

Astola, Laura; Stigter, Hans; Gomez Roldan, Maria Victoria; van Eeuwijk, Fred; Hall, Robert D; Groenenboom, Marian; Molenaar, Jaap J

2016-01-01

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

Composition and structure of Pinus koraiensis mixed forest respond to spatial climatic changes.

PubMed

Zhang, Jingli; Zhou, Yong; Zhou, Guangsheng; Xiao, Chunwang

2014-01-01

Although some studies have indicated that climate changes can affect Pinus koraiensis mixed forest, the responses of composition and structure of Pinus koraiensis mixed forests to climatic changes are unknown and the key climatic factors controlling the composition and structure of Pinus koraiensis mixed forest are uncertain. Field survey was conducted in the natural Pinus koraiensis mixed forests along a latitudinal gradient and an elevational gradient in Northeast China. In order to build the mathematical models for simulating the relationships of compositional and structural attributes of the Pinus koraiensis mixed forest with climatic and non-climatic factors, stepwise linear regression analyses were performed, incorporating 14 dependent variables and the linear and quadratic components of 9 factors. All the selected new models were computed under the +2°C and +10% precipitation and +4°C and +10% precipitation scenarios. The Max Temperature of Warmest Month, Mean Temperature of Warmest Quarter and Precipitation of Wettest Month were observed to be key climatic factors controlling the stand densities and total basal areas of Pinus koraiensis mixed forest. Increased summer temperatures and precipitations strongly enhanced the stand densities and total basal areas of broadleaf trees but had little effect on Pinus koraiensis under the +2°C and +10% precipitation scenario and +4°C and +10% precipitation scenario. These results show that the Max Temperature of Warmest Month, Mean Temperature of Warmest Quarter and Precipitation of Wettest Month are key climatic factors which shape the composition and structure of Pinus koraiensis mixed forest. Although the Pinus koraiensis would persist, the current forests dominated by Pinus koraiensis in the region would all shift and become broadleaf-dominated forests due to the dramatic increase of broadleaf trees under the future global warming and increased precipitation.

Chaotic Behaviuor of the Navier-Stokes Solutions, Gyroscopes and Storm Surging

NASA Astrophysics Data System (ADS)

Tchiguirinskaia, Ioulia; Schertzer, Daniel

2015-04-01

Storm surges are phenomena inflicting wide damages all over the planet. Unfortunately they are badly represented in classical forecast model schemes because their multiscale nature is at odd with the scale truncation of these models. For similar reasons, classical data analysis often compelled to considered them as 'outliers' of the normal atmospheric activity, whereas as in fact they result from the same physical mechanisms that create less extreme behavior. A better representation of storm surges requires a multicale understanding of how a cascade of seemingly harmless instabilities can generate major ones. This correspond to the conjectured, outstanding intermittency.of the chaotic behaviour of the Navier-Stokes solutions. However, our limited, mathematical understanding of the Navier-Stokes equations prevent us to directly use them to investigate this question. We therefore use the most relevant cascade model to theoretically tackle this question of intermittency, i.e. the Scaling Gyroscopes Cascade (SGC). Indeed, this model is obtained with the help of a non trivial tree-decomposition of the Lie structure of the Navier-Stokes equations. the SGC model is deduced from these equations by preserving only a certain type of direct interactions, while the resulting indirect interactions are built dynamically along the tree-structure of the cascade. Because its fundamental element corresponds to a 'top' -i.e., an object with which almost anyone began to discover the puzzling nonlinear properties of rotation!- the SGC model remains rather simple, yet not simplistic! In particular, the SGC model enables us to investigate in details the occurrence of the critical singularity of a first order multifractal phase transition, which theoretically define storm surges. Overall, these theoretical findings could significantly reduce numerous uncertainties of environmental risk assessments.

Dry season limnological conditions and basin geology exhibit complex relationships with δ13C and δ15N of carbon sources in four Neotropical floodplains.

PubMed

Zaia Alves, Gustavo H; Hoeinghaus, David J; Manetta, Gislaine I; Benedito, Evanilde

2017-01-01

Studies in freshwater ecosystems are seeking to improve understanding of carbon flow in food webs and stable isotopes have been influential in this work. However, variation in isotopic values of basal production sources could either be an asset or a hindrance depending on study objectives. We assessed the potential for basin geology and local limnological conditions to predict stable carbon and nitrogen isotope values of six carbon sources at multiple locations in four Neotropical floodplain ecosystems (Paraná, Pantanal, Araguaia, and Amazon). Limnological conditions exhibited greater variation within than among systems. δ15N differed among basins for most carbon sources, but δ13C did not (though high within-basin variability for periphyton, phytoplankton and particulate organic carbon was observed). Although δ13C and δ15N values exhibited significant correlations with some limnological factors within and among basins, those relationships differed among carbon sources. Regression trees for both carbon and nitrogen isotopes for all sources depicted complex and in some cases nested relationships, and only very limited similarity was observed among trees for different carbon sources. Although limnological conditions predicted variation in isotope values of carbon sources, we suggest the resulting models were too complex to enable mathematical corrections of source isotope values among sites based on these parameters. The importance of local conditions in determining variation in source isotope values suggest that isotopes may be useful for examining habitat use, dispersal and patch dynamics within heterogeneous floodplain ecosystems, but spatial variability in isotope values needs to be explicitly considered when testing ecosystem models of carbon flow in these systems.

Mating disruption of citrus leafminer mediated by a noncompetitive mechanism at a remarkably low pheromone release rate.

PubMed

Stelinski, L L; Miller, J R; Rogers, M E

2008-08-01

The citrus leafminer, Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), is a worldwide pest of citrus. A season-long investigation was conducted that evaluated mating disruption for this pest. Effective disruption of the male P. citrella orientation to pheromone traps (98%) and reduced flush infestation by larvae was achieved for 221 d with two deployments of a 3:1 blend of (Z,Z,E)-7,11,13-hexadecatrienal/(Z,Z)-7,11-hexadecadienal at a remarkably low rate of 1.5 g active ingredient (AI)/ha per deployment. To gain insight into the mechanism that mediates the disruption of P. citrella, male moth catch was quantified in replicated plots of citrus treated with varying densities of pheromone dispensers. The densities of septum dispensers compared were: 0 (0/ha, 0.0 g AI/ha), 0.2 (one every fifth tree or 35/ha, 0.05 g AI/ha), 1 (215/ha, 0.29 g AI/ha), and 5 per tree (1,100/ha, 1.5 g AI/ha). Profile analysis by previously published mathematical methods matched predictions of noncompetitive mating disruption. Behavioral observations of male P. citrella in the field revealed that males did not approach mating disruption dispensers in any of the dispenser density treatments. The current report presents the first set of profile analyses combined with direct behavioral observations consistent with previously published theoretical predictions for a noncompetitive mechanism of mating disruption. The results suggest that disruption of P. citrella should be effective even at high population densities given the density-independent nature of disruption for this species and the remarkably low rate of pheromone per hectare required for efficacy.

Identification of Lightning Gaps in Mangrove Forests Using Airborne LIDAR Measurements

NASA Astrophysics Data System (ADS)

Zhang, K.

2006-12-01

Mangrove forests are highly dynamic ecosystems and change frequently due to tropical storms, frost, and lightning. These factors can cause gaps in mangrove forests by damaging trees. Compared to gaps generated by storms and frost, gaps caused by lightning strikes are small, ranging from 50 to 300 m2. However, these small gaps may play a critical role in mangrove forest dynamics because of the frequent occurrence of lightning in tropical areas. It has been hypothesized that the turnover of mangrove forests is mainly due to the death and regeneration of trees in lightning gaps. However, there is a lack of data for gap occurrence in mangrove forests to verify this hypothesis. It is impractical to measure gaps through a field survey on a large scale because of the logistic difficulties of muddy mangrove forests. Airborne light detection and ranging (LIDAR) technology is an effective alternative because it provides direct measurements of ground and canopy elevations remotely. This study developed a method to identify lightning gaps in mangrove forests in terms of LIDAR measurements. First, LIDAR points are classified into vegetation and ground measurements using the progressive morphological filter. Second, a digital canopy model (DCM) is generated by subtracting a digital terrain model (DTM) from a digital surface model (DSM). The DSM is generated by interpolating raw LIDAR measurements, and DTM is produced by interpolating ground measurements. Third, a black top-hat mathematical morphological transformation is used to identify canopy gaps. Comparison of identified gap polygons with raw LIDAR measurements and field surveys shows that the proposed method identifies lightning gaps in mangrove forests successfully. The area of lightning gaps in mangrove forests in Everglades National Park is about 3% of total forest area, which verifies that lightning gaps play a critical role in mangrove forest turnover.

Dry season limnological conditions and basin geology exhibit complex relationships with δ13C and δ15N of carbon sources in four Neotropical floodplains

PubMed Central

Hoeinghaus, David J.; Manetta, Gislaine I.; Benedito, Evanilde

2017-01-01

Studies in freshwater ecosystems are seeking to improve understanding of carbon flow in food webs and stable isotopes have been influential in this work. However, variation in isotopic values of basal production sources could either be an asset or a hindrance depending on study objectives. We assessed the potential for basin geology and local limnological conditions to predict stable carbon and nitrogen isotope values of six carbon sources at multiple locations in four Neotropical floodplain ecosystems (Paraná, Pantanal, Araguaia, and Amazon). Limnological conditions exhibited greater variation within than among systems. δ15N differed among basins for most carbon sources, but δ13C did not (though high within-basin variability for periphyton, phytoplankton and particulate organic carbon was observed). Although δ13C and δ15N values exhibited significant correlations with some limnological factors within and among basins, those relationships differed among carbon sources. Regression trees for both carbon and nitrogen isotopes for all sources depicted complex and in some cases nested relationships, and only very limited similarity was observed among trees for different carbon sources. Although limnological conditions predicted variation in isotope values of carbon sources, we suggest the resulting models were too complex to enable mathematical corrections of source isotope values among sites based on these parameters. The importance of local conditions in determining variation in source isotope values suggest that isotopes may be useful for examining habitat use, dispersal and patch dynamics within heterogeneous floodplain ecosystems, but spatial variability in isotope values needs to be explicitly considered when testing ecosystem models of carbon flow in these systems. PMID:28358822

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

Abstract The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees’ branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. PMID:28472435

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes.

PubMed

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

2016-01-01

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

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes

PubMed Central

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

2016-01-01

Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and functioning. We furthermore conclude that artificial tree-hole analogues represent a useful experimental alternative to test effects of changes in forest management on natural communities. PMID:27187741

Trees in the Landscape.

ERIC Educational Resources Information Center

Webb, Richard; Forbatha, Ann

1982-01-01

Strategies for using trees in classroom instruction are provided. Includes: (1) activities (such as tree identification, mapping, measuring tree height/width); (2) list of asthetic, architectural, engineering, climate, and wildlife functions of trees; (3) tree discussion questions; and (4) references. (JN)

Tree-mediated methane emissions from tropical and temperate peatlands.

NASA Astrophysics Data System (ADS)

Pangala, S. R.; Gauci, V.; Hornibrook, E. R. C.; Gowing, D. J.

2012-04-01

Methane production and transport processes in peatlands are fairly well understood, but growing evidence for emission of methane through trees has highlighted the need to revisit methane transport processes. In wetland trees, morphological adaptations such as development of hypertrophied lenticels, aerenchyma and adventitious roots in response to soil anoxia mediates gas transport, transporting both oxygen from the atmosphere to oxygen-deprived roots and soil-produced methane from the root-zone to the atmosphere. Although, tree-mediated methane emissions from temperate tree species have been confirmed, methane emissions from tropical tree species and processes that control tree-mediated methane emissions remain unclear. This study explains the role of trees in transporting soil-produced methane to the atmosphere and uncovers the principal mechanisms of tree-mediated methane emissions. Methane emissions from eight tropical tree species and two temperate tree species were studied in situ. The mechanisms and controls on tree-mediated methane emissions were investigated using three year old common alder (Alnus glutinosa; 50 trees) grown under two artificially controlled water-table positions. Methane fluxes from whole mesocosms, the soil surface and tree stems were measured using static closed chambers. Both temperate and tropical tree species released significant quantities of methane, with tropical trees dominating ecosystem level methane fluxes. In temperate peatlands, both the methane gas transport mechanism and quantity of methane emitted from stems is tree-species dependent. In Alnus glutinosa, no correlations were observed between stomatal behaviour and tree-mediated methane emissions, however, stem methane emissions were positively correlated with both stem lenticel density and dissolved soil methane concentration. In Alnus glutinosa, no emissions were observed from leaf surfaces. The results demonstrate that exclusion of tree-mediated methane emissions from flux measurement campaigns in forested peatlands will lead to an underestimation of ecosystem-wide methane emissions.

The Inference of Gene Trees with Species Trees

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

2015-01-01

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

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

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

Olszyk, D.M.; Takemoto, B.K.; Kats, G.

1992-01-01

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

Size Matters a Lot: Drought-Affected Italian Oaks Are Smaller and Show Lower Growth Prior to Tree Death.

PubMed

Colangelo, Michele; Camarero, Jesús J; Borghetti, Marco; Gazol, Antonio; Gentilesca, Tiziana; Ripullone, Francesco

2017-01-01

Hydraulic theory suggests that tall trees are at greater risk of drought-triggered death caused by hydraulic failure than small trees. In addition the drop in growth, observed in several tree species prior to death, is often interpreted as an early-warning signal of impending death. We test these hypotheses by comparing size, growth, and wood-anatomy patterns of living and now-dead trees in two Italian oak forests showing recent mortality episodes. The mortality probability of trees is modeled as a function of recent growth and tree size. Drift-diffusion-jump (DDJ) metrics are used to detect early-warning signals. We found that the tallest trees of the anisohydric Italian oak better survived drought contrary to what was predicted by the theory. Dead trees were characterized by a lower height and radial-growth trend than living trees in both study sites. The growth reduction of now-dead trees started about 10 years prior to their death and after two severe spring droughts during the early 2000s. This critical transition in growth was detected by DDJ metrics in the most affected site. Dead trees were also more sensitive to drought stress in this site indicating different susceptibility to water shortage between trees. Dead trees did not form earlywood vessels with smaller lumen diameter than surviving trees but tended to form wider latewood vessels with a higher percentage of vessel area. Since living and dead trees showed similar competition we did not expect that moderate thinning and a reduction in tree density would increase the short-term survival probability of trees.

Stand conditions and tree characteristics affect quality of longleaf pine for red-cockaded woodpecker cavity trees

Treesearch

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

1997-01-01

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

Cavity tree selection by red-cockaded woodpeckers in relation to tree age

Treesearch

D. Craig Rudolph; Richard N. Conner

1991-01-01

We aged over 1350 Red-cockaded Woodpecker (Picoides borealis) cavity trees and a comparable number of randomly selected trees. Resulting data strongly support the hypothesis that Red-cockaded Woodpeckers preferentially select older trees. Ages of recently initiated cavity trees in the Texas study areas generally were similar to those of cavity trees...

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.

[The Application of the Fault Tree Analysis Method in Medical Equipment Maintenance].

PubMed

Liu, Hongbin

2015-11-01

In this paper, the traditional fault tree analysis method is presented, detailed instructions for its application characteristics in medical instrument maintenance is made. It is made significant changes when the traditional fault tree analysis method is introduced into the medical instrument maintenance: gave up the logic symbolic, logic analysis and calculation, gave up its complicated programs, and only keep its image and practical fault tree diagram, and the fault tree diagram there are also differences: the fault tree is no longer a logical tree but the thinking tree in troubleshooting, the definition of the fault tree's nodes is different, the composition of the fault tree's branches is also different.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

PubMed

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-11-18

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

PubMed Central

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-01-01

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

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

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

PubMed

Hannerz, Mats; Westin, Johan

2005-09-01

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

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

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Recursive algorithms for phylogenetic tree counting.

PubMed

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

2013-10-28

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

Directional phytoscreening: contaminant gradients in trees for plume delineation.

PubMed

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

2013-08-20

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

Measuring (bio)physical tree properties using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

2017-04-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

A quantitative evaluation of the three dimensional reconstruction of patients' coronary arteries.

PubMed

Klein, J L; Hoff, J G; Peifer, J W; Folks, R; Cooke, C D; King, S B; Garcia, E V

1998-04-01

Through extensive training and experience angiographers learn to mentally reconstruct the three dimensional (3D) relationships of the coronary arterial branches. Graphic computer technology can assist angiographers to more quickly visualize the coronary 3D structure from limited initial views and then help to determine additional helpful views by predicting subsequent angiograms before they are obtained. A new computer method for facilitating 3D reconstruction and visualization of human coronary arteries was evaluated by reconstructing biplane left coronary angiograms from 30 patients. The accuracy of the reconstruction was assessed in two ways: 1) by comparing the vessel's centerlines of the actual angiograms with the centerlines of a 2D projection of the 3D model projected into the exact angle of the actual angiogram; and 2) by comparing two 3D models generated by different simultaneous pairs on angiograms. The inter- and intraobserver variability of reconstruction were evaluated by mathematically comparing the 3D model centerlines of repeated reconstructions. The average absolute corrected displacement of 14,662 vessel centerline points in 2D from 30 patients was 1.64 +/- 2.26 mm. The average corrected absolute displacement of 3D models generated from different biplane pairs was 7.08 +/- 3.21 mm. The intraobserver variability of absolute 3D corrected displacement was 5.22 +/- 3.39 mm. The interobserver variability was 6.6 +/- 3.1 mm. The centerline analyses show that the reconstruction algorithm is mathematically accurate and reproducible. The figures presented in this report put these measurement errors into clinical perspective showing that they yield an accurate representation of the clinically relevant information seen on the actual angiograms. These data show that this technique can be clinically useful by accurately displaying in three dimensions the complex relationships of the branches of the coronary arterial tree.

A guide to phylogenetic metrics for conservation, community ecology and macroecology.

PubMed

Tucker, Caroline M; Cadotte, Marc W; Carvalho, Silvia B; Davies, T Jonathan; Ferrier, Simon; Fritz, Susanne A; Grenyer, Rich; Helmus, Matthew R; Jin, Lanna S; Mooers, Arne O; Pavoine, Sandrine; Purschke, Oliver; Redding, David W; Rosauer, Dan F; Winter, Marten; Mazel, Florent

2017-05-01

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices. © 2016 The Authors. Biological Reviews published by John Wiley © Sons Ltd on behalf of Cambridge Philosophical Society.

A global parallel model based design of experiments method to minimize model output uncertainty.

PubMed

Bazil, Jason N; Buzzard, Gregory T; Rundell, Ann E

2012-03-01

Model-based experiment design specifies the data to be collected that will most effectively characterize the biological system under study. Existing model-based design of experiment algorithms have primarily relied on Fisher Information Matrix-based methods to choose the best experiment in a sequential manner. However, these are largely local methods that require an initial estimate of the parameter values, which are often highly uncertain, particularly when data is limited. In this paper, we provide an approach to specify an informative sequence of multiple design points (parallel design) that will constrain the dynamical uncertainty of the biological system responses to within experimentally detectable limits as specified by the estimated experimental noise. The method is based upon computationally efficient sparse grids and requires only a bounded uncertain parameter space; it does not rely upon initial parameter estimates. The design sequence emerges through the use of scenario trees with experimental design points chosen to minimize the uncertainty in the predicted dynamics of the measurable responses of the system. The algorithm was illustrated herein using a T cell activation model for three problems that ranged in dimension from 2D to 19D. The results demonstrate that it is possible to extract useful information from a mathematical model where traditional model-based design of experiments approaches most certainly fail. The experiments designed via this method fully constrain the model output dynamics to within experimentally resolvable limits. The method is effective for highly uncertain biological systems characterized by deterministic mathematical models with limited data sets. Also, it is highly modular and can be modified to include a variety of methodologies such as input design and model discrimination.

Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling

PubMed Central

Santos, Guido; Lai, Xin; Eberhardt, Martin; Vera, Julio

2018-01-01

Pneumococcal infection is the most frequent cause of pneumonia, and one of the most prevalent diseases worldwide. The population groups at high risk of death from bacterial pneumonia are infants, elderly and immunosuppressed people. These groups are more vulnerable because they have immature or impaired immune systems, the efficacy of their response to vaccines is lower, and antibiotic treatment often does not take place until the inflammatory response triggered is already overwhelming. The immune response to bacterial lung infections involves dynamic interactions between several types of cells whose activation is driven by intracellular molecular networks. A feasible approach to the integration of knowledge and data linking tissue, cellular and intracellular events and the construction of hypotheses in this area is the use of mathematical modeling. For this paper, we used a multi-level computational model to analyse the role of cellular and molecular interactions during the first 10 h after alveolar invasion of Streptococcus pneumoniae bacteria. By “multi-level” we mean that we simulated the interplay between different temporal and spatial scales in a single computational model. In this instance, we included the intracellular scale of processes driving lung epithelial cell activation together with the scale of cell-to-cell interactions at the alveolar tissue. In our analysis, we combined systematic model simulations with logistic regression analysis and decision trees to find genotypic-phenotypic signatures that explain differences in bacteria strain infectivity. According to our simulations, pneumococci benefit from a high dwelling probability and a high proliferation rate during the first stages of infection. In addition to this, the model predicts that during the very early phases of infection the bacterial capsule could be an impediment to the establishment of the alveolar infection because it impairs bacterial colonization. PMID:29868515

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling.

PubMed

Santos, Guido; Lai, Xin; Eberhardt, Martin; Vera, Julio

2018-01-01

Pneumococcal infection is the most frequent cause of pneumonia, and one of the most prevalent diseases worldwide. The population groups at high risk of death from bacterial pneumonia are infants, elderly and immunosuppressed people. These groups are more vulnerable because they have immature or impaired immune systems, the efficacy of their response to vaccines is lower, and antibiotic treatment often does not take place until the inflammatory response triggered is already overwhelming. The immune response to bacterial lung infections involves dynamic interactions between several types of cells whose activation is driven by intracellular molecular networks. A feasible approach to the integration of knowledge and data linking tissue, cellular and intracellular events and the construction of hypotheses in this area is the use of mathematical modeling. For this paper, we used a multi-level computational model to analyse the role of cellular and molecular interactions during the first 10 h after alveolar invasion of Streptococcus pneumoniae bacteria. By "multi-level" we mean that we simulated the interplay between different temporal and spatial scales in a single computational model. In this instance, we included the intracellular scale of processes driving lung epithelial cell activation together with the scale of cell-to-cell interactions at the alveolar tissue. In our analysis, we combined systematic model simulations with logistic regression analysis and decision trees to find genotypic-phenotypic signatures that explain differences in bacteria strain infectivity. According to our simulations, pneumococci benefit from a high dwelling probability and a high proliferation rate during the first stages of infection. In addition to this, the model predicts that during the very early phases of infection the bacterial capsule could be an impediment to the establishment of the alveolar infection because it impairs bacterial colonization.

A guide to phylogenetic metrics for conservation, community ecology and macroecology

PubMed Central

Cadotte, Marc W.; Carvalho, Silvia B.; Davies, T. Jonathan; Ferrier, Simon; Fritz, Susanne A.; Grenyer, Rich; Helmus, Matthew R.; Jin, Lanna S.; Mooers, Arne O.; Pavoine, Sandrine; Purschke, Oliver; Redding, David W.; Rosauer, Dan F.; Winter, Marten; Mazel, Florent

2016-01-01

ABSTRACT The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices. PMID:26785932

The Adventures of Captain John Smith, Pocahontas and a Sundial: Cosmology, Mathematics, and Power at the Time of Jamestown

NASA Astrophysics Data System (ADS)

Schechner, Sara J.

2007-12-01

While exploring the Chickahominy River in Virginia by canoe in December 1607, Captain John Smith was ambushed by 200 Powhatan Indians and chased into the swamp. Wounded by arrows and mired in the cold mud, Smith surrendered and was led to their chieftain, Opechancanough. Smith played for time. He pulled out his pocket sundial and proceeded to deliver a lecture on astronomy. The Indians marveled at the dancing needle of the magnetic compass, which they could plainly see but not touch because of the glass cover. They apparently thought less of his discourse in a foreign language on the sun, moon, and planets, as within the hour, Smith's captors had him tied to a tree and were ready to shoot him. But then, Opechancanough held the sundial aloft and spared Smith's life. For the next month, Smith was paraded around various Indian villages before being condemned to have his head bashed in. Pocahontas, however, threw herself across Smith's body in order to save his life. This legendary episode reveals more than Smith's ingenuity. His compass sundial, shaped and marked like a celestial globe, was a microcosm of his universe. It embodied the belief that the smallest things mirrored the large, that number was the key to God's creation, and that by means of mathematical instruments, men could dominate that world (or at least extricate themselves from tight spots!). This paper will examine the astronomical ideas and instruments on which these beliefs were based, and show how ultimately, Smith's sundial also represented the clash of two cosmologies-that of the Indians and European settlers.

Positive geometries and canonical forms

NASA Astrophysics Data System (ADS)

Arkani-Hamed, Nima; Bai, Yuntao; Lam, Thomas

2017-11-01

Recent years have seen a surprising connection between the physics of scattering amplitudes and a class of mathematical objects — the positive Grassmannian, positive loop Grassmannians, tree and loop Amplituhedra — which have been loosely referred to as "positive geometries". The connection between the geometry and physics is provided by a unique differential form canonically determined by the property of having logarithmic singularities (only) on all the boundaries of the space, with residues on each boundary given by the canonical form on that boundary. The structures seen in the physical setting of the Amplituhedron are both rigid and rich enough to motivate an investigation of the notions of "positive geometries" and their associated "canonical forms" as objects of study in their own right, in a more general mathematical setting. In this paper we take the first steps in this direction. We begin by giving a precise definition of positive geometries and canonical forms, and introduce two general methods for finding forms for more complicated positive geometries from simpler ones — via "triangulation" on the one hand, and "push-forward" maps between geometries on the other. We present numerous examples of positive geometries in projective spaces, Grassmannians, and toric, cluster and flag varieties, both for the simplest "simplex-like" geometries and the richer "polytope-like" ones. We also illustrate a number of strategies for computing canonical forms for large classes of positive geometries, ranging from a direct determination exploiting knowledge of zeros and poles, to the use of the general triangulation and push-forward methods, to the representation of the form as volume integrals over dual geometries and contour integrals over auxiliary spaces. These methods yield interesting representations for the canonical forms of wide classes of positive geometries, ranging from the simplest Amplituhedra to new expressions for the volume of arbitrary convex polytopes.

Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari).

PubMed

Gil, Zulma Nancy; Benavides, Pablo; De Souza, Og; Acevedo, Flor Edith; Lima, Eraldo

2015-01-01

The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was [Formula: see text], being [Formula: see text] the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

The challenge of cerebral magnetic resonance imaging in neonates: A new method using mathematical morphology for the segmentation of structures including diffuse excessive high signal intensities.

PubMed

Xu, Yongchao; Morel, Baptiste; Dahdouh, Sonia; Puybareau, Élodie; Virzì, Alessio; Urien, Héléne; Géraud, Thierry; Adamsbaum, Catherine; Bloch, Isabelle

2018-05-17

Preterm birth is a multifactorial condition associated with increased morbidity and mortality. Diffuse excessive high signal intensity (DEHSI) has been recently described on T2-weighted MR sequences in this population and thought to be associated with neuropathologies. To date, no robust and reproducible method to assess the presence of white matter hyperintensities has been developed, perhaps explaining the current controversy over their prognostic value. The aim of this paper is to propose a new semi-automated framework to detect DEHSI on neonatal brain MR images having a particular pattern due to the physiological lack of complete myelination of the white matter. A novel method for semi- automatic segmentation of neonatal brain structures and DEHSI, based on mathematical morphology and on max-tree representations of the images is thus described. It is a mandatory first step to identify and clinically assess homogeneous cohorts of neonates for DEHSI and/or volume of any other segmented structures. Implemented in a user-friendly interface, the method makes it straightforward to select relevant markers of structures to be segmented, and if needed, apply eventually manual corrections. This method responds to the increasing need for providing medical experts with semi-automatic tools for image analysis, and overcomes the limitations of visual analysis alone, prone to subjectivity and variability. Experimental results demonstrate that the method is accurate, with excellent reproducibility and with very few manual corrections needed. Although the method was intended initially for images acquired at 1.5T, which corresponds to the usual clinical practice, preliminary results on images acquired at 3T suggest that the proposed approach can be generalized. Copyright © 2018 Elsevier B.V. All rights reserved.

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Parallel multiscale simulations of a brain aneurysm

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

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

Modeling the effects of palm-house proximity on the theoretical risk of Chagas disease transmission in a rural locality of the Orinoco basin, Colombia.

PubMed

Erazo, Diana; Cordovez, Juan

2016-11-18

Chagas disease is a major public health concern in Latin America and it is transmitted by insects of the subfamily Triatominae, including Rhodnius spp. Since palm trees are ubiquitous in Colombia and a habitat for Rhodnius spp., the presence of palms near villages could increase contact rates between vectors and humans. Therefore, knowing whether a relationship exists between the proximity of palms to villages and the abundance and distribution of vectors therein, may be critical for Chagas disease prevention programs. Adapting a mathematical model for R. prolixus population dynamics in a small village, we model the implications of changing distances between palms and dwellings, to the risk of Chagas disease infection. We implemented a mathematical model that reflects R. prolixus population dynamics in a small village located in the department of Casanare (Colombia) to study the role of palm-house proximity. We varied the distance between palms and houses by monitoring the network global efficiency metric. We constructed 1,000 hypothetical villages varying distances and each one was run 100 times. According to the model, as palm-house proximity increases, houses were more likely to be visited by triatomine bugs. The number of bugs per unit time increased progressively in a non-linear fashion with high variability. We stress the importance of village configuration on the model output. From a theoretical perspective, palm-house proximity may have a positive effect on the incidence of Chagas disease. The model predicts a 1% increase in new human cases per year when houses and palms are brought closer by 75%.

Size Matters a Lot: Drought-Affected Italian Oaks Are Smaller and Show Lower Growth Prior to Tree Death

PubMed Central

Colangelo, Michele; Camarero, Jesús J.; Borghetti, Marco; Gazol, Antonio; Gentilesca, Tiziana; Ripullone, Francesco

2017-01-01

Hydraulic theory suggests that tall trees are at greater risk of drought-triggered death caused by hydraulic failure than small trees. In addition the drop in growth, observed in several tree species prior to death, is often interpreted as an early-warning signal of impending death. We test these hypotheses by comparing size, growth, and wood-anatomy patterns of living and now-dead trees in two Italian oak forests showing recent mortality episodes. The mortality probability of trees is modeled as a function of recent growth and tree size. Drift-diffusion-jump (DDJ) metrics are used to detect early-warning signals. We found that the tallest trees of the anisohydric Italian oak better survived drought contrary to what was predicted by the theory. Dead trees were characterized by a lower height and radial-growth trend than living trees in both study sites. The growth reduction of now-dead trees started about 10 years prior to their death and after two severe spring droughts during the early 2000s. This critical transition in growth was detected by DDJ metrics in the most affected site. Dead trees were also more sensitive to drought stress in this site indicating different susceptibility to water shortage between trees. Dead trees did not form earlywood vessels with smaller lumen diameter than surviving trees but tended to form wider latewood vessels with a higher percentage of vessel area. Since living and dead trees showed similar competition we did not expect that moderate thinning and a reduction in tree density would increase the short-term survival probability of trees. PMID:28270816

Paleoecological insights on fixed tree island development in the Florida Everglades: I. environmental controls: Chapter 4

USGS Publications Warehouse

Willard, Debra A.; Murray, James B.; Holmes, Charles W.; Korvela, Michael S.; Mason, Daniel; Orem, William H.; Towles, D. Timothy; Sklar, Fred H.; van der Valk, A.

2002-01-01

Palynological and geochemical analyses of sediment cores collected on two tree islands in the Florida Everglades indicate long-term hydrologic and chemical differences between tree islands and surrounding marshes and sloughs. Gumbo Limbo and Nuthouse tree islands are elongate, teardrop-shaped islands in Water Conservation Area 3B. Prior to tree island formation at both sites, pollen records indicate that sites on modern tree island heads were covered with sawgrass marshes with abundant weedy annuals. Such vegetation is characteristic of moderate water depths and hydroperiods with frequent droughts or disturbances. Contemporaneously deposited sediments on tree island tails indicate progressively deeper water conditions with increasing distance from the head; wetlands surrounding tree islands were covered by sloughs with deep water and long hydroperiods. Tree island formation occurred at about 1200 BC on Gumbo Limbo Island, with mature tree island vegetation established by about 800 AD. On Nuthouse Island, tree island formation occurred around 300 AD, shifting to mature tree island vegetation around 1400 AD. Thus, tree island formation began on these islands between 3.2 Ka and 1.7 Ka. Maturation of tree islands took between 1,000 and 2,000 years, and vegetation on these tree islands has been relatively stable for the last 600–1,200 years. Phosphorus levelson tree island heads have been extremely high (approximately six times greaterthan baseline levels in marshes) throughout the history of the sites, and phosphorus content in tree island tails began increasing when tree island formation occurred. Elevated phosphorus content may reflect the long-termpresence of wading birds at these sites and provide a proxy for reconstructing the historic distribution of wading bird populations.

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

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

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

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

Tree-ring δ13C and δ18O, leaf δ13C and wood and leaf N status demonstrate tree growth strategies and predict susceptibility to disturbance

PubMed Central

Billings, S.A.; Boone, A.S.; Stephen, F.M.

2016-01-01

Understanding how tree growth strategies may influence tree susceptibility to disturbance is an important goal, especially given projected increases in diverse ecological disturbances this century. We use growth responses of tree rings to climate, relationships between tree-ring stable isotopic signatures of carbon (δ13C) and oxygen (δ18O), wood nitrogen concentration [N], and contemporary leaf [N] and δ13C values to assess potential historic drivers of tree photosynthesis in dying and apparently healthy co-occurring northern red oak (Quercus rubra L. (Fagaceae)) during a region-wide oak decline event in Arkansas, USA. Bole growth of both healthy and dying trees responded negatively to drought severity (Palmer Drought Severity Index) and temperature; healthy trees exhibited a positive, but small, response to growing season precipitation. Contrary to expectations, tree-ring δ13C did not increase with drought severity. A significantly positive relationship between tree-ring δ13C and δ18O was evident in dying trees (P < 0.05) but not in healthy trees. Healthy trees’ wood exhibited lower [N] than that of dying trees throughout most of their lives (P < 0.05), and we observed a significant, positive relationship (P < 0.05) in healthy trees between contemporary leaf δ13C and leaf N (by mass), but not in dying trees. Our work provides evidence that for plants in which strong relationships between δ13C and δ18O are not evident, δ13C may be governed by plant N status. The data further imply that historic photosynthesis in healthy trees was linked to N status and, perhaps, C sink strength to a greater extent than in dying trees, in which tree-ring stable isotopes suggest that historic photosynthesis was governed primarily by stomatal regulation. This, in turn, suggests that assessing the relative dominance of photosynthetic capacity vs stomatal regulation as drivers of trees’ C accrual may be a feasible means of predicting tree responses to some disturbance events. Our work demonstrates that a dual isotope, tree-ring approach can be integrated with tree N status to begin to unravel a fundamental question in forest ecology: why do some trees die during a disturbance, while other conspecifics with apparently similar access to resources remain healthy? PMID:26960389

Digging for knowledge

NASA Astrophysics Data System (ADS)

Szu, Harold; Jenkins, Jeffrey; Hsu, Charles; Goehl, Steve; Miao, Liden; Cader, Masud; Benachenhou, Dalila

2009-04-01

The "smile of a mother" is always recognized, whenever and wherever. But why is my PC always dumb and unable to recognize me or my needs, whoever or whatever? This paper postulates that such a 6 W's query and search system needs matching storage. Such a lament will soon be mended with a smarter PC, or a smarter Google engine, a network computer, working in the field of data retrieval, feature extraction, reduction, and knowledge precipitation. Specifically, the strategy of modern information storage and retrieval shall work like our brains, which are constantly overwhelmed by 5 pairs of identical tapes taken by eyes, ears, etc. 5 high fidelity sensors generate 5 pairs of high definition tapes which produce the seeing and hearing etc. in our perception. This amounts to 10 tapes recorded in a non-abridged fashion. How can we store and retrieve them when we need to? We must reduce the redundancy, enhancing the signal noise ratio, and fusing invariant features using a simple set of mathematical operations to write according to the union and read by the intersection in the higher dimensional vector space. For example, (see paper for equation) where the query must be phrased in terms of the union of imprecise or partial set of 6w's denoted by the union of lower case w's. The upper case W's are the archival storage of a primer tree. A simplified humanistic representation may be called the 6W space (who, what, where, when, why, how), also referred to as the Newspaper geometry. It seems like mapping the 6W to the 3W (World Wide Web) is becoming relatively easier. It may thus become efficient and robust by rapidly digging for knowledge through the set operations of union, writing, and intersection, reading, upon the design of 6 W query searching engine matched efficiently by the 6W vector index databases. In fact, Newspaper 6D geometry may be reduced furthermore by PCA (Principal Component Analysis) eigenvector mathematics and mapped into the 2D causality space comprised of the causes (What, How, Why) and the effects (Where, When and Who). If this hypothesis of brain strategy were true, one must then develop a 6W query language to support a 6Wordered set storage of linkage pointers in high D space. In other words, one can easily map the basic 1st Gen. Google Web, 1-D statistical PageRanking databases, to a nested 6W tree where each branch of sub-6-W is stemming from the prime 6 W tree, using a system of automated text mining assisted by syntactic semantics to discern the properties of the 6W for that query. Goehl et al. has demonstrated previously that such is doable, but one may need more tools to support the knowledge extraction and automated feature reduction. In this paper, we have set out to demonstrate lossless down sampling using the 2nd Gen wavelet transform, the so-called "1-D Cartesian lifting processing of Swelden" adopted by JPEG 2000. "The loss of statistics, if any (including PageRanking and 1-D lifting), is the loss of geometry insights," such as 2-D vector time series, video, whose 1-D lifting Cartesian product will loss the diagonal changes insights.

Using tree diversity to compare phylogenetic heuristics.

PubMed

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

2009-04-29

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

Tree-ring isotopes reveal drought sensitivity in trees killed by spruce beetle outbreaks in south-central Alaska.

PubMed

Csank, Adam Z; Miller, Amy E; Sherriff, Rosemary L; Berg, Edward E; Welker, Jeffrey M

2016-10-01

Increasing temperatures have resulted in reduced growth and increased tree mortality across large areas of western North American forests. We use tree-ring isotope chronologies (δ 13 C and δ 18 O) from live and dead trees from four locations in south-central Alaska, USA, to test whether white spruce trees killed by recent spruce beetle (Dendroctonus rufipennis Kirby) outbreaks showed evidence of drought stress prior to death. Trees that were killed were more sensitive to spring/summer temperature and/or precipitation than trees that survived. At two of our sites, we found greater correlations between the δ 13 C and δ 18 O chronologies and spring/summer temperatures in dead trees than in live trees, suggesting that trees that are more sensitive to temperature-induced drought stress are more likely to be killed. At one site, the difference between δ 13 C in live and dead trees was related to winter/spring precipitation, with dead trees showing stronger correlations between δ 13 C and precipitation, again suggesting increased water stress in dead trees. At all sites where δ 18 O was measured, δ 18 O chronologies showed the greatest difference in climate response between live and dead groups, with δ 18 O in live trees correlating more strongly with late winter precipitation than dead trees. Our results indicate that sites where trees are already sensitive to warm or dry early growing-season conditions experienced the most beetle-kill, which has important implications for forecasting future mortality events in Alaska. © 2016 by the Ecological Society of America.

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

PubMed Central

Cui, Yun; Jansson, Jesper

2012-01-01

Abstract A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host–parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists. PMID:22963134

Polynomial-time algorithms for building a consensus MUL-tree.

PubMed

Cui, Yun; Jansson, Jesper; Sung, Wing-Kin

2012-09-01

A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host-parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists.

Estimating the probability of survival of individual shortleaf pine (Pinus echinata mill.) trees

Treesearch

Sudip Shrestha; Thomas B. Lynch; Difei Zhang; James M. Guldin

2012-01-01

A survival model is needed in a forest growth system which predicts the survival of trees on individual basis or on a stand basis (Gertner, 1989). An individual-tree modeling approach is one of the better methods available for predicting growth and yield as it provides essential information about particular tree species; tree size, tree quality and tree present status...

The Concept of Cosmic Tree in Armenian and Iranian Cosmologies

NASA Astrophysics Data System (ADS)

Farmanyan, S. V.; Mickaelian, A. M.

2016-09-01

Cosmic Tree or Tree of Life is a common motif in various world theologies, mythologies, and philosophies. In the present study we focus on Armenian and Iranian Cosmic Tree. In ancient Armenia, the Tree of Life (Կենաց Ծառ) is a religious symbol and is drawn on walls of fortresses and carved on the armour of warriors. According to ancient Armenians the center of the Universe is located at the crown of the tree or the column, which is the closest to the sky. We explore the idea of cosmic tree in the riddles, prayers, medieval rituals and miniatures. In the riddles, the tree mostly symbolizes the celestial phenomena (Sun, Stars, and Heavens), different units of time (years, months, weeks, days, and seasons), the people, Jerusalem, the apostles and Jesus Christ. The branches of the tree were equally divided on the right and left sides of the stem, with each branch having one leaf, and one leaf on the apex of the tree. Servants stood on each side of the tree with one of their hands up as if they are taking care of the tree. In pre-Islamic Persian mythology, the Gaokerena world tree is a large, sacred Haoma tree which bears all seeds. Ahriman created a frog to invade the tree and destroy it, aiming at preventing all trees from growing on the Earth. As a reaction, God (Ahura Mazda) created two kar fish staring at the frog to guard the tree. The concept of world tree in Persian Mythology is very closely related to the concept of the Tree of Life. Another related issue in ancient mythology of Iran is the myth of Mashya and Mashyane, two trees who were the ancestors of all living beings. This myth can be considered as a prototype for the creation myth where living beings are created by Gods (who have human forms). We come to the conclusion that in both cultures, no matter of the present different religions, the perception of Cosmic Tree is interconnected to the life on our planet and served as a metaphor for common descent in the evolutionary sense.

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

PubMed

Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

2018-04-05

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

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

PubMed Central

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

2015-01-01

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

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

PubMed

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

2018-03-01

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

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

PubMed Central

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

2018-01-01

Abstract Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data. PMID:29106675

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.

NBOD2- PROGRAM TO DERIVE AND SOLVE EQUATIONS OF MOTION FOR COUPLED N-BODY SYSTEMS

NASA Technical Reports Server (NTRS)

Frisch, H. P.

1994-01-01

The analysis of the dynamic characteristics of a complex system, such as a spacecraft or a robot, is usually best accomplished through the study of a simulation model. The simulation model must have the same dynamic characteristics as the complex system, while lending itself to mathematical quantification. The NBOD2 computer program was developed to aid in the analysis of spacecraft attitude dynamics. NBOD2 is a very general program that may be applied to a large class of problems involving coupled N-body systems. NBOD2 provides the dynamics analyst with the capability to automatically derive and numerically solve the equations of motion for any system that can be modeled as a topological tree of coupled rigid bodies, flexible bodies, point masses, and symmetrical momentum wheels. NBOD2 uses a topological tree model of the dynamic system to derive the vector-dyadic equations of motion for the system. The user builds this topological tree model by using rigid and flexible bodies, point masses, and symmetrical momentum wheels with appropriate connections. To insure that the relative motion between contiguous bodies is kinematically constrained, NBOD2 assumes that contiguous rigid and flexible bodies are connected by physically reliable 0, 1, 2, and 3-degrees-of-freedom gimbals. These gimbals prohibit relative translational motion, while permitting up to 3 degrees of relative rotational freedom at hinge points. Point masses may have 0, 1, 2, or 3-degrees of relative translational freedom, and symmetric momentum wheels may have a single degree of rotational freedom relative to the body in which they are imbedded. Flexible bodies may possess several degrees of vibrational freedom in addition to the degrees of freedom associated with the connection gimbals. Data concerning the natural modes and vibrations of the flexible bodies must be supplied by the user. NBOD2 combines the best features of the discrete-body approach and the nested body approach to reduce the topological tree to a complete set of nonlinear equations of motion in vector-dyadic form for the system being analyzed. NBOD2 can then numerically solve the equations of motion. Input to NBOD2 consists of a user-supplied description of the system to be modeled. The NBOD2 system includes an interactive, tutorial, input support program to aid the NBOD2 user in preparing input data. Output from NBOD2 consists of a listing of the complete set of nonlinear equations of motion in vector-dyadic form and any userspecified set of system state variables. The NBOD2 program is written in FORTRAN 77 for batch execution and has been implemented on a DEC VAX-11/780 computer. The NBOD2 program was developed in 1978 and last updated in 1982.

NE-TWIGS update: Incorporating tree quality

Treesearch

Daniel A. Yaussy

1993-01-01

A method to distribute tree quality was incorporated into the NE-TWIGS individual-tree growth and yield simulator. The program uses potential tree grade to allow changes in actual tree grade over time. Volume is reported by grade and value is calculated using tree grades. Example screens are shown.

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

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

2013-01-01

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

Whole-tree distribution and temporal variation of non-structural carbohydrates in broadleaf evergreen trees.

PubMed

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

2018-04-01

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

Interspecific variation in growth responses to tree size, competition and climate of western Canadian boreal mixed forests.

PubMed

Jiang, Xinyu; Huang, Jian-Guo; Cheng, Jiong; Dawson, Andria; Stadt, Kenneth J; Comeau, Philip G; Chen, Han Y H

2018-08-01

Tree growth of boreal forest plays an important role on global carbon (C) cycle, while tree growth in the western Canadian boreal mixed forests has been predicted to be negatively affected by regional drought. Individual tree growth can be controlled by many factors, such as competition, climate, tree size and age. However, information about contributions of different factors to tree growth is still limited in this region. In order to address this uncertainty, tree rings of two dominant tree species, trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench.) Voss), were sampled from boreal mixed forest stands distributed across Alberta, Canada. Tree growth rates over different time intervals (10years interval, 1998-2007; 20years interval, 1988-2007; 30years interval, 1978-2007) were calculated to study the effects of different factors (tree size, competition, climate, and age) on tree growth. Results indicated that tree growth of two species were both primarily affected by competition or tree size, while climatic indices showed less effects on tree growth. Growth of trembling aspen was significantly affected by inter- and intraspecific competition, while growth of white spruce was primarily influenced by tree size, followed by competition. Positive relationship was found between growth of white spruce and competition index of coniferous group, suggesting an intraspecific mutualism mechanism within coniferous group. Our results further suggested that competition driven succession was the primary process of forest composition shift in the western Canadian boreal mixed forest. Although drought stress increased tree mortality, decline of stem density under climate change released competition stress of surviving trees, which in turn sustained growth of surviving trees. Therefore, climatic indices showed fewer effects on growth of dominant tree species compared to other factors in our study. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

i-Tree: Tools to assess and manage structure, function, and value of community forests

NASA Astrophysics Data System (ADS)

Hirabayashi, S.; Nowak, D.; Endreny, T. A.; Kroll, C.; Maco, S.

2011-12-01

Trees in urban communities can mitigate many adverse effects associated with anthropogenic activities and climate change (e.g. urban heat island, greenhouse gas, air pollution, and floods). To protect environmental and human health, managers need to make informed decisions regarding urban forest management practices. Here we present the i-Tree suite of software tools (www.itreetools.org) developed by the USDA Forest Service and their cooperators. This software suite can help urban forest managers assess and manage the structure, function, and value of urban tree populations regardless of community size or technical capacity. i-Tree is a state-of-the-art, peer-reviewed Windows GUI- or Web-based software that is freely available, supported, and continuously refined by the USDA Forest Service and their cooperators. Two major features of i-Tree are 1) to analyze current canopy structures and identify potential planting spots, and 2) to estimate the environmental benefits provided by the trees, such as carbon storage and sequestration, energy conservation, air pollution removal, and storm water reduction. To cover diverse forest topologies, various tools were developed within the i-Tree suite: i-Tree Design for points (individual trees), i-Tree Streets for lines (street trees), and i-Tree Eco, Vue, and Canopy (in the order of complexity) for areas (community trees). Once the forest structure is identified with these tools, ecosystem services provided by trees can be estimated with common models and protocols, and reports in the form of texts, charts, and figures are then created for users. Since i-Tree was developed with a client/server architecture, nationwide data in the US such as location-related parameters, weather, streamflow, and air pollution data are stored in the server and retrieved to a user's computer at run-time. Freely available remote-sensed images (e.g. NLCD and Google maps) are also employed to estimate tree canopy characteristics. As the demand for i-Tree grows internationally, environmental databases from more countries will be coupled with the software suite. Two more i-Tree applications, i-Tree Forecast and i-Tree Landscape are now under development. i-Tree Forecast simulates canopy structures for up to 100 years based on planting and mortality rates and adds capabilities for other i-Tree applications to estimate the benefits of future canopy scenarios. While most i-Tree applications employ a spatially lumped approach, i-Tree landscape employs a spatially distributed approach that allows users to map changes in canopy cover and ecosystem services through time and space. These new i-Tree tools provide an advanced platform for urban managers to assess the impact of current and future urban forests. i-Tree allows managers to promote effective urban forest management and sound arboricultural practices by providing information for advocacy and planning, baseline data for making informed decisions, and standardization for comparisons with other communities.

Urban park tree inventories

Treesearch

Joe R. McBride; David J. Nowak

1989-01-01

A survey of published reports on urban park tree inventories in the United States and the United Kingdom reveal two types of inventories: (1) Tree Location Inventories and (2) Generalized Information Inventories. Tree location inventories permit managers to relocate specific park trees, along with providing individual tree characteristics and condition data. In...

Simple street tree sampling

Treesearch

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

2015-01-01

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

The Tree Worker's Manual.

ERIC Educational Resources Information Center

Smithyman, S. J.

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

What Makes a Tree a Tree?

ERIC Educational Resources Information Center

NatureScope, 1986

1986-01-01

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

INTRODUCTION TO PHYTOTECHNOLOGIES

EPA Science Inventory

A tree is a tree is a tree; or is it? To a child a tree is to climb, to a landscape architect a tree shapes the view, while to an environmental engineer a tree may be a self-assembling, solar- powered pump and treat system. Phytoremediation is the art and science of using plant...

Ring profiler: a new method for estimating tree-ring density for improved estimates of carbon storage

Treesearch

David W. Vahey; C. Tim Scott; J.Y. Zhu; Kenneth E. Skog

2012-01-01

Methods for estimating present and future carbon storage in trees and forests rely on measurements or estimates of tree volume or volume growth multiplied by specific gravity. Wood density can vary by tree ring and height in a tree. If data on density by tree ring could be obtained and linked to tree size and stand characteristics, it would be possible to more...

Management, morphological, and environmental factors influencing Douglas-fir bark furrows in the Oregon Coast Range

USGS Publications Warehouse

Sheridan, Christopher D.; Puettmann, Klaus J.; Huso, Manuela M.P.; Hagar, Joan C.; Falk, Kristen R.

2013-01-01

Many land managers in the Pacific Northwest have the goal of increasing late-successional forest structures. Despite the documented importance of Douglas-fir tree bark structure in forested ecosystems, little is known about factors influencing bark development and how foresters can manage development. This study investigated the relative importance of tree size, growth, environmental factors, and thinning on Douglas-fir bark furrow characteristics in the Oregon Coast Range. Bark furrow depth, area, and bark roughness were measured for Douglas-fir trees in young heavily thinned and unthinned sites and compared to older reference sites. We tested models for relationships between bark furrow response and thinning, tree diameter, diameter growth, and environmental factors. Separately, we compared bark responses measured on trees used by bark-foraging birds with trees with no observed usage. Tree diameter and diameter growth were the most important variables in predicting bark characteristics in young trees. Measured environmental variables were not strongly related to bark characteristics. Bark furrow characteristics in old trees were influenced by tree diameter and surrounding tree densities. Young trees used by bark foragers did not have different bark characteristics than unused trees. Efforts to enhance Douglas-fir bark characteristics should emphasize retention of larger diameter trees' growth enhancement.

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

PubMed

Kordi, Misagh; Bansal, Mukul S

2017-06-01

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

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.

Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

PubMed

Goloboff, Pablo A

2014-10-01

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner trees and for moving around plateaus can be useful when analyzing phylogenomic data sets formed by concatenation of genes with uneven taxon representation ("sparse" supermatrices), which are likely to present a tree landscape with extensive plateaus. Copyright © 2014 Elsevier Inc. All rights reserved.

Ascorbic Acid Alleviates Water Stress in Young Peach Trees and Improves Their Performance after Rewatering.

PubMed

Penella, Consuelo; Calatayud, Ángeles; Melgar, Juan C

2017-01-01

Exogenous application of biochemicals has been found to improve water stress tolerance in herbaceous crops but there are limited studies on deciduous fruit trees. The goal of this research was to study if ascorbic acid applications could improve physiological mechanisms associated with water stress tolerance in young fruit trees. Ascorbic acid was foliarly applied at a concentration of 250 ppm to water-stressed and well-watered peach trees (control) of two cultivars ('Scarletprince' and 'CaroTiger'). Trees received either one or two applications, and 1 week after the second application all trees were rewatered to field capacity. Upon rewatering, CO 2 assimilation and stomatal conductance of water-stressed 'Scarletprince' trees sprayed with ascorbic acid (one or two applications) were similar to those of well-irrigated trees, but water-stressed trees that had not received ascorbic acid did not recover photosynthetical functions. Also, water status in sprayed water-stressed 'Scarletprince' trees was improved to values similar to control trees. On the other hand, water-stressed 'CaroTiger' trees needed two applications of ascorbic acid to reach values of CO 2 assimilation similar to control trees but these applications did not improve their water status. In general terms, different response mechanisms to cope with water stress in presence of ascorbic acid were found in each cultivar, with 'Scarletprince' trees preferentially using proline as compatible solute and 'CaroTiger' trees relying on stomatal regulation. The application of ascorbic acid reduced cell membrane damage and increased catalase activity in water-stressed trees of both cultivars. These results suggest that foliar applications of ascorbic acid could be used as a management practice for improving water stress tolerance of young trees under suboptimal water regimes.

Ascorbic Acid Alleviates Water Stress in Young Peach Trees and Improves Their Performance after Rewatering

PubMed Central

Penella, Consuelo; Calatayud, Ángeles; Melgar, Juan C.

2017-01-01

Exogenous application of biochemicals has been found to improve water stress tolerance in herbaceous crops but there are limited studies on deciduous fruit trees. The goal of this research was to study if ascorbic acid applications could improve physiological mechanisms associated with water stress tolerance in young fruit trees. Ascorbic acid was foliarly applied at a concentration of 250 ppm to water-stressed and well-watered peach trees (control) of two cultivars (‘Scarletprince’ and ‘CaroTiger’). Trees received either one or two applications, and 1 week after the second application all trees were rewatered to field capacity. Upon rewatering, CO2 assimilation and stomatal conductance of water-stressed ‘Scarletprince’ trees sprayed with ascorbic acid (one or two applications) were similar to those of well-irrigated trees, but water-stressed trees that had not received ascorbic acid did not recover photosynthetical functions. Also, water status in sprayed water-stressed ‘Scarletprince’ trees was improved to values similar to control trees. On the other hand, water-stressed ‘CaroTiger’ trees needed two applications of ascorbic acid to reach values of CO2 assimilation similar to control trees but these applications did not improve their water status. In general terms, different response mechanisms to cope with water stress in presence of ascorbic acid were found in each cultivar, with ‘Scarletprince’ trees preferentially using proline as compatible solute and ‘CaroTiger’ trees relying on stomatal regulation. The application of ascorbic acid reduced cell membrane damage and increased catalase activity in water-stressed trees of both cultivars. These results suggest that foliar applications of ascorbic acid could be used as a management practice for improving water stress tolerance of young trees under suboptimal water regimes. PMID:28979284

Foliar ozone injury on different-sized Prumus serotina Ehrh. trees

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

Fredericksen, T.S.; Skelly, J.M.; Steiner, K.C.

1995-06-01

Black cherry (Prunus serotina Ehrh.) is a common tree species in the eastern U.S. that is highly sensitive to ozone relative to other associated deciduous tree species. Because of difficulties in conducting exposure-response experiments on large trees, air pollution studies have often utilized seedlings and extrapolated the results to predict the potential response of larger forest trees. However, physiological differences between seedlings and mature forest trees may alter responses to air pollutants. A comparative study of seedling, sapling, and canopy black cherry trees was conducted to determine the response of different-sized trees to known ozone exposures and amounts of ozonemore » uptake. Apparent foliar sensitivity to ozone, observed as a dark adaxial leaf stipple, decreased with increasing tree size. An average of 46% of seedling leaf area was symptomatic by early September, compared to 15% - 20% for saplings and canopy trees. In addition to visible symptoms, seedlings also appeared to have greater rates of early leaf abscission than larger trees. Greater sensitivity (i.e., foliar symptoms) per unit exposure with decreasing tree size was closely correlated with rates of stomatal conductance. However, after accounting for differences in stomatal conductance, sensitivity appeared to increase with tree size.« less

Trees as templates for tropical litter arthropod diversity.

PubMed

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

2010-09-01

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

Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics

PubMed Central

Ilstedt, U.; Bargués Tobella, A.; Bazié, H. R.; Bayala, J.; Verbeeten, E.; Nyberg, G.; Sanou, J.; Benegas, L.; Murdiyarso, D.; Laudon, H.; Sheil, D.; Malmer, A.

2016-01-01

Water scarcity contributes to the poverty of around one-third of the world’s people. Despite many benefits, tree planting in dry regions is often discouraged by concerns that trees reduce water availability. Yet relevant studies from the tropics are scarce, and the impacts of intermediate tree cover remain unexplored. We developed and tested an optimum tree cover theory in which groundwater recharge is maximized at an intermediate tree density. Below this optimal tree density the benefits from any additional trees on water percolation exceed their extra water use, leading to increased groundwater recharge, while above the optimum the opposite occurs. Our results, based on groundwater budgets calibrated with measurements of drainage and transpiration in a cultivated woodland in West Africa, demonstrate that groundwater recharge was maximised at intermediate tree densities. In contrast to the prevailing view, we therefore find that moderate tree cover can increase groundwater recharge, and that tree planting and various tree management options can improve groundwater resources. We evaluate the necessary conditions for these results to hold and suggest that they are likely to be common in the seasonally dry tropics, offering potential for widespread tree establishment and increased benefits for hundreds of millions of people. PMID:26908158

Differences in xylogenesis between dominant and suppressed trees.

PubMed

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

2018-05-01

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

Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics

NASA Astrophysics Data System (ADS)

Ilstedt, U.; Bargués Tobella, A.; Bazié, H. R.; Bayala, J.; Verbeeten, E.; Nyberg, G.; Sanou, J.; Benegas, L.; Murdiyarso, D.; Laudon, H.; Sheil, D.; Malmer, A.

2016-02-01

Water scarcity contributes to the poverty of around one-third of the world’s people. Despite many benefits, tree planting in dry regions is often discouraged by concerns that trees reduce water availability. Yet relevant studies from the tropics are scarce, and the impacts of intermediate tree cover remain unexplored. We developed and tested an optimum tree cover theory in which groundwater recharge is maximized at an intermediate tree density. Below this optimal tree density the benefits from any additional trees on water percolation exceed their extra water use, leading to increased groundwater recharge, while above the optimum the opposite occurs. Our results, based on groundwater budgets calibrated with measurements of drainage and transpiration in a cultivated woodland in West Africa, demonstrate that groundwater recharge was maximised at intermediate tree densities. In contrast to the prevailing view, we therefore find that moderate tree cover can increase groundwater recharge, and that tree planting and various tree management options can improve groundwater resources. We evaluate the necessary conditions for these results to hold and suggest that they are likely to be common in the seasonally dry tropics, offering potential for widespread tree establishment and increased benefits for hundreds of millions of people.

Regolith properties under trees and the biomechanical effects caused by tree root systems as recognized by electrical resistivity tomography (ERT)

NASA Astrophysics Data System (ADS)

Pawlik, Łukasz; Kasprzak, Marek

2018-01-01

Following previous findings regarding the influence of vascular plants (mainly trees) on weathering, soil production and hillslope stability, in this study, we attempted to test a hypothesis regarding significant impacts of tree root systems on soil and regolith properties. Different types of impacts from tree root system (direct and indirect) are commonly gathered under the key term of "biomechanical effects". To add to the discussion of the biomechanical effects of trees, we used a non-invasive geophysical method, electrical resistivity tomography (ERT), to investigate the profiles of four different configurations at three study sites within the Polish section of the Outer Western Carpathians. At each site, one long profile (up to 189 m) of a large section of a hillslope and three short profiles (up to 19.5 m), that is, microsites occupied by trees or their remnants, were made. Short profiles included the tree root zone of a healthy large tree, the tree stump of a decaying tree and the pit-and-mound topography formed after a tree uprooting. The resistivity of regolith and bedrock presented on the long profiles and in comparison with the short profiles through the microsites it can be seen how tree roots impact soil and regolith properties and add to the complexity of the whole soil/regolith profile. Trees change soil and regolith properties directly through root channels and moisture migration and indirectly through the uprooting of trees and the formation of pit-and-mound topography. Within tree stump microsites, the impact of tree root systems, evaluated by a resistivity model, was smaller compared to microsites with living trees or those with pit-and-mound topography but was still visible even several decades after the trees were windbroken or cut down. The ERT method is highly useful for quick evaluation of the impact of tree root systems on soils and regolith. This method, in contrast to traditional soil analyses, offers a continuous dataset for the entire microsite and at depths not normally reached by standard soil excavations. The non-invasive nature of ERT studies is especially important for protected areas as it was shown in the present study.

How does tree age influence damage and recovery in forests impacted by freezing rain and snow?

PubMed

Zhu, LiRong; Zhou, Ting; Chen, BaoMing; Peng, ShaoLin

2015-05-01

The response and recovery mechanisms of forests to damage from freezing rain and snow events are a key topic in forest research and management. However, the relationship between the degree of damage and tree age, i.e., whether seedlings, young trees, or adult trees are most vulnerable, remains unclear and is rarely reported. We investigated the effect of tree age on the degrees of vegetation damage and subsequent recovery in three subtropical forest types-coniferous, mixed, and broad-leaved-in the Tianjing Mountains, South China, after a series of rare icy rain and freezing snow events in 2008. The results showed that damage and recovery rates were both dependent on tree age, with the proportion of damaged vegetation increasing with age (estimated by diameter at breast height, DBH) in all three forest types and gradually plateauing. Significant variation occurred among forest types. Young trees in the coniferous forest were more vulnerable than those in the broad-leaved forest. The type of damage also varied with tree age in different ways in the three forest types. The proportion of young seedlings that were uprooted (the most severe type of damage) was highest in the coniferous forest. In the mixed forest, young trees were significantly more likely to be uprooted than seedlings and adult trees, while in the broad-leaved forest, the proportion of uprooted adult trees was significantly higher than that of seedlings and young trees. There were also differences among forest types in how tree age affected damage recovery. In the coniferous forest, the recovery rate of trees with broken trunks or crowns (DBH > 2.5 cm) increased with tree age. However, in the mixed and broad-leaved forests, no obvious correlation between the recovery rate of trees with broken trunks or crowns and tree age was observed. Trees with severe root damage did not recover; they were uprooted and died. In these forests, vegetation damage and recovery showed tree age dependencies, which varied with tree shape, forest type, and damage type. Understanding this dependency will guide restoration after freezing rain and snow disturbances.

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

Urban tree database and allometric equations

Treesearch

E. Gregory McPherson; Natalie S. van Doorn; Paula J.  Peper

2016-01-01

Information on urban tree growth underpins models used to calculate the effects of trees on the environment and human well-being. Maximum tree size and other growth data are used by urban forest managers, landscape architects, and planners to select trees most suitable to the amount of growing space, thereby reducing costly future conflicts between trees and...

75 FR 48927 - Sierra National Forest, Bass Lake Ranger District, California, Fish Camp Project

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-12

... stocked and thinning is needed. This thinning is needed to reduce inter-tree competition and improve tree... densities are above what can be sustained, with inter-tree competition increasing and tree vigor beginning... communities and reduce inter tree competition to improve tree vigor and increase stand resistance to drought...

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-20

...] WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application August 13, 2010. AGENCY... subadvisory agreements without shareholder approval. Applicants: WisdomTree Asset Management, Inc (``WTAM'' or ``Adviser'') and WisdomTree Trust (``Trust''). Filing Dates: The application was filed on December 23, 2009...

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

ERIC Educational Resources Information Center

Hollister, Sarah

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

Trees of Yap: a field guide

Treesearch

Marjorie V. Cushing Falanruw

2015-01-01

Descriptions, drawings, and photographs are presented for trees found on the Yap Islands in the Federated States of Micronesia. Included are all recorded native trees and most introduced trees as well as new records of native and introduced trees. Additional information is provided on tree distribution, status, vernacular names in Micronesia, and English names when...

Folding Automaton for Trees

NASA Astrophysics Data System (ADS)

Subashini, N.; Thiagarajan, K.

2018-04-01

In this paper we observed the definition of folding technique in graph theory and we derived the corresponding automaton for trees. Also derived some propositions on symmetrical structure tree, non-symmetrical structure tree, point symmetrical structure tree, edge symmetrical structure tree along with finite number of points. This approach provides to derive one edge after n’ number of foldings.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks

PubMed Central

2017-01-01

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com PMID:28407035

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

PubMed

Vaughan, Timothy G

2017-08-01

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

Roost networks of northern myotis (Myotis septentrionalis) in a managed landscape

USGS Publications Warehouse

Johnson, J.B.; Mark, Ford W.; Edwards, J.W.

2012-01-01

Maternity groups of many bat species conform to fission-fusion models and movements among diurnal roost trees and individual bats belonging to these groups use networks of roost trees. Forest disturbances may alter roost networks and characteristics of roost trees. Therefore, at the Fernow Experimental Forest in West Virginia, we examined roost tree networks of northern myotis (Myotis septentrionalis) in forest stands subjected to prescribed fire and in unmanipulated control treatments in 2008 and 2009. Northern myotis formed social groups whose roost areas and roost tree networks overlapped to some extent. Roost tree networks largely resembled scale-free network models, as 61% had a single central node roost tree. In control treatments, central node roost trees were in early stages of decay and surrounded by greater basal area than other trees within the networks. In prescribed fire treatments, central node roost trees were small in diameter, low in the forest canopy, and surrounded by low basal area compared to other trees in networks. Our results indicate that forest disturbances, including prescribed fire, can affect availability and distribution of roosts within roost tree networks. ?? 2011 Elsevier B.V.

Large variations in diurnal and seasonal patterns of sap flux among Aleppo pine trees in semi-arid forest reflect tree-scale hydraulic adjustments

NASA Astrophysics Data System (ADS)

Preisler, Yakir; Tatarinov, Fyodor; Rohatyn, Shani; Rotenberg, Eyal; Grünzweig, José M.; Klein, Tamir; Yakir, Dan

2015-04-01

Adjustments and adaptations of trees to drought vary across different biomes, species and habitats, with important implications for tree mortality and forest dieback associated with global climate change. The aim of this study was to investigate possible links between the patterns of variations in water flux dynamics and drought resistance in Aleppo pine (Pinus halepensis) trees in a semi-arid stand (Yatir forest, Israel). We measured sap flow (SF) and variations in stem diameter, complemented with short-term campaigns of leaf-scale measurements of water vapour and CO2 gas exchange, branch water potential and hydraulic conductivity, as well as eddy flux measurements of evapotranspiration (ET) from a permanent flux tower at the site. SF rates were well synchronized with ET, reaching maximum rates during midday in all trees during the rainy season (Dec-Apr). However, during the dry season (May-Nov), the daily trend in the rates of SF greatly varied among trees, allowing classification into three tree classes: 1) trees with SF maximum rate constantly occurring in mid-day (12:00-13:00); 2)trees showing a shift to an early morning SF peak (04:00-06:00); and 3) trees shifting their daily SF peak to the evening (16:00-18:00). This classification did not change during the four years study period, between 2010 and 2014. Checking for correlation of tree parameters as DBH, tree height, crown size, and competition indices with rates of SF, indicated that timing of maximum SF in summer was mainly related to tree size (DBH), when large trees tended to have a later SF maximum. Dendrometer measurements indicated that large trees (high DBH) had maximum daily diameter in the morning during summer and winter, while small trees typically had maximum daily diameter during midday and afternoon in winter and summer, respectively. Leaf-scale transpiration (T) measurements showed typical morning peak in all trees, and another peak in the afternoon in large trees only. Different diurnal curves observed during the dry season, indicated that water potential and hydraulic conductivity values in larger trees restored from midday depression earlier than in smaller ones. The results demonstrate large heterogeneity in the behaviour related to tree water relations among trees of the same species and in the same stand. The combination of diurnal leaf-scale measurements, SF and changes in DBH demonstrated the different strategies of individual trees of different sizes. Large trees with sufficient internal water storage can more freely manipulate their water storage capacity, with reduced dependence on environmental conditions (e.g., morning and afternoon peaks of T). On the other hand, during the dry summer small trees with insufficient internal water storage are strongly restricted by low soil water availability and extreme environmental conditions, which is expressed in only one peak of T, midday to afternoon shift of diurnal DBH maximum, and shift in SF to predawn when soil water potential is highest. Refilling of internal water storage seems to be in the afternoon/evening since T becomes smaller than SF and DBH increases. Reliance on external water availability in small trees might be insufficient during long drought episodes when soil water content decreases below threshold required for extraction by the trees, leading to increased tree mortality in small DBH trees.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.

PubMed

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

2016-12-01

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

Mechanisms of Douglas-fir resistance to western spruce budworm defoliation: bud burst phenology, photosynthetic compensation and growth rate.

PubMed

Chen, Z; Kolb, T E; Clancy, K M

2001-10-01

We compared growth rates among mature interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) trees showing resistance or susceptibility to defoliation caused by western spruce budworm (Choristoneura occidentalis Freeman), and among clones and half-sib seedling progeny of these trees in a greenhouse. We also investigated bud burst phenology and photosynthetic responses of clones to budworm defoliation in greenhouse experiments. Resistant mature trees had a higher radial growth rate than susceptible trees, especially during periods of budworm defoliation. Clones from resistant trees grew larger crowns than clones from susceptible trees, whereas stem base diameter at the ground line and height did not differ. Half-sib seedling progeny from resistant trees had larger stem diameter, height, and total biomass than progeny from susceptible trees. Mean 5-year radial growth increment of mature trees was more strongly correlated with growth of seedlings than with growth of clones. Clones from resistant trees had later bud burst than clones from susceptible trees, and budworm defoliation of clones depended on the degree of synchrony between bud burst phenology and budworm larval feeding. Clones of resistant and susceptible mature trees showed similar responses of net photosynthetic rate to 2 years of budworm defoliation. We conclude that phenotypic differences in crown condition of Douglas-fir trees following western spruce budworm defoliation are influenced by tree genotype and that high growth rate and late bud burst phenology promote tree resistance to budworm defoliation.

Comprehensive monitoring of Bangladesh tree cover inside and outside of forests, 2000-2014

NASA Astrophysics Data System (ADS)

Potapov, P.; Siddiqui, B. N.; Iqbal, Z.; Aziz, T.; Zzaman, B.; Islam, A.; Pickens, A.; Talero, Y.; Tyukavina, A.; Turubanova, S.; Hansen, M. C.

2017-10-01

A novel approach for satellite-based comprehensive national tree cover change assessment was developed and applied in Bangladesh, a country where trees outside of forests play an important role in the national economy and carbon sequestration. Tree cover change area was quantified using the integration of wall-to-wall Landsat-based mapping with a higher spatial resolution sample-based assessment. The total national tree canopy cover area was estimated as 3165 500 ± 186 600 ha in the year 2000, with trees outside forests making up 54% of total canopy cover. Total tree canopy cover increased by 135 700 (± 116 600) ha (4.3%) during the 2000-2014 time interval. Bangladesh exhibits a national tree cover dynamic where net change is rather small, but gross dynamics significant and variable by forest type. Despite the overall gain in tree cover, results revealed the ongoing clearing of natural forests, especially within the Chittagong hill tracts. While forests decreased their tree cover area by 83 600 ha, the trees outside forests (including tree plantations, village woodlots, and agroforestry) increased their canopy area by 219 300 ha. Our results demonstrated method capability to quantify tree canopy cover dynamics within a fine-scale agricultural landscape. Our approach for comprehensive monitoring of tree canopy cover may be recommended for operational implementation in Bangladesh and other countries with significant tree cover outside of forests.

Size matters a lot: tree height and prior growth predict drought-induced tree death in Italian oak forests

NASA Astrophysics Data System (ADS)

Ripullone, F.; Colangelo, M.; Camarero, J. J.; Gazol, A.; Borghetti, M.; Gentilesca, T.

2016-12-01

Climate warming is expected to amplify drought stress resulting in the occurrence of more widespread dieback episodes and increasing mortality rates. This has pushed the search of reliable and robust early-warning indicators of impending drought-triggered tree death. Recent studies highlight how level of defoliation or age of trees strictly coact with drought in leading to forest decline. In addition, tree size and the tree-to-tree competition for water could also contribute to tree death in drought-prone sites. In this regard, it has been predicted that tall trees with isohydric stomatal regulation are most likely to die due to drought stress. Here, we test this hypothesis by analyzing size, age, competition and growth data in a Mediterranean oak species characterized by anisohydric behaviour, showing recent drought-induced mortality in two Italian forest sites. At both study sites, tree height was associated to the probability of dying. However, this association was opposite to published predictions because living trees were taller than dead trees at both sites. Neither age nor competition intensity played significant roles as drivers of tree mortality. Regarding growth data, trends in basal area increment were significantly smaller in dead than in living trees. Differences were most marked at mid (15 years prior to death) than at short (10 years) or long-term (35 year) scales. This is probably not related to intrinsic growth features of the study species but it can be explained because the most severe drought since 1950 occurred in 2000 at the study area, i.e. 15 years prior to the increase of tree mortality and when growth of living and dead trees started diverging. Lastly, we discuss potential factors which may explain why smaller individuals of anisohydric tree species such as Mediterranean oaks are prone to drought-induced tree death.

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.

[Competition among dominant tree species in a natural spruce-fir forest in Changbai Mountain].

PubMed

Ren, Mei Mei; Yang, Hua

2016-10-01

Dominant tree species are the main species in different layers of mixed-species forests. Examining competitive relationships among dominant tree species is important for proper management of mixedwood forests. In this study, we established a 100 m×100 m plot of uniform condition on Jingouling Forest Farm, Wangqing County, Jilin Province. The dominant tree species of the young forest community were first determined through dominance index analysis approach and the competitive relationships among dominant tree species were then examined using tree competition index that described intra- and inter-specific competition from the above and sides of individual tree crown. The results indicated three dominant tree species in this mixed-species community were Abies nephrolepis, Picea koraiensis and Pinus koraiensis. A. nephrolepis, Picea koraiensis, Pinus koraiensis, Betula costata, Tilia amurensis, Acer tegmentosum and Betula platyphylla were the main competitors of the dominant tree species, while A. nephrolepis was the major competitor for all three dominant tree species (1412.48), followed by Picea koraiensis (439.17) and Pinus koraiensis (245.28), they all had side squeeze effect (64.9%, 65.2% and 66.0% of the total competition for the three dominant tree species, respectively). The level of side and above competition decreased with individual tree DBH (diameter at breast height); the percentage of side competition was nearly equal to that of above competition in small trees and increased with tree size, reaching nearly 100% in large canopy trees. For the three dominant tree species, the side and above competition of three dominant tree species mainly came from A. nephrolepis, Picea koraiensis, Pinus koraiensis, T. amurensis, B. costata, A. tegmentosum and B. platyphylla, and the inter-specific competition was more intense than intra-specific competition (58.4%, 87.1%, 83.7% of the total competition for the three dominant species), both of which decreased with the increase of individual tree DBH.

The relationship among mathematics anxiety, beliefs about mathematics, mathematics self-efficacy, and mathematics performance in associate degree nursing students.

PubMed

Walsh, Kathleen A

2008-01-01

This research explored nursing students' mathematics anxiety, beliefs about mathematics, and mathematics self-efficacy in relation to performance on a medication mathematics test. Results revealed that the participants experienced some mathematics anxiety and had positive beliefs about mathematics and mathematics self-efficacy. Qualitative responses indicated that participants worried about the consequences of failing the medication mathematics test and that practice helped reduce this anxiety. In addition, participants acknowledged the importance of correct dosage calculations for nursing practice. Implications for nursing education are discussed.

Measuring Tree Properties and Responses Using Low-Cost Accelerometers

DOE PAGES

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; ...

2017-05-11

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of momentum, heat, water, and CO 2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree properties such as mass and canopy interception of precipitation are often expensive or difficult due to challenging environments. This paper aims to demonstrate the concept of using robust and affordable accelerometers to measure tree properties and responses. Tree sway is dependent on mass, canopy structure, drag coefficient, and wind forcing.more » By measuring tree acceleration, we can relate the tree motion to external forcing (e.g., wind, precipitation and related canopy interception) and tree physical properties (e.g., mass, elasticity). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, canopy interception of precipitation, and canopy–atmosphere turbulent exchange.« less

Measuring Tree Properties and Responses Using Low-Cost Accelerometers

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

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of momentum, heat, water, and CO 2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree properties such as mass and canopy interception of precipitation are often expensive or difficult due to challenging environments. This paper aims to demonstrate the concept of using robust and affordable accelerometers to measure tree properties and responses. Tree sway is dependent on mass, canopy structure, drag coefficient, and wind forcing.more » By measuring tree acceleration, we can relate the tree motion to external forcing (e.g., wind, precipitation and related canopy interception) and tree physical properties (e.g., mass, elasticity). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, canopy interception of precipitation, and canopy–atmosphere turbulent exchange.« less

Measuring Tree Properties and Responses Using Low-Cost Accelerometers

PubMed Central

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Guerin, Marceau; Oliveira, Rafael S.; Wagner, Jim; Selker, John; van de Giesen, Nick

2017-01-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of momentum, heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree properties such as mass and canopy interception of precipitation are often expensive or difficult due to challenging environments. This paper aims to demonstrate the concept of using robust and affordable accelerometers to measure tree properties and responses. Tree sway is dependent on mass, canopy structure, drag coefficient, and wind forcing. By measuring tree acceleration, we can relate the tree motion to external forcing (e.g., wind, precipitation and related canopy interception) and tree physical properties (e.g., mass, elasticity). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, canopy interception of precipitation, and canopy–atmosphere turbulent exchange. PMID:28492477

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.

[Hydraulic limitation on photosynthetic rate of old Populus simonii trees in sandy soil of north Shaanxi Province].

PubMed

Zuo, Li-Xiang; Li, Yang-Yang; Chen, Jia-Cun

2014-06-01

'Old and dwarf trees' on the loess plateau region mainly occurred among mature trees rather than among small trees. To elucidate the mechanism of tree age on 'old and dwarf trees' formation, taking Populus simonii, a tree species that accounted for the largest portion of 'old and dwarf trees' on the loess plateau, as an example, the growth, photosynthesis and hydraulic traits of P. simonii trees with different ages (young: 13-15 years, mid-aged: 31-34 years, and old: 49-54 years) were measured. The results showed that the dieback length increased, and net photosynthetic rate, stomatal conductance, transpiration rate, and whole plant hydraulic conductance decreased significantly with the increasing tree age. Both net photosynthetic rate and stomatal conductance measured at different dates were significantly and positively related to the whole plant hydraulic conductance, suggesting that the decreasing photosynthetic rate of old trees was possibly caused by the declined hydraulic conductance. Although the resistance to cavitation in stems and leaves was stronger in old trees than in young and mid-aged trees, there were no differences in midday native stem embolization degree and leaf hydraulic conductance based on the vulnerability curve estimation, suggesting that the increased hydraulic resistance of the soil-root system is probably the most important reason for decreasing the whole plant hydraulic conductance of old trees.

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

PubMed

Wu, Yufeng

2012-03-01

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

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.

Decision-analytic modeling studies: An overview for clinicians using multiple myeloma as an example.

PubMed

Rochau, U; Jahn, B; Qerimi, V; Burger, E A; Kurzthaler, C; Kluibenschaedl, M; Willenbacher, E; Gastl, G; Willenbacher, W; Siebert, U

2015-05-01

The purpose of this study was to provide a clinician-friendly overview of decision-analytic models evaluating different treatment strategies for multiple myeloma (MM). We performed a systematic literature search to identify studies evaluating MM treatment strategies using mathematical decision-analytic models. We included studies that were published as full-text articles in English, and assessed relevant clinical endpoints, and summarized methodological characteristics (e.g., modeling approaches, simulation techniques, health outcomes, perspectives). Eleven decision-analytic modeling studies met our inclusion criteria. Five different modeling approaches were adopted: decision-tree modeling, Markov state-transition modeling, discrete event simulation, partitioned-survival analysis and area-under-the-curve modeling. Health outcomes included survival, number-needed-to-treat, life expectancy, and quality-adjusted life years. Evaluated treatment strategies included novel agent-based combination therapies, stem cell transplantation and supportive measures. Overall, our review provides a comprehensive summary of modeling studies assessing treatment of MM and highlights decision-analytic modeling as an important tool for health policy decision making. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

NASA Astrophysics Data System (ADS)

Cooper, Edwin L.; Overstreet, Nicola

2014-03-01

Recent evidence supports that prokaryotes exhibit adaptive immunity in the form of CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) and Cas (CRISPR associated proteins). The CRISPR-Cas system confers resistance to exogenous genetic elements such as phages and plasmids by allowing for the recognition and silencing of these genetic elements. Moreover, CRISPR-Cas serves as a memory of past exposures. This suggests that the evolution of the immune system has counterparts among the prokaryotes, not exclusively among eukaryotes. Mathematical models have been proposed which simulate the evolutionary patterns of CRISPR, however large gaps in our understanding of CRISPR-Cas function and evolution still exist. The CRISPR-Cas system is analogous to small RNAs involved in resistance mechanisms throughout the tree of life, and a deeper understanding of the evolution of small RNA pathways is necessary before the relationship between these convergent systems is to be determined. Presented in this review are novel RNAi therapies based on CRISPR-Cas analogs and the potential for future therapies based on CRISPR-Cas system components.

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

Branch-Based Model for the Diameters of the Pulmonary Airways: Accounting for Departures From Self-Consistency and Registration Errors

PubMed Central

Neradilek, Moni B.; Polissar, Nayak L.; Einstein, Daniel R.; Glenny, Robb W.; Minard, Kevin R.; Carson, James P.; Jiao, Xiangmin; Jacob, Richard E.; Cox, Timothy C.; Postlethwait, Edward M.; Corley, Richard A.

2017-01-01

We examine a previously published branch-based approach for modeling airway diameters that is predicated on the assumption of self-consistency across all levels of the tree. We mathematically formulate this assumption, propose a method to test it and develop a more general model to be used when the assumption is violated. We discuss the effect of measurement error on the estimated models and propose methods that take account of error. The methods are illustrated on data from MRI and CT images of silicone casts of two rats, two normal monkeys, and one ozone-exposed monkey. Our results showed substantial departures from self-consistency in all five subjects. When departures from self-consistency exist, we do not recommend using the self-consistency model, even as an approximation, as we have shown that it may likely lead to an incorrect representation of the diameter geometry. The new variance model can be used instead. Measurement error has an important impact on the estimated morphometry models and needs to be addressed in the analysis. PMID:22528468

Modelling daily water temperature from air temperature for the Missouri River.

PubMed

Zhu, Senlin; Nyarko, Emmanuel Karlo; Hadzima-Nyarko, Marijana

2018-01-01

The bio-chemical and physical characteristics of a river are directly affected by water temperature, which thereby affects the overall health of aquatic ecosystems. It is a complex problem to accurately estimate water temperature. Modelling of river water temperature is usually based on a suitable mathematical model and field measurements of various atmospheric factors. In this article, the air-water temperature relationship of the Missouri River is investigated by developing three different machine learning models (Artificial Neural Network (ANN), Gaussian Process Regression (GPR), and Bootstrap Aggregated Decision Trees (BA-DT)). Standard models (linear regression, non-linear regression, and stochastic models) are also developed and compared to machine learning models. Analyzing the three standard models, the stochastic model clearly outperforms the standard linear model and nonlinear model. All the three machine learning models have comparable results and outperform the stochastic model, with GPR having slightly better results for stations No. 2 and 3, while BA-DT has slightly better results for station No. 1. The machine learning models are very effective tools which can be used for the prediction of daily river temperature.

ɛ-connectedness, finite approximations, shape theory and coarse graining in hyperspaces

NASA Astrophysics Data System (ADS)

Alonso-Morón, Manuel; Cuchillo-Ibanez, Eduardo; Luzón, Ana

2008-12-01

We use upper semifinite hyperspaces of compacta to describe ε-connectedness and to compute homology from finite approximations. We find a new connection between ε-connectedness and the so-called Shape Theory. We construct a geodesically complete R-tree, by means of ε-components at different resolutions, whose behavior at infinite captures the topological structure of the space of components of a given compact metric space. We also construct inverse sequences of finite spaces using internal finite approximations of compact metric spaces. These sequences can be converted into inverse sequences of polyhedra and simplicial maps by means of what we call the Alexandroff-McCord correspondence. This correspondence allows us to relate upper semifinite hyperspaces of finite approximation with the Vietoris-Rips complexes of such approximations at different resolutions. Two motivating examples are included in the introduction. We propose this procedure as a different mathematical foundation for problems on data analysis. This process is intrinsically related to the methodology of shape theory. This paper reinforces Robins’s idea of using methods from shape theory to compute homology from finite approximations.

Branch-Based Model for the Diameters of the Pulmonary Airways: Accounting for Departures From Self-Consistency and Registration Errors

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

Neradilek, Moni B.; Polissar, Nayak L.; Einstein, Daniel R.

2012-04-24

We examine a previously published branch-based approach to modeling airway diameters that is predicated on the assumption of self-consistency across all levels of the tree. We mathematically formulate this assumption, propose a method to test it and develop a more general model to be used when the assumption is violated. We discuss the effect of measurement error on the estimated models and propose methods that account for it. The methods are illustrated on data from MRI and CT images of silicone casts of two rats, two normal monkeys and one ozone-exposed monkey. Our results showed substantial departures from self-consistency inmore » all five subjects. When departures from selfconsistency exist we do not recommend using the self-consistency model, even as an approximation, as we have shown that it may likely lead to an incorrect representation of the diameter geometry. Measurement error has an important impact on the estimated morphometry models and needs to be accounted for in the analysis.« less

Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models

DOE PAGES

Carlberg, Kevin T.

2014-11-05

Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less

A formulation for studying dynamics of N connected flexible deployable members

NASA Astrophysics Data System (ADS)

Ibrahim, A. M.; Modi, V. J.

A relatively general formulation for studying dynamics of a system, consisting of N connected flexible deployable members (beams, plates, shells, membranes, strings) forming a topological tree or a closed configuration, is presented. The mathematical description of the system can be, in general, a combination of discrete and distributed coordinates. Joints, elastic and dissipative, permit relative rotation and translation between bodies. The elastic deformations (lateral, axial, and torsional) can be discretized using admissible functions, finite elements or lumped mass method. Rotations of the members, as well as of the entire system, can be described using a set of orientation angles, Euler parameters or Rodrigues vectors. The formulation accounts for: the presence of momentum or reaction wheels (gimballed or fixed); thrusters distributed over the flexible and rigid portions; and any prescribed forms of energy dissipation mechanisms. Of course, the generalized forces can simulate desired environmental effects. The formulation is valid for orbiting as well as ground based and marine systems. Application of the formulation is illustrated through several examples, in spacecraft dynamics, which are of contemporary interest.

Method for estimating potential tree-grade distributions for northeastern forest species

Treesearch

Daniel A. Yaussy; Daniel A. Yaussy

1993-01-01

Generalized logistic regression was used to distribute trees into four potential tree grades for 20 northeastern species groups. The potential tree grade is defined as the tree grade based on the length and amount of clear cuttings and defects only, disregarding minimum grading diameter. The algorithms described use site index and tree diameter as the predictive...

National Forest Health Monitoring Program Maryland and Massachusetts Street Tree Monitoring Pilot Projects

Treesearch

Buckelew Cumming Anne; Daniel Twardus; William Smith

2006-01-01

Urban forests have many components: park trees, small woodlands, riparian buffers, street trees, and others. While some communities conduct city-wide inventories of street tree populations, there has been no comprehensive, statewide sampling to characterize the structure, health, and function of street tree populations. A statewide Street Tree Monitoring pilot study...

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.

Modeling Missing Remeasurement Tree Heights in Forest Inventory Data

Treesearch

Raymond M. Sheffield; Callie J. Schweitzer

2005-01-01

Missing tree heights are often problematic in compiling forest inventory remeasurement data. Heights for cut and mortality trees are usually not available; calculations of removal or mortality volumes must utilize either a modeled height at the time of tree death or the height assigned to the tree at a previous remeasurement. Less often, tree heights are not available...

Modeling missing remeasurement tree heights in forest inventory data

Treesearch

Raymond M. Sheffield; Callie J. Schweitzer

2002-01-01

Missing tree heights are often problematic in compiling forest inventory renleasureinent data. Heights for cut and niortality trees are usually not available; calculations of removal or mortality volumes must utilize either a modeled height at the time of tree death or the height assigned to the tree at a previous remeasurement. Less often, tree heights are not...

Epicormic branching on hardwood trees bordering forest openings

Treesearch

G.R., Jr. Trimble; Donald W. Seegrist; Donald W. Seegrist

1973-01-01

Epicormic branching in hardwoods can degrade logs and reduce the dollar returns from growing trees. A study made around clearcut openings of various sizes showed that the following variables were related to the degree of epicormic branching on trees bordering the openings: size of opening, species, tree dominance class, exposure of tree bole, and position on tree bole...

Urban Sacramento oak reforestation: 17 years and 20,000 trees

Treesearch

Zarah Wyly; Erika Teach

2015-01-01

The Sacramento Tree Foundation (Tree Foundation), a nonprofit organization operating in the greater Sacramento California region, has been engaged in planting native oak trees in urban and suburban areas since 1998. Through an effort to provide efficient access to tree mitigation services and support compliance with local tree protection ordinances, more than 20,038...

Community Tree Planting Guide

Treesearch

Katie Himanga; Douglas Jones; Jean Miller; Janette Monear; Gail Steinman; Katherine Widin

2001-01-01

Tree Trust has been helping people plant trees in their communities since 1976. Our goal is to educate people about the importance of trees in their community and guide them through the process of successful tree-planting projects. Franklin Delano Roosevelt once said ?to exist as a nation, to prosper as a state, and to live as a people, we must have trees?....

Are trees long-lived?

Treesearch

Kevin T. Smith

2009-01-01

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

Timber volume and aboveground live tree biomass estimations for landscape analyses in the Pacific Northwest

Treesearch

Xiaoping Zhou; Miles A. Hemstrom

2010-01-01

Timber availability, aboveground tree biomass, and changes in aboveground carbon pools are important consequences of landscape management. There are several models available for calculating tree volume and aboveground tree biomass pools. This paper documents species-specific regional equations for tree volume and aboveground live tree biomass estimation that might be...

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

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

Tree Colors: Color Schemes for Tree-Structured Data.

PubMed

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

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

Quotable Quotes in Mathematics

ERIC Educational Resources Information Center

Lo, Bruce W. N.

1983-01-01

As a way to dispel negative feelings toward mathematics, a variety of quotations are given. They are categorized by: what mathematics is, mathematicians, mathematics and other disciplines, different areas of mathematics, mathematics and humor, applications of mathematics, and pure versus applied mathematics. (MNS)

Ecological Importance of Large-Diameter Trees in a Temperate Mixed-Conifer Forest

PubMed Central

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

2012-01-01

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

From Google Maps to a fine-grained catalog of street trees

NASA Astrophysics Data System (ADS)

Branson, Steve; Wegner, Jan Dirk; Hall, David; Lang, Nico; Schindler, Konrad; Perona, Pietro

2018-01-01

Up-to-date catalogs of the urban tree population are of importance for municipalities to monitor and improve quality of life in cities. Despite much research on automation of tree mapping, mainly relying on dedicated airborne LiDAR or hyperspectral campaigns, tree detection and species recognition is still mostly done manually in practice. We present a fully automated tree detection and species recognition pipeline that can process thousands of trees within a few hours using publicly available aerial and street view images of Google MapsTM. These data provide rich information from different viewpoints and at different scales from global tree shapes to bark textures. Our work-flow is built around a supervised classification that automatically learns the most discriminative features from thousands of trees and corresponding, publicly available tree inventory data. In addition, we introduce a change tracker that recognizes changes of individual trees at city-scale, which is essential to keep an urban tree inventory up-to-date. The system takes street-level images of the same tree location at two different times and classifies the type of change (e.g., tree has been removed). Drawing on recent advances in computer vision and machine learning, we apply convolutional neural networks (CNN) for all classification tasks. We propose the following pipeline: download all available panoramas and overhead images of an area of interest, detect trees per image and combine multi-view detections in a probabilistic framework, adding prior knowledge; recognize fine-grained species of detected trees. In a later, separate module, track trees over time, detect significant changes and classify the type of change. We believe this is the first work to exploit publicly available image data for city-scale street tree detection, species recognition and change tracking, exhaustively over several square kilometers, respectively many thousands of trees. Experiments in the city of Pasadena, California, USA show that we can detect >70% of the street trees, assign correct species to >80% for 40 different species, and correctly detect and classify changes in >90% of the cases.

Local versus landscape-scale effects of savanna trees on grasses

USGS Publications Warehouse

Riginos, C.; Grace, J.B.; Augustine, D.J.; Young, T.P.

2009-01-01

1. Savanna ecosystems - defined by the coexistence of trees and grasses - cover more than one-fifth the world's land surface and harbour most of the world's rangelands, livestock and large mammal diversity. Savanna trees can have a variety of effects on grasses, with consequences for the wild and domestic herbivores that depend on them. 2.Studies of these effects have focused on two different spatial scales. At the scale of individual trees, many studies have shown net positive effects of trees on sub-canopy grass nutrient concentrations and biomass. At the landscape scale, other studies have shown negative effects of high tree densities on grass productivity. These disparate results have led to different conclusions about the effects of trees on forage quality and ungulate nutrition in savannas. 3.We integrate these approaches by examining the effects of trees on grasses at both spatial scales and across a range of landscape-scale tree densities. 4.We quantified grass biomass, species composition and nutrient concentrations in these different contexts in an Acacia drepanolobium savanna in Laikipia, Kenya. Individual trees had positive effects on grass biomass, most likely because trees enrich soil nitrogen. Grass leaf phosphorus in sub-canopy areas, however, was depressed. The effects of individual trees could explain the effects of increasing landscape-scale tree cover for the biomass of only two of the four dominant grass species. 5.The negative effects of trees on grass and soil phosphorus, combined with depressed grass productivity in areas of high tree cover, suggest that ungulate nutrition may be compromised in areas with many trees. 6.Synthesis. We conclude that few, isolated trees may have positive local effects on savanna grasses and forage, but in areas of high tree density the negative landscape-scale effects of trees are likely to outweigh these positive effects. In savannas and other patchy landscapes, attempts to predict the consequences of changes in patch abundances for ecosystem services (e.g. rangeland productivity and carbon sequestration) will depend on our understanding of the extent to which local, patch-scale dynamics do or do not predict landscape-scale dynamics. ?? 2009 British Ecological Society.

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

PubMed

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

2018-01-01

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

Local-scale drivers of tree survival in a temperate forest.

PubMed

Wang, Xugao; Comita, Liza S; Hao, Zhanqing; Davies, Stuart J; Ye, Ji; Lin, Fei; Yuan, Zuoqiang

2012-01-01

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1-20 cm dbh) and medium trees (20-40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management.

Transpiration and whole-tree conductance in ponderosa pine trees of different heights.

PubMed

Ryan, M G; Bond, B J; Law, B E; Hubbard, R M; Woodruff, D; Cienciala, E; Kucera, J

2000-09-01

Changes in leaf physiology with tree age and size could alter forest growth, water yield, and carbon fluxes. We measured tree water flux (Q) for 14 ponderosa pine trees in two size classes (12 m tall and ∼40 years old, and 36 m tall and ∼ 290 years old) to determine if transpiration (E) and whole-tree conductance (g t ) differed between the two sizes of trees. For both size classes, E was approximately equal to Q measured 2 m above the ground: Q was most highly correlated with current, not lagged, water vapor pressure deficit, and night Q was <12% of total daily flux. E for days 165-195 and 240-260 averaged 0.97 mmol m -2 (leaf area, projected) s -1 for the 12-m trees and 0.57 mmol m -2 (leaf area) s -1 for the 36-m trees. When photosynthetically active radiation (I P ) exceeded the light saturation for photosynthesis in ponderosa pine (900 µmol m -2 (ground) s -1 ), differences in E were more pronounced: 2.4 mmol m -2 (leaf area) s -1 for the 12-m trees and 1.2 mmol m -2 s -1 for the 36-m trees, yielding g t of 140 mmol m -2 (leaf area) s -1 for the 12-m trees and 72 mmol m -2 s -1 for the 36-m trees. Extrapolated to forests with leaf area index =1, the 36-m trees would transpire 117 mm between 1 June and 31 August compared to 170 mm for the 12-m trees, a difference of 15% of average annual precipitation. Lower g t in the taller trees also likely lowers photosynthesis during the growing season.

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.

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

PubMed Central

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

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics. PMID:29515616

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

Local-Scale Drivers of Tree Survival in a Temperate Forest

PubMed Central

Wang, Xugao; Comita, Liza S.; Hao, Zhanqing; Davies, Stuart J.; Ye, Ji; Lin, Fei; Yuan, Zuoqiang

2012-01-01

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1–20 cm dbh) and medium trees (20–40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management. PMID:22347996

Tree Species Richness Promotes Invertebrate Herbivory on Congeneric Native and Exotic Tree Saplings in a Young Diversity Experiment.

PubMed

Wein, Annika; Bauhus, Jürgen; Bilodeau-Gauthier, Simon; Scherer-Lorenzen, Michael; Nock, Charles; Staab, Michael

2016-01-01

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

Effects of lightning on trees: A predictive model based on in situ electrical resistivity.

PubMed

Gora, Evan M; Bitzer, Phillip M; Burchfield, Jeffrey C; Schnitzer, Stefan A; Yanoviak, Stephen P

2017-10-01

The effects of lightning on trees range from catastrophic death to the absence of observable damage. Such differences may be predictable among tree species, and more generally among plant life history strategies and growth forms. We used field-collected electrical resistivity data in temperate and tropical forests to model how the distribution of power from a lightning discharge varies with tree size and identity, and with the presence of lianas. Estimated heating density (heat generated per volume of tree tissue) and maximum power (maximum rate of heating) from a standardized lightning discharge differed 300% among tree species. Tree size and morphology also were important; the heating density of a hypothetical 10 m tall Alseis blackiana was 49 times greater than for a 30 m tall conspecific, and 127 times greater than for a 30 m tall Dipteryx panamensis . Lianas may protect trees from lightning by conducting electric current; estimated heating and maximum power were reduced by 60% (±7.1%) for trees with one liana and by 87% (±4.0%) for trees with three lianas. This study provides the first quantitative mechanism describing how differences among trees can influence lightning-tree interactions, and how lianas can serve as natural lightning rods for trees.

Coalescent methods for estimating phylogenetic trees.

PubMed

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

2009-10-01

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

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

PubMed

Ji, Wenjing; Zhao, Bin

2018-03-15

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

Facilitation or Competition? Tree Effects on Grass Biomass across a Precipitation Gradient

PubMed Central

Moustakas, Aristides; Kunin, William E.; Cameron, Tom C.; Sankaran, Mahesh

2013-01-01

Savanna ecosystems are dominated by two distinct plant life forms, grasses and trees, but the interactions between them are poorly understood. Here, we quantified the effects of isolated savanna trees on grass biomass as a function of distance from the base of the tree and tree height, across a precipitation gradient in the Kruger National Park, South Africa. Our results suggest that mean annual precipitation (MAP) mediates the nature of tree-grass interactions in these ecosystems, with the impact of trees on grass biomass shifting qualitatively between 550 and 737 mm MAP. Tree effects on grass biomass were facilitative in drier sites (MAP≤550 mm), with higher grass biomass observed beneath tree canopies than outside. In contrast, at the wettest site (MAP = 737 mm), grass biomass did not differ significantly beneath and outside tree canopies. Within this overall precipitation-driven pattern, tree height had positive effect on sub-canopy grass biomass at some sites, but these effects were weak and not consistent across the rainfall gradient. For a more synthetic understanding of tree-grass interactions in savannas, future studies should focus on isolating the different mechanisms by which trees influence grass biomass, both positively and negatively, and elucidate how their relative strengths change over broad environmental gradients. PMID:23451137

How Does Tree Density Affect Water Loss of Peatlands? A Mesocosm Experiment

PubMed Central

Limpens, Juul; Holmgren, Milena; Jacobs, Cor M. J.; Van der Zee, Sjoerd E. A. T. M.; Karofeld, Edgar; Berendse, Frank

2014-01-01

Raised bogs have accumulated more atmospheric carbon than any other terrestrial ecosystem on Earth. Climate-induced expansion of trees and shrubs may turn these ecosystems from net carbon sinks into sources when associated with reduced water tables. Increasing water loss through tree evapotranspiration could potentially deepen water tables, thus stimulating peat decomposition and carbon release. Bridging the gap between modelling and field studies, we conducted a three-year mesocosm experiment subjecting natural bog vegetation to three birch tree densities, and studied the changes in subsurface temperature, water balance components, leaf area index and vegetation composition. We found the deepest water table in mesocosms with low tree density. Mesocosms with high tree density remained wettest (i.e. highest water tables) whereas the control treatment without trees had intermediate water tables. These differences are attributed mostly to differences in evapotranspiration. Although our mesocosm results cannot be directly scaled up to ecosystem level, the systematic effect of tree density suggests that as bogs become colonized by trees, the effect of trees on ecosystem water loss changes with time, with tree transpiration effects of drying becoming increasingly offset by shading effects during the later phases of tree encroachment. These density-dependent effects of trees on water loss have important implications for the structure and functioning of peatbogs. PMID:24632565

Conifer Stored Resources and Resistance to a Fungus Associated with the Spruce Bark Beetle Ips typographus

PubMed Central

Lahr, Eleanor C.; Krokene, Paal

2013-01-01

Bark beetles and associated fungi are among the greatest natural threats to conifers worldwide. Conifers have potent defenses, but resistance to beetles and fungal pathogens may be reduced if tree stored resources are consumed by fungi rather than used for tree defense. Here, we assessed the relationship between tree stored resources and resistance to Ceratocystis polonica, a phytopathogenic fungus vectored by the spruce bark beetle Ips typographus. We measured phloem and sapwood nitrogen, non-structural carbohydrates (NSC), and lipids before and after trees were attacked by I. typographus (vectoring C. polonica) or artificially inoculated with C. polonica alone. Tree resistance was assessed by measuring phloem lesions and the proportion of necrotic phloem around the tree's circumference following attack or inoculation. While initial resource concentrations were unrelated to tree resistance to C. polonica, over time, phloem NSC and sapwood lipids declined in the trees inoculated with C. polonica. Greater resource declines correlated with less resistant trees (trees with larger lesions or more necrotic phloem), suggesting that resource depletion may be caused by fungal consumption rather than tree resistance. Ips typographus may then benefit indirectly from reduced tree defenses caused by fungal resource uptake. Our research on tree stored resources represents a novel way of understanding bark beetle-fungal-conifer interactions. PMID:23967298

Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

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

Mapping tree density at a global scale

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Non-unique key B-Tree implementation

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

Ries, D.R.

1980-12-23

The B-Trees are an indexed method to allow fast retrieval and order preserving updates to a FRAMIS relation based on a designated set of keys in the relation. A B-Tree access method is being implemented to provide indexed and sequential (in index order) access to FRAMIS relations. The implementation modifies the basic B-Tree structure to correctly allow multiple key values and still maintain the balanced page fill property of B-Trees. The data structures of the B-Tree are presented first, including the FRAMIS solution to the duplicate key value problem. Then the access level routines and utilities are presented. These routinesmore » include the original B-Tree creation; searching the B-Tree; and inserting, deleting, and replacing tuples on the B-Tree. In conclusion, the uses of the B-Tree access structures at the semantic level to enhance the FRAMIS performance are discussed. 10 figures.« less

Mapping tree density at a global scale.

PubMed

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

2015-09-10

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

Carbon storage and sequestration by trees in VIT University campus

NASA Astrophysics Data System (ADS)

Saral, A. Mary; SteffySelcia, S.; Devi, Keerthana

2017-11-01

The present study addresses carbon storage and sequestration by trees grown in VIT University campus, Vellore. Approximately twenty trees were selected from Woodstockarea. The above ground biomass and below ground biomass were calculated. The above ground biomass includes non-destructive anddestructive sampling. The Non-destructive method includes the measurement of height of thetree and diameter of the tree. The height of the tree is calculated using Total Station instrument and diameter is calculated using measuring tape. In the destructive method the weight of samples (leaves) and sub-samples (fruits, flowers) of the tree were considered. To calculate the belowground biomass soil samples are taken and analyzed. The results obtained were used to predict the carbon storage. It was found that out of twenty tree samples Millingtonia hortensis which is commonly known as Cork tree possess maximum carbon storage (14.342kg/tree) and carbon sequestration (52.583kg/tree) respectively.

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models

PubMed Central

Mitchell, Jonathan S.; Chang, Jonathan

2017-01-01

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM’s likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA’s numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that “unobserved rate shifts” appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\sim}$\\end{document}20% of simulated trees in MEA’s data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth–death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth. PMID:28334223

Deciphering the enigma of undetected species, phylogenetic, and functional diversity based on Good-Turing theory.

PubMed

Chao, Anne; Chiu, Chun-Huo; Colwell, Robert K; Magnago, Luiz Fernando S; Chazdon, Robin L; Gotelli, Nicholas J

2017-11-01

Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith's phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.'s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under which the estimators are nearly unbiased, thus offering new insights. Simulation results are reported to numerically verify the performance of the derived estimators. We illustrate all estimators and assess their sampling uncertainty with an empirical dataset for Brazilian rain forest trees. These estimators should be widely applicable to many current problems in ecology, such as the effects of climate change on spatial and temporal beta diversity and the contribution of trait diversity to ecosystem multi-functionality. © 2017 by the Ecological Society of America.

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models.

PubMed

Rabosky, Daniel L; Mitchell, Jonathan S; Chang, Jonathan

2017-07-01

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\\sim}$20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

The pipe model theory half a century on: a review.

PubMed

Lehnebach, Romain; Beyer, Robert; Letort, Véronique; Heuret, Patrick

2018-01-23

More than a half century ago, Shinozaki et al. (Shinozaki K, Yoda K, Hozumi K, Kira T. 1964b. A quantitative analysis of plant form - the pipe model theory. II. Further evidence of the theory and its application in forest ecology. Japanese Journal of Ecology14: 133-139) proposed an elegant conceptual framework, the pipe model theory (PMT), to interpret the observed linear relationship between the amount of stem tissue and corresponding supported leaves. The PMT brought a satisfactory answer to two vividly debated problems that were unresolved at the moment of its publication: (1) What determines tree form and which rules drive biomass allocation to the foliar versus stem compartments in plants? (2) How can foliar area or mass in an individual plant, in a stand or at even larger scales be estimated? Since its initial formulation, the PMT has been reinterpreted and used in applications, and has undoubtedly become an important milestone in the mathematical interpretation of plant form and functioning. This article aims to review the PMT by going back to its initial formulation, stating its explicit and implicit properties and discussing them in the light of current biological knowledge and experimental evidence in order to identify the validity and range of applicability of the theory. We also discuss the use of the theory in tree biomechanics and hydraulics as well as in functional-structural plant modelling. Scrutinizing the PMT in the light of modern biological knowledge revealed that most of its properties are not valid as a general rule. The hydraulic framework derived from the PMT has attracted much more attention than its mechanical counterpart and implies that only the conductive portion of a stem cross-section should be proportional to the supported foliage amount rather than the whole of it. The facts that this conductive portion is experimentally difficult to measure and varies with environmental conditions and tree ontogeny might cause the commonly reported non-linear relationships between foliage and stem metrics. Nevertheless, the PMT can still be considered as a portfolio of properties providing a unified framework to integrate and analyse functional-structural relationships. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Releasing young hardwood crop trees-use of a chain saw costs less than herbicides

Treesearch

Gary W. Miller; Gary W. Miller

1984-01-01

A crown-touching release of 12-year-old black cherry and yellow-poplar crop trees on a good site required removing an average of 14 trees for every crop tree. An average of 80 crop trees per acre was left free-to-grow with an average growing space of 4.7 feet on all sides of the crown. Basal spraying cost $0.80 per crop tree, stem injecting cost $0.61 per crop tree,...

The Relationship of Mathematics Anxiety and Mathematical Knowledge to the Learning of Mathematical Pedagogy by Preservice Elementary Teachers.

ERIC Educational Resources Information Center

Battista, Michael T.

1986-01-01

Examined how preservice elementary teachers' (N=38) mathematical knowledge and mathematics anxiety affect their success in a mathematics methods course. Also examined the hypothesis that a mathematics methods course can reduce the mathematics anxiety of these teachers. One finding is that mathematics anxiety does not inhibit their learning of…

Mathematics Teachers' Perceptions of Their Students' Mathematical Competence: Relations to Mathematics Achievement, Affect, and Engagement in Singapore and Australia

ERIC Educational Resources Information Center

Areepattamannil, Shaljan; Kaur, Berinderjeet

2013-01-01

This study, drawing on data from the Trends in International Mathematics and Science Study (TIMSS) 2011, examined whether mathematics teachers' perceptions of their students' mathematical competence were related to mathematics achievement, affect toward mathematics, and engagement in mathematics lessons among Grade 8 students in Singapore and…

Tree detection in orchards from VHR satellite images using scale-space theory

NASA Astrophysics Data System (ADS)

Mahour, Milad; Tolpekin, Valentyn; Stein, Alfred

2016-10-01

This study focused on extracting reliable and detailed information from very High Resolution (VHR) satellite images for the detection of individual trees in orchards. The images contain detailed information on spectral and geometrical properties of trees. Their scale level, however, is insufficient for spectral properties of individual trees, because adjacent tree canopies interlock. We modeled trees using a bell shaped spectral profile. Identifying the brightest peak was challenging due to sun illumination effects caused 1 by differences in positions of the sun and the satellite sensor. Crown boundary detection was solved by using the NDVI from the same image. We used Gaussian scale-space methods that search for extrema in the scale-space domain. The procedures were tested on two orchards with different tree types, tree sizes and tree observation patterns in Iran. Validation was done using reference data derived from an UltraCam digital aerial photo. Local extrema of the determinant of the Hessian corresponded well to the geographical coordinates and the size of individual trees. False detections arising from a slight asymmetry of trees were distinguished from multiple detections of the same tree with different extents. Uncertainty assessment was carried out on the presence and spatial extents of individual trees. The study demonstrated how the suggested approach can be used for image segmentation for orchards with different types of trees. We concluded that Gaussian scale-space theory can be applied to extract information from VHR satellite images for individual tree detection. This may lead to improved decision making for irrigation and crop water requirement purposes in future studies.

Climate variability drives recent tree mortality in Europe.

PubMed

Neumann, Mathias; Mues, Volker; Moreno, Adam; Hasenauer, Hubert; Seidl, Rupert

2017-11-01

Tree mortality is an important process in forest ecosystems, frequently hypothesized to be highly climate sensitive. Yet, tree death remains one of the least understood processes of forest dynamics. Recently, changes in tree mortality have been observed in forests around the globe, which could profoundly affect ecosystem functioning and services provisioning to society. We describe continental-scale patterns of recent tree mortality from the only consistent pan-European forest monitoring network, identifying recent mortality hotspots in southern and northern Europe. Analyzing 925,462 annual observations of 235,895 trees between 2000 and 2012, we determine the influence of climate variability and tree age on interannual variation in tree mortality using Cox proportional hazard models. Warm summers as well as high seasonal variability in precipitation increased the likelihood of tree death. However, our data also suggest that reduced cold-induced mortality could compensate increased mortality related to peak temperatures in a warming climate. Besides climate variability, age was an important driver of tree mortality, with individual mortality probability decreasing with age over the first century of a trees life. A considerable portion of the observed variation in tree mortality could be explained by satellite-derived net primary productivity, suggesting that widely available remote sensing products can be used as an early warning indicator of widespread tree mortality. Our findings advance the understanding of patterns of large-scale tree mortality by demonstrating the influence of seasonal and diurnal climate variation, and highlight the potential of state-of-the-art remote sensing to anticipate an increased likelihood of tree mortality in space and time. © 2017 John Wiley & Sons Ltd.

Occurrence of termites (Isoptera) on living and standing dead trees in a tropical dry forest in Mexico.

PubMed

Calderón-Cortés, Nancy; Escalera-Vázquez, Luis H; Oyama, Ken

2018-01-01

Termites play a key role as ecosystem engineers in numerous ecological processes though their role in the dynamics of wood degradation in tropical dry forests, particularly at the level of the crown canopy, has been little studied. In this study, we analysed the occurrence of termites in the forest canopy by evaluating the density and proportion of living and standing dead trees associated with termites in deciduous and riparian habitats of the tropical dry forest in Chamela, Mexico. The results indicated that 60-98% of standing dead trees and 23-59% of living trees in Chamela were associated with termites. In particular, we found that the density of standing dead trees was higher in deciduous forests (0.057-0.066 trees/m 2 ) than in riparian forests (0.022 and 0.027 trees/m 2 ), even though the proportion of trees was not significantly different among habitats. Additionally, we found a higher density of trees associated with termites in trees of smaller size classes (0.01-0.09 trees/m 2 ) than in larger class sizes (0-0.02 trees/m 2 ). Interestingly, 72% of variation in the density of trees associated with termites is explained by the density of standing dead trees. Overall, these results indicate that standing dead tree availability might be the main factor regulating termite populations in Chamela forest and suggest that termites could play a key role in the decomposition of above-ground dead wood, mediating the incorporation of suspended and standing dead wood into the soil.

Walking tree heuristics for biological string alignment, gene location, and phylogenies

NASA Astrophysics Data System (ADS)

Cull, P.; Holloway, J. L.; Cavener, J. D.

1999-03-01

Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. We propose a family of heuristics called walking trees to align biologically reasonable strings. Both edit-distance and walking tree methods can locate specific genes within a large string when the genes' sequences are given. When we attempt to match whole strings, the walking tree matches most genes, while the edit-distance method fails. We also give examples in which the walking tree matches substrings even if they have been moved or inverted. The edit-distance method was not designed to handle these problems. We include an example in which the walking tree "discovered" a gene. Calculating scores for whole genome matches gives a method for approximating evolutionary distance. We show two evolutionary trees for the picornaviruses which were computed by the walking tree heuristic. Both of these trees show great similarity to previously constructed trees. The point of this demonstration is that WHOLE genomes can be matched and distances calculated. The first tree was created on a Sequent parallel computer and demonstrates that the walking tree heuristic can be efficiently parallelized. The second tree was created using a network of work stations and demonstrates that there is suffient parallelism in the phylogenetic tree calculation that the sequential walking tree can be used effectively on a network.

Occurrence of termites (Isoptera) on living and standing dead trees in a tropical dry forest in Mexico

PubMed Central

Escalera-Vázquez, Luis H.; Oyama, Ken

2018-01-01

Termites play a key role as ecosystem engineers in numerous ecological processes though their role in the dynamics of wood degradation in tropical dry forests, particularly at the level of the crown canopy, has been little studied. In this study, we analysed the occurrence of termites in the forest canopy by evaluating the density and proportion of living and standing dead trees associated with termites in deciduous and riparian habitats of the tropical dry forest in Chamela, Mexico. The results indicated that 60–98% of standing dead trees and 23–59% of living trees in Chamela were associated with termites. In particular, we found that the density of standing dead trees was higher in deciduous forests (0.057–0.066 trees/m2) than in riparian forests (0.022 and 0.027 trees/m2), even though the proportion of trees was not significantly different among habitats. Additionally, we found a higher density of trees associated with termites in trees of smaller size classes (0.01–0.09 trees/m2) than in larger class sizes (0–0.02 trees/m2). Interestingly, 72% of variation in the density of trees associated with termites is explained by the density of standing dead trees. Overall, these results indicate that standing dead tree availability might be the main factor regulating termite populations in Chamela forest and suggest that termites could play a key role in the decomposition of above-ground dead wood, mediating the incorporation of suspended and standing dead wood into the soil. PMID:29785342

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.

Plant defense, herbivory, and the growth of Cordia alliodora trees and their symbiotic Azteca ant colonies.

PubMed

Pringle, Elizabeth G; Dirzo, Rodolfo; Gordon, Deborah M

2012-11-01

The effects of herbivory on plant fitness are integrated over a plant's lifetime, mediated by ontogenetic changes in plant defense, tolerance, and herbivore pressure. In symbiotic ant-plant mutualisms, plants provide nesting space and food for ants, and ants defend plants against herbivores. The benefit to the plant of sustaining the growth of symbiotic ant colonies depends on whether defense by the growing ant colony outpaces the plant's growth in defendable area and associated herbivore pressure. These relationships were investigated in the symbiotic mutualism between Cordia alliodora trees and Azteca pittieri ants in a Mexican tropical dry forest. As ant colonies grew, worker production remained constant relative to ant-colony size. As trees grew, leaf production increased relative to tree size. Moreover, larger trees hosted lower densities of ants, suggesting that ant-colony growth did not keep pace with tree growth. On leaves with ants experimentally excluded, herbivory per unit leaf area increased exponentially with tree size, indicating that larger trees experienced higher herbivore pressure per leaf area than smaller trees. Even with ant defense, herbivory increased with tree size. Therefore, although larger trees had larger ant colonies, ant density was lower in larger trees, and the ant colonies did not provide sufficient defense to compensate for the higher herbivore pressure in larger trees. These results suggest that in this system the tree can decrease herbivory by promoting ant-colony growth, i.e., sustaining space and food investment in ants, as long as the tree continues to grow.

Per tree estimates with n-tree distance sampling: an application to increment core data

Treesearch

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...

Compensatory value of an urban forest: an application of the tree-value formula

Treesearch

David J. Nowak

1993-01-01

Understanding the value of an urban forest can give decisionmakers a better foundation for urban tree management. According to the tree-valuation formula of the Council of Tree and Landscape Appraisers, the estimated compensatory value of the urban forest in Oakland, California, (21% tree cover) is $385.7 million, with residential trees accounting for 58.6% of the...

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...

Monitoring Million Trees LA: Tree performance during the early years and future benefits

Treesearch

E. Gregory McPherson

2014-01-01

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

Interim hardwood tree grades for factory lumber

Treesearch

Leland F. Hanks; Leland F. Hanks

1971-01-01

Hardwood trees have for many years been measured in such a way that tree volume could be estimated; and in recent years the prediction of tree quality by using tree grades has become of interest to owners, sellers, and buyers of timber. Several tree-grading systems have been developed, but none has been publicized and used on a widespread scale. The Forest Service...

Evaluation of the seasonal and annual abortifacient risk of western juniper trees on Oregon rangelands: Abortion risk of western juniper trees

USDA-ARS?s Scientific Manuscript database

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

i-Tree and urban FIA—what's the connection?

Treesearch

David J. Nowak

2015-01-01

The i-Tree program (www.itreetools.org) was developed to assess ecosystem services and values from trees and forests based on measured forest data. The i-Tree program is currently being integrated with FIA data to assess various ecosystem services and values from urban FIA data. This presentation will overview the history and use of i-Tree; the various tools of i-Tree...

Determinants of establishment survival for residential trees in Sacramento County, CA

Treesearch

Lara A. Roman; John J. Battles; Joe R. McBride

2014-01-01

Urban forests can provide ecosystem services that motivate tree planting campaigns, and tree survival is a key element of program success and projected benefits. We studied survival in a shade tree give-away program in Sacramento, CA, monitoring a cohort of young trees for five years on single-family residential properties. We used conditional inference trees to...

HOW to Recognize and Reduce Tree Hazards in Recreation Sites

Treesearch

Kathyn Robbins

1986-01-01

An understanding of the many factors affecting tree hazards in recreation sites will help predict which trees are most likely to fail. Hazard tree management deals with probabilities of failure. This guide, written for anyone involved in management or maintenance of public use areas that contain trees, is intended to help minimize the risk associated with hazard trees...

User's Manual for Total-Tree Multiproduct Cruise Program

Treesearch

Alexander Clark; Thomas M. Burgan; Richard C. Field; Peter E. Dress

1985-01-01

This interactive computer program uses standard tree-cruise data to estimate the weight and volume of the total tree, saw logs, plylogs, chipping logs, pulpwood, crown firewood, and logging residue in timber stands.Input is cumulative cruise data for tree counts by d.b.h. and height. Output is in tables: board-foot volume by d.b.h.; total-tree and tree-component...