Measuring and modelling interception loss by an isolated olive tree in a traditional olive grove - pasture system

NASA Astrophysics Data System (ADS)

Nóbrega, Cristina; Pereira, Fernando L.; Valente, Fernanda

2015-04-01

Water losses associated to the rainfall interception process by trees can be an important component of the local hydrologic balance and must be accounted for when implementing any sustainable water management programme. In many dry areas of the Mediterranean region where agro-forestry systems are common, those programmes are crucial to foster adequate water conservation measures. Recent studies have shown that the evaluation of interception loss in sparse forests or tree plantations should be made for individual trees, being the total value determined as the sum of the individual contributions. Following this approach, rainfall interception was measured and modelled over two years, in an isolated Olea europeaea L. tree, in a traditional low-density olive grove in Castelo Branco, central Portugal. Total interception loss over the experimental period was 243.5 mm, on a tree crown projected area basis, corresponding to 18.0% of gross rainfall (Pg). Modelling made for each rainfall event using the sparse version of the Gash model, slightly underestimated interception loss with a value of 240.5 mm, i.e., 17.8 % ofPg. Modelling quality, evaluated according to a number of criteria, was good, allowing the conclusion that the methodology used was adequate. Modelling was also made on a daily basis, i.e., assuming a single storm per rainday. In this case, interception loss was overestimated by 12%, mostly because 72% of all rainfall events lasted for more than a day.

A survival tree method for the analysis of discrete event times in clinical and epidemiological studies.

PubMed

Schmid, Matthias; Küchenhoff, Helmut; Hoerauf, Achim; Tutz, Gerhard

2016-02-28

Survival trees are a popular alternative to parametric survival modeling when there are interactions between the predictor variables or when the aim is to stratify patients into prognostic subgroups. A limitation of classical survival tree methodology is that most algorithms for tree construction are designed for continuous outcome variables. Hence, classical methods might not be appropriate if failure time data are measured on a discrete time scale (as is often the case in longitudinal studies where data are collected, e.g., quarterly or yearly). To address this issue, we develop a method for discrete survival tree construction. The proposed technique is based on the result that the likelihood of a discrete survival model is equivalent to the likelihood of a regression model for binary outcome data. Hence, we modify tree construction methods for binary outcomes such that they result in optimized partitions for the estimation of discrete hazard functions. By applying the proposed method to data from a randomized trial in patients with filarial lymphedema, we demonstrate how discrete survival trees can be used to identify clinically relevant patient groups with similar survival behavior. Copyright © 2015 John Wiley & Sons, Ltd.

Wood anatomical analysis of Alnus incana and Betula pendula injured by a debris-flow event.

PubMed

Arbellay, Estelle; Stoffel, Markus; Bollschweiler, Michelle

2010-10-01

Vessel chronologies in ring-porous species have been successfully employed in the past to extract the climate signal from tree rings. Environmental signals recorded in vessels of ring-porous species have also been used in previous studies to reconstruct discrete events of drought, flooding and insect defoliation. However, very little is known about the ability of diffuse-porous species to record environmental signals in their xylem cells. Moreover, time series of wood anatomical features have only rarely been used to reconstruct former geomorphic events. This study was therefore undertaken to characterize the wood anatomical response of diffuse-porous Alnus incana (L.) Moench and Betula pendula Roth to debris-flow-induced wounding. Tree microscopic response to wounding was assessed through the analysis of wood anatomical differences between injured rings formed in the debris-flow event year and uninjured rings formed in the previous year. The two ring types were examined close and opposite to the injury in order to determine whether wound effects on xylem cells decrease with increasing tangential distance from the injury. Image analysis was used to measure vessel parameters as well as fiber and parenchyma cell (FPC) parameters. The results of this study indicate that injured rings are characterized by smaller vessels as compared with uninjured rings. By contrast, FPC parameters were not found to significantly differ between injured and uninjured rings. Vessel and FPC parameters mainly remained constant with increasing tangential distance from the injury, except for a higher proportion of vessel lumen area opposite to the injury within A. incana. This study highlights the existence of anatomical tree-ring signatures-in the form of smaller vessels-related to past debris-flow activity and addresses a new methodological approach to date injuries inflicted on trees by geomorphic processes.

The Academic Tree of Howard V. Malmstadt: From Early Scientific Exploration to Modern Analytical Chemistry.

PubMed

Storey, Andrew P; Hieftje, Gary M

2016-12-01

Over the last several decades, science has benefited tremendously by the implementation of digital electronic components for analytical instrumentation. A pioneer in this area of scientific inquiry was Howard Malmstadt. Frequently, such revolutions in scientific history can be viewed as a series of discoveries without a great deal of attention as to how mentorship shapes the careers and methodologies of those who made great strides forward for science. This paper focuses on the verifiable relationships of those who are connected through the academic tree of Malmstadt and how their experiences and the context of world events influenced their scientific pursuits. Particular attention is dedicated to the development of American chemistry departments and the critical role played by many of the individuals in the tree in this process. © The Author(s) 2016.

Bow-tie diagrams for risk management in anaesthesia.

PubMed

Culwick, M D; Merry, A F; Clarke, D M; Taraporewalla, K J; Gibbs, N M

2016-11-01

Bow-tie analysis is a risk analysis and management tool that has been readily adopted into routine practice in many high reliability industries such as engineering, aviation and emergency services. However, it has received little exposure so far in healthcare. Nevertheless, its simplicity, versatility, and pictorial display may have benefits for the analysis of a range of healthcare risks, including complex and multiple risks and their interactions. Bow-tie diagrams are a combination of a fault tree and an event tree, which when combined take the shape of a bow tie. Central to bow-tie methodology is the concept of an undesired or 'Top Event', which occurs if a hazard progresses past all prevention controls. Top Events may also occasionally occur idiosyncratically. Irrespective of the cause of a Top Event, mitigation and recovery controls may influence the outcome. Hence the relationship of hazard to outcome can be viewed in one diagram along with possible causal sequences or accident trajectories. Potential uses for bow-tie diagrams in anaesthesia risk management include improved understanding of anaesthesia hazards and risks, pre-emptive identification of absent or inadequate hazard controls, investigation of clinical incidents, teaching anaesthesia risk management, and demonstrating risk management strategies to third parties when required.

Genome-Wide Identification of Evolutionarily Conserved Alternative Splicing Events in Flowering Plants

PubMed Central

Chamala, Srikar; Feng, Guanqiao; Chavarro, Carolina; Barbazuk, W. Brad

2015-01-01

Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNA-Seq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants. AS events within 40–70% of the expressed multi-exonic genes per species were found, 27,120 of which are conserved among two or more of the taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the nine species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential. Examining AS in gene families identifies those with high rates of AS, and conservation can distinguish ancient events vs. recent or species specific adaptations. The MADS-box and SR protein families are found to represent families with low and high occurrences of AS, respectively, yet their AS events were likely present in the MRCA of angiosperms. PMID:25859541

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.

STUDYING FOREST ROOT SYSTEMS - AN OVERVIEW OF METHODOLOGICAL PROBLEMS

EPA Science Inventory

The study of tree root systems is central to understanding forest ecosystem carbon and nutrient cycles, nutrient and water uptake, C allocation patterns by trees, soil microbial populations, adaptation of trees to stress, soil organic matter production, etc. Methodological probl...

Nuclear power plant digital system PRA pilot study with the dynamic flow-graph methodology

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

Yau, M.; Motamed, M.; Guarro, S.

2006-07-01

Current Probabilistic Risk Assessment (PRA) methodology is well established in analyzing hardware and some of the key human interactions. However processes for analyzing the software functions of digital systems within a plant PRA framework, and accounting for the digital system contribution to the overall risk are not generally available nor are they well understood and established. A recent study reviewed a number of methodologies that have potential applicability to modeling and analyzing digital systems within a PRA framework. This study identified the Dynamic Flow-graph Methodology (DFM) and the Markov Methodology as the most promising tools. As a result of thismore » study, a task was defined under the framework of a collaborative agreement between the U.S. Nuclear Regulatory Commission (NRC) and the Ohio State Univ. (OSU). The objective of this task is to set up benchmark systems representative of digital systems used in nuclear power plants and to evaluate DFM and the Markov methodology with these benchmark systems. The first benchmark system is a typical Pressurized Water Reactor (PWR) Steam Generator (SG) Feedwater System (FWS) level control system based on an earlier ASCA work with the U.S. NRC 2, upgraded with modern control laws. ASCA, Inc. is currently under contract to OSU to apply DFM to this benchmark system. The goal is to investigate the feasibility of using DFM to analyze and quantify digital system risk, and to integrate the DFM analytical results back into the plant event tree/fault tree PRA model. (authors)« less

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

PubMed

Knowles, Lacey L; Klimov, Pavel B

2011-11-01

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

A risk assessment methodology to evaluate the risk failure of managed aquifer recharge in the Mediterranean Basin

NASA Astrophysics Data System (ADS)

Rodríguez-Escales, Paula; Canelles, Arnau; Sanchez-Vila, Xavier; Folch, Albert; Kurtzman, Daniel; Rossetto, Rudy; Fernández-Escalante, Enrique; Lobo-Ferreira, João-Paulo; Sapiano, Manuel; San-Sebastián, Jon; Schüth, Christoph

2018-06-01

Managed aquifer recharge (MAR) can be affected by many risks. Those risks are related to different technical and non-technical aspects of recharge, like water availability, water quality, legislation, social issues, etc. Many other works have acknowledged risks of this nature theoretically; however, their quantification and definition has not been developed. In this study, the risk definition and quantification has been performed by means of fault trees and probabilistic risk assessment (PRA). We defined a fault tree with 65 basic events applicable to the operation phase. After that, we have applied this methodology to six different managed aquifer recharge sites located in the Mediterranean Basin (Portugal, Spain, Italy, Malta, and Israel). The probabilities of the basic events were defined by expert criteria, based on the knowledge of the different managers of the facilities. From that, we conclude that in all sites, the perception of the expert criteria of the non-technical aspects were as much or even more important than the technical aspects. Regarding the risk results, we observe that the total risk in three of the six sites was equal to or above 0.90. That would mean that the MAR facilities have a risk of failure equal to or higher than 90 % in the period of 2-6 years. The other three sites presented lower risks (75, 29, and 18 % for Malta, Menashe, and Serchio, respectively).

A methodology for risk analysis based on hybrid Bayesian networks: application to the regasification system of liquefied natural gas onboard a floating storage and regasification unit.

PubMed

Martins, Marcelo Ramos; Schleder, Adriana Miralles; Droguett, Enrique López

2014-12-01

This article presents an iterative six-step risk analysis methodology based on hybrid Bayesian networks (BNs). In typical risk analysis, systems are usually modeled as discrete and Boolean variables with constant failure rates via fault trees. Nevertheless, in many cases, it is not possible to perform an efficient analysis using only discrete and Boolean variables. The approach put forward by the proposed methodology makes use of BNs and incorporates recent developments that facilitate the use of continuous variables whose values may have any probability distributions. Thus, this approach makes the methodology particularly useful in cases where the available data for quantification of hazardous events probabilities are scarce or nonexistent, there is dependence among events, or when nonbinary events are involved. The methodology is applied to the risk analysis of a regasification system of liquefied natural gas (LNG) on board an FSRU (floating, storage, and regasification unit). LNG is becoming an important energy source option and the world's capacity to produce LNG is surging. Large reserves of natural gas exist worldwide, particularly in areas where the resources exceed the demand. Thus, this natural gas is liquefied for shipping and the storage and regasification process usually occurs at onshore plants. However, a new option for LNG storage and regasification has been proposed: the FSRU. As very few FSRUs have been put into operation, relevant failure data on FSRU systems are scarce. The results show the usefulness of the proposed methodology for cases where the risk analysis must be performed under considerable uncertainty. © 2014 Society for Risk Analysis.

Development and application of the dynamic system doctor to nuclear reactor probabilistic risk assessments.

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

Kunsman, David Marvin; Aldemir, Tunc; Rutt, Benjamin

2008-05-01

This LDRD project has produced a tool that makes probabilistic risk assessments (PRAs) of nuclear reactors - analyses which are very resource intensive - more efficient. PRAs of nuclear reactors are being increasingly relied on by the United States Nuclear Regulatory Commission (U.S.N.R.C.) for licensing decisions for current and advanced reactors. Yet, PRAs are produced much as they were 20 years ago. The work here applied a modern systems analysis technique to the accident progression analysis portion of the PRA; the technique was a system-independent multi-task computer driver routine. Initially, the objective of the work was to fuse the accidentmore » progression event tree (APET) portion of a PRA to the dynamic system doctor (DSD) created by Ohio State University. Instead, during the initial efforts, it was found that the DSD could be linked directly to a detailed accident progression phenomenological simulation code - the type on which APET construction and analysis relies, albeit indirectly - and thereby directly create and analyze the APET. The expanded DSD computational architecture and infrastructure that was created during this effort is called ADAPT (Analysis of Dynamic Accident Progression Trees). ADAPT is a system software infrastructure that supports execution and analysis of multiple dynamic event-tree simulations on distributed environments. A simulator abstraction layer was developed, and a generic driver was implemented for executing simulators on a distributed environment. As a demonstration of the use of the methodological tool, ADAPT was applied to quantify the likelihood of competing accident progression pathways occurring for a particular accident scenario in a particular reactor type using MELCOR, an integrated severe accident analysis code developed at Sandia. (ADAPT was intentionally created with flexibility, however, and is not limited to interacting with only one code. With minor coding changes to input files, ADAPT can be linked to other such codes.) The results of this demonstration indicate that the approach can significantly reduce the resources required for Level 2 PRAs. From the phenomenological viewpoint, ADAPT can also treat the associated epistemic and aleatory uncertainties. This methodology can also be used for analyses of other complex systems. Any complex system can be analyzed using ADAPT if the workings of that system can be displayed as an event tree, there is a computer code that simulates how those events could progress, and that simulator code has switches to turn on and off system events, phenomena, etc. Using and applying ADAPT to particular problems is not human independent. While the human resources for the creation and analysis of the accident progression are significantly decreased, knowledgeable analysts are still necessary for a given project to apply ADAPT successfully. This research and development effort has met its original goals and then exceeded them.« less

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

DTIC Science & Technology

2016-06-01

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

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

PubMed Central

Blanco-Pastor, José Luis; Vargas, Pablo; Pfeil, Bernard E.

2012-01-01

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora. PMID:22768061

From Goal-Oriented Requirements to Event-B Specifications

NASA Technical Reports Server (NTRS)

Aziz, Benjamin; Arenas, Alvaro E.; Bicarregui, Juan; Ponsard, Christophe; Massonet, Philippe

2009-01-01

In goal-oriented requirements engineering methodologies, goals are structured into refinement trees from high-level system-wide goals down to fine-grained requirements assigned to specific software/ hardware/human agents that can realise them. Functional goals assigned to software agents need to be operationalised into specification of services that the agent should provide to realise those requirements. In this paper, we propose an approach for operationalising requirements into specifications expressed in the Event-B formalism. Our approach has the benefit of aiding software designers by bridging the gap between declarative requirements and operational system specifications in a rigorous manner, enabling powerful correctness proofs and allowing further refinements down to the implementation level. Our solution is based on verifying that a consistent Event-B machine exhibits properties corresponding to requirements.

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

NASA Astrophysics Data System (ADS)

Sahin, Dagistan

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

Deep Borehole Emplacement Mode Hazard Analysis Revision 0

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

Sevougian, S. David

This letter report outlines a methodology and provides resource information for the Deep Borehole Emplacement Mode Hazard Analysis (DBEMHA). The main purpose is identify the accident hazards and accident event sequences associated with the two emplacement mode options (wireline or drillstring), to outline a methodology for computing accident probabilities and frequencies, and to point to available databases on the nature and frequency of accidents typically associated with standard borehole drilling and nuclear handling operations. Risk mitigation and prevention measures, which have been incorporated into the two emplacement designs (see Cochran and Hardin 2015), are also discussed. A key intent ofmore » this report is to provide background information to brief subject matter experts involved in the Emplacement Mode Design Study. [Note: Revision 0 of this report is concentrated more on the wireline emplacement mode. It is expected that Revision 1 will contain further development of the preliminary fault and event trees for the drill string emplacement mode.]« less

Direct evaluation of fault trees using object-oriented programming techniques

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1989-01-01

Object-oriented programming techniques are used in an algorithm for the direct evaluation of fault trees. The algorithm combines a simple bottom-up procedure for trees without repeated events with a top-down recursive procedure for trees with repeated events. The object-oriented approach results in a dynamic modularization of the tree at each step in the reduction process. The algorithm reduces the number of recursive calls required to solve trees with repeated events and calculates intermediate results as well as the solution of the top event. The intermediate results can be reused if part of the tree is modified. An example is presented in which the results of the algorithm implemented with conventional techniques are compared to those of the object-oriented approach.

Predicting Tree Mortality Die-off Events Associated with Hotter Drought and Assessing Their Global Consequences via Ecoclimate Teleconnections.

NASA Astrophysics Data System (ADS)

Breshears, D. D.; Allen, C. D.; McDowell, N. G.; Adams, H. D.; Barnes, M.; Barron-Gafford, G.; Bradford, J. B.; Cobb, N.; Field, J. P.; Froend, R.; Fontaine, J. B.; Garcia, E.; Hardy, G. E. S. J.; Huxman, T. E.; Kala, J.; Lague, M. M.; Martinez-Yrizar, A.; Matusick, G.; Minor, D. M.; Moore, D. J.; Ng, M.; Ruthrof, K. X.; Saleska, S. R.; Stark, S. C.; Swann, A. L. S.; Villegas, J. C.; Williams, A. P.; Zou, C.

2017-12-01

Evidence that tree mortality is increasingly likely occur in extensive die-off events across the terrestrial biosphere continues to mount. The consequences of such extensive mortality events are potentially profound, not only for the locations where die-off events occur, but also for other locations that could be impacted via ecoclimate teleconnections, whereby the land surface changes associated with die-off in one location could alter atmospheric circulation patterns and affect vegetation elsewhere. Here, we (1) recap the background of tree mortality as an emerging environmental issue, (2) highlight recent advances that could help us improve predictions of the vulnerability to tree mortality, including the underlying importance of hydraulic failure, the potential to develop climatic envelopes specific to tree mortality events, and consideration of the role of heat waves; and (3) initial bounding simulations that indicate the potential for tree die-off events in different locations to alter ecoclimate teleconnections. As we move toward globally coordinated carbon accounting and management, the high vulnerability to tree die-off events and the potential for such events to affect vegetation elsewhere will both need to be accounted for.

Methodology development for quantitative optimization of security enhancement in medical information systems -Case study in a PACS and a multi-institutional radiotherapy database-.

PubMed

Haneda, Kiyofumi; Umeda, Tokuo; Koyama, Tadashi; Harauchi, Hajime; Inamura, Kiyonari

2002-01-01

The target of our study is to establish the methodology for analyzing level of security requirements, for searching suitable security measures and for optimizing security distribution to every portion of medical practice. Quantitative expression must be introduced to our study as possible for the purpose of easy follow up of security procedures and easy evaluation of security outcomes or results. Results of system analysis by fault tree analysis (FTA) clarified that subdivided system elements in detail contribute to much more accurate analysis. Such subdivided composition factors very much depended on behavior of staff, interactive terminal devices, kinds of service, and routes of network. As conclusion, we found the methods to analyze levels of security requirements for each medical information systems employing FTA, basic events for each composition factor and combination of basic events. Methods for searching suitable security measures were found. Namely risk factors for each basic event, number of elements for each composition factor and candidates of security measure elements were found. Method to optimize the security measures for each medical information system was proposed. Namely optimum distribution of risk factors in terms of basic events were figured out, and comparison of them between each medical information systems became possible.

ARAMIS project: a comprehensive methodology for the identification of reference accident scenarios in process industries.

PubMed

Delvosalle, Christian; Fievez, Cécile; Pipart, Aurore; Debray, Bruno

2006-03-31

In the frame of the Accidental Risk Assessment Methodology for Industries (ARAMIS) project, this paper aims at presenting the work carried out in the part of the project devoted to the definition of accident scenarios. This topic is a key-point in risk assessment and serves as basis for the whole risk quantification. The first result of the work is the building of a methodology for the identification of major accident hazards (MIMAH), which is carried out with the development of generic fault and event trees based on a typology of equipment and substances. The term "major accidents" must be understood as the worst accidents likely to occur on the equipment, assuming that no safety systems are installed. A second methodology, called methodology for the identification of reference accident scenarios (MIRAS) takes into account the influence of safety systems on both the frequencies and possible consequences of accidents. This methodology leads to identify more realistic accident scenarios. The reference accident scenarios are chosen with the help of a tool called "risk matrix", crossing the frequency and the consequences of accidents. This paper presents both methodologies and an application on an ethylene oxide storage.

Forest tree responses to extreme drought and some biotic events: Towards a selection according to hazard tolerance?

NASA Astrophysics Data System (ADS)

Bréda, Nathalie; Badeau, Vincent

2008-09-01

The aim of this paper is to illustrate how some extreme events could affect forest ecosystems. Forest tree response can be analysed using dendroecological methods, as tree-ring widths are strongly controlled by climatic or biotic events. Years with such events induce similar tree responses and are called pointer years. They can result from extreme climatic events like frost, a heat wave, spring water logging, drought or insect damage… Forest tree species showed contrasting responses to climatic hazards, depending on their sensitivity to water shortage or temperature hardening, as illustrated from our dendrochronological database. For foresters, a drought or a pest disease is an extreme event if visible and durable symptoms are induced (leaf discolouration, leaf loss, perennial organs mortality, tree dieback and mortality). These symptoms here are shown, lagging one or several years behind a climatic or biotic event, from forest decline cases in progress since the 2003 drought or attributed to previous severe droughts or defoliations in France. Tree growth or vitality recovery is illustrated, and the functional interpretation of the long lasting memory of trees is discussed. A coupled approach linking dendrochronology and ecophysiology helps in discussing vulnerability of forest stands, and suggests management advices in order to mitigate extreme drought and cope with selective mortality.

Testing for Independence between Evolutionary Processes.

PubMed

Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

2016-09-01

Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Methodology for Modeling Nuclear Power Plant Passive Component Aging in Probabilistic Risk Assessment under the Impact of Operating Conditions, Surveillance and Maintenance Activities

NASA Astrophysics Data System (ADS)

Guler Yigitoglu, Askin

In the context of long operation of nuclear power plants (NPPs) (i.e., 60-80 years, and beyond), investigation of the aging of passive systems, structures and components (SSCs) is important to assess safety margins and to decide on reactor life extension as indicated within the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program. In the traditional probabilistic risk assessment (PRA) methodology, evaluating the potential significance of aging of passive SSCs on plant risk is challenging. Although passive SSC failure rates can be added as initiating event frequencies or basic event failure rates in the traditional event-tree/fault-tree methodology, these failure rates are generally based on generic plant failure data which means that the true state of a specific plant is not reflected in a realistic manner on aging effects. Dynamic PRA methodologies have gained attention recently due to their capability to account for the plant state and thus address the difficulties in the traditional PRA modeling of aging effects of passive components using physics-based models (and also in the modeling of digital instrumentation and control systems). Physics-based models can capture the impact of complex aging processes (e.g., fatigue, stress corrosion cracking, flow-accelerated corrosion, etc.) on SSCs and can be utilized to estimate passive SSC failure rates using realistic NPP data from reactor simulation, as well as considering effects of surveillance and maintenance activities. The objectives of this dissertation are twofold: The development of a methodology for the incorporation of aging modeling of passive SSC into a reactor simulation environment to provide a framework for evaluation of their risk contribution in both the dynamic and traditional PRA; and the demonstration of the methodology through its application to pressurizer surge line pipe weld and steam generator tubes in commercial nuclear power plants. In the proposed methodology, a multi-state physics based model is selected to represent the aging process. The model is modified via sojourn time approach to reflect the operational and maintenance history dependence of the transition rates. Thermal-hydraulic parameters of the model are calculated via the reactor simulation environment and uncertainties associated with both parameters and the models are assessed via a two-loop Monte Carlo approach (Latin hypercube sampling) to propagate input probability distributions through the physical model. The effort documented in this thesis towards this overall objective consists of : i) defining a process for selecting critical passive components and related aging mechanisms, ii) aging model selection, iii) calculating the probability that aging would cause the component to fail, iv) uncertainty/sensitivity analyses, v) procedure development for modifying an existing PRA to accommodate consideration of passive component failures, and, vi) including the calculated failure probability in the modified PRA. The proposed methodology is applied to pressurizer surge line pipe weld aging and steam generator tube degradation in pressurized water reactors.

TESTING TREE-CLASSIFIER VARIANTS AND ALTERNATE MODELING METHODOLOGIES IN THE EAST GREAT BASIN MAPPING UNIT OF THE SOUTHWEST REGIONAL GAP ANALYSIS PROJECT (SW REGAP)

EPA Science Inventory

We tested two methods for dataset generation and model construction, and three tree-classifier variants to identify the most parsimonious and thematically accurate mapping methodology for the SW ReGAP project. Competing methodologies were tested in the East Great Basin mapping un...

Machine learning algorithms for meteorological event classification in the coastal area using in-situ data

NASA Astrophysics Data System (ADS)

Sokolov, Anton; Gengembre, Cyril; Dmitriev, Egor; Delbarre, Hervé

2017-04-01

The problem is considered of classification of local atmospheric meteorological events in the coastal area such as sea breezes, fogs and storms. The in-situ meteorological data as wind speed and direction, temperature, humidity and turbulence are used as predictors. Local atmospheric events of 2013-2014 were analysed manually to train classification algorithms in the coastal area of English Channel in Dunkirk (France). Then, ultrasonic anemometer data and LIDAR wind profiler data were used as predictors. A few algorithms were applied to determine meteorological events by local data such as a decision tree, the nearest neighbour classifier, a support vector machine. The comparison of classification algorithms was carried out, the most important predictors for each event type were determined. It was shown that in more than 80 percent of the cases machine learning algorithms detect the meteorological class correctly. We expect that this methodology could be applied also to classify events by climatological in-situ data or by modelling data. It allows estimating frequencies of each event in perspective of climate change.

Automated flood extent identification using WorldView imagery for the insurance industry

NASA Astrophysics Data System (ADS)

Geller, Christina

2017-10-01

Flooding is the most common and costly natural disaster around the world, causing the loss of human life and billions in economic and insured losses each year. In 2016, pluvial and fluvial floods caused an estimated 5.69 billion USD in losses worldwide with the most severe events occurring in Germany, France, China, and the United States. While catastrophe modeling has begun to help bridge the knowledge gap about the risk of fluvial flooding, understanding the extent of a flood - pluvial and fluvial - in near real-time allows insurance companies around the world to quantify the loss of property that their clients face during a flooding event and proactively respond. To develop this real-time, global analysis of flooded areas and the associated losses, a new methodology utilizing optical multi-spectral imagery from DigitalGlobe (DGI) WorldView satellite suite is proposed for the extraction of pluvial and fluvial flood extents. This methodology involves identifying flooded areas visible to the sensor, filling in the gaps left by the built environment (i.e. buildings, trees) with a nearest neighbor calculation, and comparing the footprint against an Industry Exposure Database (IE) to calculate a loss estimate. Full-automation of the methodology allows production of flood extents and associated losses anywhere around the world as required. The methodology has been tested and proven effective for the 2016 flood in Louisiana, USA.

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

ERIC Educational Resources Information Center

Barker, Bruce O.; Petersen, Paul D.

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

Interrogating trees as archives of sulphur deposition

NASA Astrophysics Data System (ADS)

Wynn, P. M.; Loader, N. J.; Fairchild, I. J.

2012-04-01

A principal driver of climatic variability over the past 1,000 years and essential forcing mechanism for climate, are the changes in atmospheric composition resulting from sulphur aerosols. Natural and anthropogenic aerosols released into the atmosphere disrupt the radiative balance through backscattering and absorption of incoming solar radiation and increase cloud albedo by acting as condensation nuclei. Understanding the impact of sulphur emissions upon climate beyond the last few hundred years however is not straightforward and natural archives of environmental information must be explored. Tree-rings represent one such archive as they are widely distributed and preserve environmental information within a precisely dateable, annually resolved timescale. Until recently the sulphur contained within tree-rings has largely remained beyond the reach of environmental scientists and climate modelers owing to difficulties associated with the extraction of a robust signal and uncertainties regarding post-depositional mobility. Our recent work using synchrotron radiation has established that the majority of non-labile sulphur in two conifer species is preserved within the cellular structure of the woody tissue after uptake and demonstrates an increasing trend in sulphur concentration during the 20th century and during known volcanic events. Due to the clear isotopic distinction between marine (+21), geological (+10 to +30), atmospheric pollution (-3 to +9 ) and volcanic sources of sulphur (0 to +5), isotopic ratios provide a diagnostic tool with which changes in the source of atmospheric sulphur can be detected in a more reliable fashion than concentration alone. Sulphur isotopes should thereby provide a fingerprint of short lived events including volcanic activity when extracted at high resolution and in conjunction with high resolution S concentrations defining the event. Here we present methodologies associated with extracting the sulphur isotopic signal from tree-rings using both elemental analyser isotope ratio mass spectrometry and ion probe technology. Preliminary data indicate success at extracting the sulphur isotopic signal from woody tissues at 2-3 year resolution. In conjunction with analytical developments in ion probe technology, high resolution records of localised sulphur forcing from tree-ring archives, including volcanic activity, no longer seem too far beyond the reach of climate scientists.

Drought-related tree mortality in drought-resistant semi-arid Aleppo pine forest

NASA Astrophysics Data System (ADS)

Preisler, Yakir; Grünzweig, José M.; Rotenberg, Eyal; Rohatyn, Shani; Yakir, Dan

2014-05-01

The frequency and intensity of drought events are expected to increase as part of global climate change. In fact, drought related tree mortality had become a widespread phenomenon in forests around the globe in the past decades. This study was conducted at the Yatir FLUXNET site, located in a 45 years old Pinus halepensis dominated forest that successfully sustained low mean annual precipitation (276mm) and extended seasonal droughts (up to 340 days between rain events). However, five recent non-consecutive drought years led to enhanced tree mortality in 2010 (5-10% of the forest population, which was not observed hitherto). The Tree mortality was characterized by patchiness, showing forest zones with either >80% mortality or no mortality at all. Areas of healthy trees were associated with deeper root distribution and increased stoniness (soil pockets & cracks). To help identify possible causes of the increased mortality and its patterns, four tree stress levels were identified based on visual appearance, and studied in more detail. This included examining from spring 2011 to summer 2013 the local trees density, root distribution, annual growth rings, needle length and chlorophyll content, rates of leaf gas exchange, and branch predawn water potential. Tree phenotypic stress level correlated with the leaf predawn water potential (-1.8 and -3.0 in healthy and stressed trees, respectively), which likely reflected tree-scale water availability. These below ground characteristics were also associated, in turn, with higher rate of assimilation (3.5 and 0.8 μmol CO2 m-2s1 in healthy and stress trees, respectively), longer needles (8.2cm and 3.4 cm in healthy and stressed trees, respectively). Annual ring widths showed differences between stress classes, with stressed trees showing 30% narrower rings on average than unstressed trees. Notably, decline in annual ring widths could be identified in currently dead or severely stressed trees 15-20 years prior to mortality or tree degradation. These results indicate, together with earlier results that showed a virtually close hydrological cycle (ET~P) for this forest, that mortality was dominated by conditions at the level of the single-tree or small group of trees. The dependency on belowground water availability of individual trees emphasizes the difficulties in drawing process-based conclusions from the mean response at the forest stand level and, alternatively, the need to investigate drought stress and survival processes at the patch scale. The capabilities of early identification, and of grading the stress level with simple tools, such as tree-rings and pre-dawn water potential, can facilitate partitioning forest stands into zones more relevant to the study and management of drought related mortality. Ultimately, an integrated approach considering both the stand and patch scales and which utilizes methodologies such as used in this study will be essential to reliably predict ecosystem response to changes in precipitation regimes and climate.

STRIDE: Species Tree Root Inference from Gene Duplication Events.

PubMed

Emms, David M; Kelly, Steven

2017-12-01

The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

77 FR 61024 - Notice of Public Meeting and Request for Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-05

... public meeting and public comments--The National Christmas Tree Lighting and the subsequent 26-day event... National Christmas Tree Lighting and the subsequent 26-day event. The general plan and theme for the event... comments and suggestions on the planning of the 2012 National Christmas Tree Lighting and the subsequent 26...

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

PubMed Central

Marcussen, Thomas; Heier, Lise; Brysting, Anne K.; Oxelman, Bengt; Jakobsen, Kjetill S.

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage—between 67% and 88%—of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. PMID:25281848

Climate change and forest trees in the Pacific Northwest: guide to vulnerability assessment methodology

Treesearch

W. Devine; C. Aubry; J. Miller; K. Potter; A. Bower

2012-01-01

This guide provides a step-by-step description of the methodology used to apply the Forest Tree Genetic Risk Assessment System (ForGRAS; Potter and Crane 2010) to the tree species of the Pacific Northwest in a recent climate change vulnerability assessment (Devine et al. 2012). We describe our modified version of the ForGRAS model, and we review the model’s basic...

A Physics-Based Engineering Methodology for Calculating Soft Error Rates of Bulk CMOS and SiGe Heterojunction Bipolar Transistor Integrated Circuits

NASA Astrophysics Data System (ADS)

Fulkerson, David E.

2010-02-01

This paper describes a new methodology for characterizing the electrical behavior and soft error rate (SER) of CMOS and SiGe HBT integrated circuits that are struck by ions. A typical engineering design problem is to calculate the SER of a critical path that commonly includes several circuits such as an input buffer, several logic gates, logic storage, clock tree circuitry, and an output buffer. Using multiple 3D TCAD simulations to solve this problem is too costly and time-consuming for general engineering use. The new and simple methodology handles the problem with ease by simple SPICE simulations. The methodology accurately predicts the measured threshold linear energy transfer (LET) of a bulk CMOS SRAM. It solves for circuit currents and voltage spikes that are close to those predicted by expensive 3D TCAD simulations. It accurately predicts the measured event cross-section vs. LET curve of an experimental SiGe HBT flip-flop. The experimental cross section vs. frequency behavior and other subtle effects are also accurately predicted.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).

PubMed

Parks, Matthew B; Nakov, Teofil; Ruck, Elizabeth C; Wickett, Norman J; Alverson, Andrew J

2018-03-01

Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Birth-death prior on phylogeny and speed dating

PubMed Central

2008-01-01

Background In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC) framework, an approach requiring computation times of hours or days when applied to large phylogenies. Results We demonstrate that a hill-climbing maximum a posteriori (MAP) adaptation of the MCMC scheme results in considerable gain in computational efficiency. We demonstrate also that a novel dynamic programming (DP) algorithm for branch length factorization, useful both in the hill-climbing and in the MCMC setting, further reduces computation time. For the problem of inferring rates and times parameters on a fixed tree, we perform simulations, comparisons between hill-climbing and MCMC on a plant rbcL gene dataset, and dating analysis on an animal mtDNA dataset, showing that our methodology enables efficient, highly accurate analysis of very large trees. Datasets requiring a computation time of several days with MCMC can with our MAP algorithm be accurately analysed in less than a minute. From the results of our example analyses, we conclude that our methodology generally avoids getting trapped early in local optima. For the cases where this nevertheless can be a problem, for instance when we in addition to the parameters also infer the tree topology, we show that the problem can be evaded by using a simulated-annealing like (SAL) method in which we favour tree swaps early in the inference while biasing our focus towards rate and time parameter changes later on. Conclusion Our contribution leaves the field open for fast and accurate dating analysis of nucleotide sequence data. Modeling branch substitutions rates and divergence times separately allows us to include birth-death priors on the times without the assumption of a molecular clock. The methodology is easily adapted to take data from fossil records into account and it can be used together with a broad range of rate and substitution models. PMID:18318893

Birth-death prior on phylogeny and speed dating.

PubMed

Akerborg, Orjan; Sennblad, Bengt; Lagergren, Jens

2008-03-04

In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC) framework, an approach requiring computation times of hours or days when applied to large phylogenies. We demonstrate that a hill-climbing maximum a posteriori (MAP) adaptation of the MCMC scheme results in considerable gain in computational efficiency. We demonstrate also that a novel dynamic programming (DP) algorithm for branch length factorization, useful both in the hill-climbing and in the MCMC setting, further reduces computation time. For the problem of inferring rates and times parameters on a fixed tree, we perform simulations, comparisons between hill-climbing and MCMC on a plant rbcL gene dataset, and dating analysis on an animal mtDNA dataset, showing that our methodology enables efficient, highly accurate analysis of very large trees. Datasets requiring a computation time of several days with MCMC can with our MAP algorithm be accurately analysed in less than a minute. From the results of our example analyses, we conclude that our methodology generally avoids getting trapped early in local optima. For the cases where this nevertheless can be a problem, for instance when we in addition to the parameters also infer the tree topology, we show that the problem can be evaded by using a simulated-annealing like (SAL) method in which we favour tree swaps early in the inference while biasing our focus towards rate and time parameter changes later on. Our contribution leaves the field open for fast and accurate dating analysis of nucleotide sequence data. Modeling branch substitutions rates and divergence times separately allows us to include birth-death priors on the times without the assumption of a molecular clock. The methodology is easily adapted to take data from fossil records into account and it can be used together with a broad range of rate and substitution models.

Qualitative Importance Measures of Systems Components - A New Approach and Its Applications

NASA Astrophysics Data System (ADS)

Chybowski, Leszek; Gawdzińska, Katarzyna; Wiśnicki, Bogusz

2016-12-01

The paper presents an improved methodology of analysing the qualitative importance of components in the functional and reliability structures of the system. We present basic importance measures, i.e. the Birnbaum's structural measure, the order of the smallest minimal cut-set, the repetition count of an i-th event in the Fault Tree and the streams measure. A subsystem of circulation pumps and fuel heaters in the main engine fuel supply system of a container vessel illustrates the qualitative importance analysis. We constructed a functional model and a Fault Tree which we analysed using qualitative measures. Additionally, we compared the calculated measures and introduced corrected measures as a tool for improving the analysis. We proposed scaled measures and a common measure taking into account the location of the component in the reliability and functional structures. Finally, we proposed an area where the measures could be applied.

Use of Bayesian event trees in semi-quantitative volcano eruption forecasting and hazard analysis

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

Use of Bayesian event trees to forecast eruptive activity during volcano crises is an increasingly common practice for the USGS-USAID Volcano Disaster Assistance Program (VDAP) in collaboration with foreign counterparts. This semi-quantitative approach combines conceptual models of volcanic processes with current monitoring data and patterns of occurrence to reach consensus probabilities. This approach allows a response team to draw upon global datasets, local observations, and expert judgment, where the relative influence of these data depends upon the availability and quality of monitoring data and the degree to which the volcanic history is known. The construction of such event trees additionally relies upon existence and use of relevant global databases and documented past periods of unrest. Because relevant global databases may be underpopulated or nonexistent, uncertainty in probability estimations may be large. Our 'hybrid' approach of combining local and global monitoring data and expert judgment facilitates discussion and constructive debate between disciplines: including seismology, gas geochemistry, geodesy, petrology, physical volcanology and technology/engineering, where difference in opinion between response team members contributes to definition of the uncertainty in the probability estimations. In collaboration with foreign colleagues, we have created event trees for numerous areas experiencing volcanic unrest. Event trees are created for a specified time frame and are updated, revised, or replaced as the crisis proceeds. Creation of an initial tree is often prompted by a change in monitoring data, such that rapid assessment of probability is needed. These trees are intended as a vehicle for discussion and a way to document relevant data and models, where the target audience is the scientists themselves. However, the probabilities derived through the event-tree analysis can also be used to help inform communications with emergency managers and the public. VDAP trees evaluate probabilities of: magmatic intrusion, likelihood of eruption, magnitude of eruption, and types of associated hazardous events and their extents. In a few cases, trees have been extended to also assess and communicate vulnerability and relative risk.

The Effects of Wildfire on Mortality and Resources for an Arboreal Marsupial: Resilience to Fire Events but Susceptibility to Fire Regime Change

PubMed Central

Banks, Sam C.; Knight, Emma J.; McBurney, Lachlan; Blair, David; Lindenmayer, David B.

2011-01-01

Background Big environmental disturbances have big ecological effects, yet these are not always what we might expect. Understanding the proximate effects of major disturbances, such as severe wildfires, on individuals, populations and habitats will be essential for understanding how predicted future increases in the frequency of such disturbances will affect ecosystems. However, researchers rarely have access to data from immediately before and after such events. Here we report on the effects of a severe and extensive forest wildfire on mortality, reproductive output and availability of key shelter resources for an arboreal marsupial. We also investigated the behavioural response of individuals to changed shelter resource availability in the post-fire environment. Methodology/Principal Findings We fitted proximity-logging radiotransmitters to mountain brushtail possums (Trichosurus cunninghami) before, during and after the 2009 wildfires in Victoria, Australia. Surprisingly, we detected no mortality associated with the fire, and despite a significant post-fire decrease in the proportion of females carrying pouch young in the burnt area, there was no short-term post-fire population decline. The major consequence of this fire for mountain brushtail possums was the loss of over 80% of hollow-bearing trees. The types of trees preferred as shelter sites (highly decayed dead standing trees) were those most likely to collapse after fire. Individuals adapted to resource decline by being more flexible in resource selection after the fire, but not by increased resource sharing. Conclusions/Significance Despite short-term demographic resilience and behavioural adaptation following this fire, the major loss of decayed hollow trees suggests the increased frequency of stand-replacing wildfires predicted under climate change will pose major challenges for shelter resource availability for hollow-dependent fauna. Hollow-bearing trees are typically biological legacies of previous forest generations in post-fire regrowth forests but will cease to be recruited to future regrowth forests if the interval between severe fires becomes too rapid for hollow formation. PMID:21826221

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

The Tunguska event in 1908: evidence from tree-ring anatomy.

PubMed

Vaganov, Evgenii A; Hughes, Malcolm K; Silkin, Pavel P; Nesvetailo, Valery D

2004-01-01

We analyzed tree rings in wood samples collected from some of the few surviving trees found close to the epicenter (within 4-5 km) of the Tunguska event that occurred on the last day of June 1908. Tree-ring growth shows a depression starting in the year after the event and continuing during a 4-5-year period. The most remarkable traces of the event were found in the rings' anatomical structure: (1) formation of "light" rings and a reduction of maximum density in 1908; (2) non-thickened tracheids (the cells that make up most of the wood volume) in the transition and latewood zones (the middle and last-formed parts of the ring, respectively); and (3) deformed tracheids, which are located on the 1908 annual ring outer boundary. In the majority of samples, normal earlywood and latewood tracheids were formed in all annual rings after 1908. The observed anomalies in wood anatomy suggest two main impacts of the Tunguska event on surviving trees--(1) defoliation and (2) direct mechanical stress on active xylem tissue. The mechanical stress needed to fell trees is less than the stress needed to cause the deformation of differentiating tracheids observed in trees close to the epicenter. In order to resolve this apparent contradiction, work is suggested on possible topographic modification of the overpressure experienced by these trees, as is an experimental test of the effects of such stresses on precisely analogous growing trees.

Inferring phylogenetic trees from the knowledge of rare evolutionary events.

PubMed

Hellmuth, Marc; Hernandez-Rosales, Maribel; Long, Yangjing; Stadler, Peter F

2018-06-01

Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters. In this contribution we analyze the phylogenetic information content from a combinatorial point of view by considering the binary relation on the set of taxa defined by the existence of a single event separating two taxa. We show that the graph-representation of this relation must be a tree. Moreover, we characterize completely the relationship between the tree of such relations and the underlying phylogenetic tree. With directed operations such as tandem-duplication-random-loss events in mind we demonstrate how non-symmetric information constrains the position of the root in the partially reconstructed phylogeny.

Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

PubMed

Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

2013-11-01

Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

Paleo-event data standards for dendrochronology

Treesearch

Elaine Kennedy Sutherland; P. Brewer; W. Gross

2017-01-01

Extreme environmental events, such as storm winds, landslides, insect infestations, and wildfire, cause loss of life, resources, and human infrastructure. Disaster riskreduction analysis can be improved with information about past frequency, intensity, and spatial patterns of extreme events. Tree-ring analyses can provide such information: tree rings reflect events as...

36 CFR 292.46 - Timber harvesting activities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... hazard trees; or to respond to natural events such as wildfire, flood, earthquake, volcanic eruption, high winds, and disease or insect infestation. (2) Where authorized, trees may be harvested by... trees, or to respond to natural events provided that the activity is consistent with the Wild and Scenic...

Volcanic hazard management in dispersed volcanism areas

NASA Astrophysics Data System (ADS)

Marrero, Jose Manuel; Garcia, Alicia; Ortiz, Ramon

2014-05-01

Traditional volcanic hazard methodologies were developed mainly to deal with the big stratovolcanoes. In such type of volcanoes, the hazard map is an important tool for decision-makers not only during a volcanic crisis but also for territorial planning. According to the past and recent eruptions of a volcano, all possible volcanic hazards are modelled and included in the hazard map. Combining the hazard map with the Event Tree the impact area can be zoned and defining the likely eruptive scenarios that will be used during a real volcanic crisis. But in areas of disperse volcanism is very complex to apply the same volcanic hazard methodologies. The event tree do not take into account unknown vents, because the spatial concepts included in it are only related with the distance reached by volcanic hazards. The volcanic hazard simulation is also difficult because the vent scatter modifies the results. The volcanic susceptibility try to solve this problem, calculating the most likely areas to have an eruption, but the differences between low and large values obtained are often very small. In these conditions the traditional hazard map effectiveness could be questioned, making necessary a change in the concept of hazard map. Instead to delimit the potential impact areas, the hazard map should show the expected behaviour of the volcanic activity and how the differences in the landscape and internal geo-structures could condition such behaviour. This approach has been carried out in La Palma (Canary Islands), combining the concept of long-term hazard map with the short-term volcanic scenario to show the expected volcanic activity behaviour. The objective is the decision-makers understand how a volcanic crisis could be and what kind of mitigation measurement and strategy could be used.

Distributed Events in Sentinel: Design and Implementation of a Global Event Detector

DTIC Science & Technology

1999-01-01

local event detector and a global event detector to detect events. Global event detector in this case plays the role of a message sending/receiving than...significant in this case . The system performance will decrease with increase in the number of applications involved in global event detection. Yet from a...Figure 8: A Global event tree (2) 1. Global composite event is detected at the GED In this case , the whole global composite event tree is sent to the

Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction

PubMed Central

Rahman, Raziur; Haider, Saad; Ghosh, Souparno; Pal, Ranadip

2015-01-01

Random forests consisting of an ensemble of regression trees with equal weights are frequently used for design of predictive models. In this article, we consider an extension of the methodology by representing the regression trees in the form of probabilistic trees and analyzing the nature of heteroscedasticity. The probabilistic tree representation allows for analytical computation of confidence intervals (CIs), and the tree weight optimization is expected to provide stricter CIs with comparable performance in mean error. We approached the ensemble of probabilistic trees’ prediction from the perspectives of a mixture distribution and as a weighted sum of correlated random variables. We applied our methodology to the drug sensitivity prediction problem on synthetic and cancer cell line encyclopedia dataset and illustrated that tree weights can be selected to reduce the average length of the CI without increase in mean error. PMID:27081304

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

PubMed

Marcussen, Thomas; Heier, Lise; Brysting, Anne K; Oxelman, Bengt; Jakobsen, Kjetill S

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the "correct" network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ("ghost subgenome lineages") significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage-between 67% and 88%-of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Constructing event trees for volcanic crises

USGS Publications Warehouse

Newhall, C.; Hoblitt, R.

2002-01-01

Event trees are useful frameworks for discussing probabilities of possible outcomes of volcanic unrest. Each branch of the tree leads from a necessary prior event to a more specific outcome, e.g., from an eruption to a pyroclastic flow. Where volcanic processes are poorly understood, probability estimates might be purely empirical - utilizing observations of past and current activity and an assumption that the future will mimic the past or follow a present trend. If processes are better understood, probabilities might be estimated from a theoritical model, either subjectively or by numerical simulations. Use of Bayes' theorem aids in the estimation of how fresh unrest raises (or lowers) the probabilities of eruptions. Use of event trees during volcanic crises can help volcanologists to critically review their analysis of hazard, and help officials and individuals to compare volcanic risks with more familiar risks. Trees also emphasize the inherently probabilistic nature of volcano forecasts, with multiple possible outcomes.

Data Analysis

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

Powell, Danny H; Elwood Jr, Robert H

2011-01-01

Analysis of the material protection, control, and accountability (MPC&A) system is necessary to understand the limits and vulnerabilities of the system to internal threats. A self-appraisal helps the facility be prepared to respond to internal threats and reduce the risk of theft or diversion of nuclear material. The material control and accountability (MC&A) system effectiveness tool (MSET) fault tree was developed to depict the failure of the MPC&A system as a result of poor practices and random failures in the MC&A system. It can also be employed as a basis for assessing deliberate threats against a facility. MSET uses faultmore » tree analysis, which is a top-down approach to examining system failure. The analysis starts with identifying a potential undesirable event called a 'top event' and then determining the ways it can occur (e.g., 'Fail To Maintain Nuclear Materials Under The Purview Of The MC&A System'). The analysis proceeds by determining how the top event can be caused by individual or combined lower level faults or failures. These faults, which are the causes of the top event, are 'connected' through logic gates. The MSET model uses AND-gates and OR-gates and propagates the effect of event failure using Boolean algebra. To enable the fault tree analysis calculations, the basic events in the fault tree are populated with probability risk values derived by conversion of questionnaire data to numeric values. The basic events are treated as independent variables. This assumption affects the Boolean algebraic calculations used to calculate results. All the necessary calculations are built into the fault tree codes, but it is often useful to estimate the probabilities manually as a check on code functioning. The probability of failure of a given basic event is the probability that the basic event primary question fails to meet the performance metric for that question. The failure probability is related to how well the facility performs the task identified in that basic event over time (not just one performance or exercise). Fault tree calculations provide a failure probability for the top event in the fault tree. The basic fault tree calculations establish a baseline relative risk value for the system. This probability depicts relative risk, not absolute risk. Subsequent calculations are made to evaluate the change in relative risk that would occur if system performance is improved or degraded. During the development effort of MSET, the fault tree analysis program used was SAPHIRE. SAPHIRE is an acronym for 'Systems Analysis Programs for Hands-on Integrated Reliability Evaluations.' Version 1 of the SAPHIRE code was sponsored by the Nuclear Regulatory Commission in 1987 as an innovative way to draw, edit, and analyze graphical fault trees primarily for safe operation of nuclear power reactors. When the fault tree calculations are performed, the fault tree analysis program will produce several reports that can be used to analyze the MPC&A system. SAPHIRE produces reports showing risk importance factors for all basic events in the operational MC&A system. The risk importance information is used to examine the potential impacts when performance of certain basic events increases or decreases. The initial results produced by the SAPHIRE program are considered relative risk values. None of the results can be interpreted as absolute risk values since the basic event probability values represent estimates of risk associated with the performance of MPC&A tasks throughout the material balance area (MBA). The RRR for a basic event represents the decrease in total system risk that would result from improvement of that one event to a perfect performance level. Improvement of the basic event with the greatest RRR value produces a greater decrease in total system risk than improvement of any other basic event. Basic events with the greatest potential for system risk reduction are assigned performance improvement values, and new fault tree calculations show the improvement in total system risk. The operational impact or cost-effectiveness from implementing the performance improvements can then be evaluated. The improvements being evaluated can be system performance improvements, or they can be potential, or actual, upgrades to the system. The RIR for a basic event represents the increase in total system risk that would result from failure of that one event. Failure of the basic event with the greatest RIR value produces a greater increase in total system risk than failure of any other basic event. Basic events with the greatest potential for system risk increase are assigned failure performance values, and new fault tree calculations show the increase in total system risk. This evaluation shows the importance of preventing performance degradation of the basic events. SAPHIRE identifies combinations of basic events where concurrent failure of the events results in failure of the top event.« less

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

PubMed

Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

2012-09-15

Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

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

NASA Astrophysics Data System (ADS)

Poliaková, Adela

2015-06-01

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

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

PubMed

Altaba, Cristian R

2009-01-01

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

What are the hydro-meteorological controls on flood characteristics?

NASA Astrophysics Data System (ADS)

Nied, Manuela; Schröter, Kai; Lüdtke, Stefan; Nguyen, Viet Dung; Merz, Bruno

2017-02-01

Flood events can be expressed by a variety of characteristics such as flood magnitude and extent, event duration or incurred loss. Flood estimation and management may benefit from understanding how the different flood characteristics relate to the hydrological catchment conditions preceding the event and to the meteorological conditions throughout the event. In this study, we therefore propose a methodology to investigate the hydro-meteorological controls on different flood characteristics, based on the simulation of the complete flood risk chain from the flood triggering precipitation event, through runoff generation in the catchment, flood routing and possible inundation in the river system and floodplains to flood loss. Conditional cumulative distribution functions and regression tree analysis delineate the seasonal varying flood processes and indicate that the effect of the hydrological pre-conditions, i.e. soil moisture patterns, and of the meteorological conditions, i.e. weather patterns, depends on the considered flood characteristic. The methodology is exemplified for the Elbe catchment. In this catchment, the length of the build-up period, the event duration and the number of gauges undergoing at least a 10-year flood are governed by weather patterns. The affected length and the number of gauges undergoing at least a 2-year flood are however governed by soil moisture patterns. In case of flood severity and loss, the controlling factor is less pronounced. Severity is slightly governed by soil moisture patterns whereas loss is slightly governed by weather patterns. The study highlights that flood magnitude and extent arise from different flood generation processes and concludes that soil moisture patterns as well as weather patterns are not only beneficial to inform on possible flood occurrence but also on the involved flood processes and resulting flood characteristics.

Early changes in physical tree characteristics during an oak decline event in the Ozark highlands

Treesearch

Martin A. Spetich

2006-01-01

An oak decline event is severely affecting up to 120 000 ha in the Ozark National Forest of Arkansas. Results of early changes in physical tree characteristics during that event are presented. In the fall and winter of 1999 and 2000, we established research plots on a site that would become a center of severe oak decline. In August 2000, standing trees > 14 cm in...

Long‐term time‐dependent probabilities for the third Uniform California Earthquake Rupture Forecast (UCERF3)

USGS Publications Warehouse

Field, Edward; Biasi, Glenn P.; Bird, Peter; Dawson, Timothy E.; Felzer, Karen R.; Jackson, David A.; Johnson, Kaj M.; Jordan, Thomas H.; Madden, Christopher; Michael, Andrew J.; Milner, Kevin; Page, Morgan T.; Parsons, Thomas E.; Powers, Peter; Shaw, Bruce E.; Thatcher, Wayne R.; Weldon, Ray J.; Zeng, Yuehua

2015-01-01

The 2014 Working Group on California Earthquake Probabilities (WGCEP 2014) presents time-dependent earthquake probabilities for the third Uniform California Earthquake Rupture Forecast (UCERF3). Building on the UCERF3 time-independent model, published previously, renewal models are utilized to represent elastic-rebound-implied probabilities. A new methodology has been developed that solves applicability issues in the previous approach for un-segmented models. The new methodology also supports magnitude-dependent aperiodicity and accounts for the historic open interval on faults that lack a date-of-last-event constraint. Epistemic uncertainties are represented with a logic tree, producing 5,760 different forecasts. Results for a variety of evaluation metrics are presented, including logic-tree sensitivity analyses and comparisons to the previous model (UCERF2). For 30-year M≥6.7 probabilities, the most significant changes from UCERF2 are a threefold increase on the Calaveras fault and a threefold decrease on the San Jacinto fault. Such changes are due mostly to differences in the time-independent models (e.g., fault slip rates), with relaxation of segmentation and inclusion of multi-fault ruptures being particularly influential. In fact, some UCERF2 faults were simply too long to produce M 6.7 sized events given the segmentation assumptions in that study. Probability model differences are also influential, with the implied gains (relative to a Poisson model) being generally higher in UCERF3. Accounting for the historic open interval is one reason. Another is an effective 27% increase in the total elastic-rebound-model weight. The exact factors influencing differences between UCERF2 and UCERF3, as well as the relative importance of logic-tree branches, vary throughout the region, and depend on the evaluation metric of interest. For example, M≥6.7 probabilities may not be a good proxy for other hazard or loss measures. This sensitivity, coupled with the approximate nature of the model and known limitations, means the applicability of UCERF3 should be evaluated on a case-by-case basis.

A scaleable methodology for assessing the impacts of urban shade on the summer electricity use of residential homes

NASA Astrophysics Data System (ADS)

Taylor, Robert Vanderlei

Our cities are experiencing unprecedented growth while net global temperatures continue to trend warmer making sustainable urban development and energy conservation pressing public issues. This research explores how urban landscaping -- in particular trees and buildings -- affect summer electricity use in residential homes. I studied the interactions of urban shade and temperature to explore how vegetation distribution and intensity could play a meaningful role in heat mitigation in urban environments. Only a few studies have reconciled modeled electricity savings from tree shade with actual electricity consumption data. This research proposes a methodology for modeling the isolated effects of urban shade (tree shade vs building shade) on buildings' summertime electricity consumption from micro to mesoscales, empirically validating the modeled shade with actual electricity billing data, and comparing the electric energetic impact of tree shade effects with building shade effects. This proposed methodology seeks to resolve three primary research questions: 1) What are the modeled quantities of urban shade associated with the area of interest (AOI)? 2) To what extent do the effects of shading from trees and buildings mitigate summertime heat in the AOI? 2) To what extent do the shade effects from trees and buildings reduce summertime electricity consumption in the AOI?

Developing a methodology to predict oak wilt distribution using classification tree analysis

Treesearch

Marla C. Downing; Vernon L. Thomas; Robin M. Reich

2006-01-01

Oak wilt (Ceratocystis fagacearum), a fungal disease that causes some species of oak trees to wilt and die rapidly, is a threat to oak forested resources in 22 states in the United States. We developed a methodology for predicting the Potential Distribution of Oak Wilt (PDOW) using Anoka County, Minnesota as our study area. The PDOW utilizes GIS; the...

Simple methodologies to estimate the energy amount stored in a tree due to an explosive seed dispersal mechanism

NASA Astrophysics Data System (ADS)

do Carmo, Eduardo; Goncalves Hönnicke, Marcelo

2018-05-01

There are different forms to introduce/illustrate the energy concepts for the basic physics students. The explosive seed dispersal mechanism found in a variety of trees could be one of them. Sibipiruna trees carry out fruits (pods) who show such an explosive mechanism. During the explosion, the pods throw out seeds several meters away. In this manuscript we show simple methodologies to estimate the energy amount stored in the Sibipiruna tree due to such a process. Two different physics approaches were used to carry out this study: by monitoring indoor and in situ the explosive seed dispersal mechanism and by measuring the elastic constant of the pod shell. An energy of the order of kJ was found to be stored in a single tree due to such an explosive mechanism.

75 FR 66125 - Notice of Public Meeting and Request for Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

...--The National Christmas Tree Lighting and the subsequent 23 day event. SUMMARY: The National Park Service is seeking public comments and suggestions on the planning of the 2010 National Christmas Tree... Christmas Tree Lighting and the subsequent 23 day event, which opens on December 9, 2010, on the Ellipse...

The influence of tree traits and storm event characteristics on stemflow production from isolated deciduous trees in an urban park

NASA Astrophysics Data System (ADS)

Carlyle-Moses, D. E.; Schooling, J. T.

2014-12-01

Urban tree canopy processes affect the volume and biogeochemistry of inputs to the hydrological cycle in cities. We studied stemflow from 37 isolated deciduous trees in an urban park in Kamloops, British Columbia which has a semi-arid climate dominated by small precipitation events. Precipitation and stemflow were measured on an event basis from June 12, 2012 to November 3, 2013. To clarify the effect of canopy traits on stemflow thresholds, rates, yields, percent, and funneling ratios, we analyzed branch angles, bark roughness, tree size, cover, leaf size, and branch and leader counts. High branch angles promoted stemflow in all trees, while bark roughness influenced stemflow differently for single- and multi-leader trees. The association between stemflow and numerous leaders deserves further study. Columnar-form trees often partitioned a large percentage of precipitation into stemflow, with event-scale values as high as 27.9 % recorded for an Armstrong Freeman Maple (Acer x freemanii 'Armstrong'). Under growing-season conditions funneling ratios as high as 196.9 were derived for an American Beech (Fagus grandifolia) individual. Among meteorological variables, rain depth was strongly correlated with stemflow yields; intra-storm break duration, rainfall intensity, rainfall inclination, wind speed, and vapour pressure deficit also played roles. Greater stemflow was associated with leafless canopies and with rain or mixed events versus snow. Results can inform climate-sensitive selection and siting of urban trees towards integrated rainwater management. For example, previous studies suggest that the reduction in storm-water generation by urban trees is accomplished through canopy interception loss alone. However, trees that partition large quantities of precipitation canopy-drainage as stemflow to the base of their trunks, where it has the potential to infiltrate into the soil media rather than fall on impervious surfaces as throughfall, may assist in reducing stormwater flow.

A Passive System Reliability Analysis for a Station Blackout

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

Brunett, Acacia; Bucknor, Matthew; Grabaskas, David

2015-05-03

The latest iterations of advanced reactor designs have included increased reliance on passive safety systems to maintain plant integrity during unplanned sequences. While these systems are advantageous in reducing the reliance on human intervention and availability of power, the phenomenological foundations on which these systems are built require a novel approach to a reliability assessment. Passive systems possess the unique ability to fail functionally without failing physically, a result of their explicit dependency on existing boundary conditions that drive their operating mode and capacity. Argonne National Laboratory is performing ongoing analyses that demonstrate various methodologies for the characterization of passivemore » system reliability within a probabilistic framework. Two reliability analysis techniques are utilized in this work. The first approach, the Reliability Method for Passive Systems, provides a mechanistic technique employing deterministic models and conventional static event trees. The second approach, a simulation-based technique, utilizes discrete dynamic event trees to treat time- dependent phenomena during scenario evolution. For this demonstration analysis, both reliability assessment techniques are used to analyze an extended station blackout in a pool-type sodium fast reactor (SFR) coupled with a reactor cavity cooling system (RCCS). This work demonstrates the entire process of a passive system reliability analysis, including identification of important parameters and failure metrics, treatment of uncertainties and analysis of results.« less

Detecting mismatches of bird migration stopover and tree phenology in response to changing climate

USGS Publications Warehouse

Kellermann, Jherime L.; van Riper, Charles

2015-01-01

Migratory birds exploit seasonal variation in resources across latitudes, timing migration to coincide with the phenology of food at stopover sites. Differential responses to climate in phenology across trophic levels can result in phenological mismatch; however, detecting mismatch is sensitive to methodology. We examined patterns of migrant abundance and tree flowering, phenological mismatch, and the influence of climate during spring migration from 2009 to 2011 across five habitat types of the Madrean Sky Islands in southeastern Arizona, USA. We used two metrics to assess phenological mismatch: synchrony and overlap. We also examined whether phenological overlap declined with increasing difference in mean event date of phenophases. Migrant abundance and tree flowering generally increased with minimum spring temperature but depended on annual climate by habitat interactions. Migrant abundance was lowest and flowering was highest under cold, snowy conditions in high elevation montane conifer habitat while bird abundance was greatest and flowering was lowest in low elevation riparian habitat under the driest conditions. Phenological synchrony and overlap were unique and complementary metrics and should both be used when assessing mismatch. Overlap declined due to asynchronous phenologies but also due to reduced migrant abundance or flowering when synchrony was actually maintained. Overlap declined with increasing difference in event date and this trend was strongest in riparian areas. Montane habitat specialists may be at greatest risk of mismatch while riparian habitat could provide refugia during dry years for phenotypically plastic species. Interannual climate patterns that we observed match climate change projections for the arid southwest, altering stopover habitat condition.

Impacts of a water stress followed by an early frost event on beech (Fagus sylvatica L.) susceptibility to Scolytine ambrosia beetles - Research strategy and first results

NASA Astrophysics Data System (ADS)

La Spina, Sylvie; de Cannière, Charles; Molenberg, Jean-Marc; Vincke, Caroline; Deman, Déborah; Grégoire, Jean-Claude

2010-05-01

Climate change tends to induce more frequent abiotic and biotic extreme events, having large impacts on tree vitality. Weakened trees are then more susceptible to secondary insect outbreaks, as it happened in Belgium in the early 2000s: after an early frost event, secondary Scolytine ambrosia beetles attacks were observed on beech trees. In this study, we test if a combination of stress, i.e. a soil water deficit preceding an early frost, could render trees more attractive to beetles. An experimental study was set in autumn 2008. Two parcels of a beech forest were covered with plastic tents to induce a water stress by rain interception. The parcels were surrounded by 2-meters depth trenches to avoid water supply by streaming. Soil water content and different indicators of tree water use (sap flow, predawn leaf water potential, tree radial growth) were followed. In autumn 2010, artificial frost injuries will be inflicted to trees using dry ice. Trees attractivity for Scolytine insects, and the success of insect colonization will then be studied. The poster will focus on experiment setting and first results (impacts of soil water deficit on trees).

Coalescence computations for large samples drawn from populations of time-varying sizes

PubMed Central

Polanski, Andrzej; Szczesna, Agnieszka; Garbulowski, Mateusz; Kimmel, Marek

2017-01-01

We present new results concerning probability distributions of times in the coalescence tree and expected allele frequencies for coalescent with large sample size. The obtained results are based on computational methodologies, which involve combining coalescence time scale changes with techniques of integral transformations and using analytical formulae for infinite products. We show applications of the proposed methodologies for computing probability distributions of times in the coalescence tree and their limits, for evaluation of accuracy of approximate expressions for times in the coalescence tree and expected allele frequencies, and for analysis of large human mitochondrial DNA dataset. PMID:28170404

Recent Mega-Thrust Tsunamigenic Earthquakes and PTHA

NASA Astrophysics Data System (ADS)

Lorito, S.

2013-05-01

The occurrence of several mega-thrust tsunamigenic earthquakes in the last decade, including but not limited to the 2004 Sumatra-Andaman, the 2010 Maule, and 2011 Tohoku earthquakes, has been a dramatic reminder of the limitations in our capability of assessing earthquake and tsunami hazard and risk. However, the increasingly high-quality geophysical observational networks allowed the retrieval of most accurate than ever models of the rupture process of mega-thrust earthquakes, thus paving the way for future improved hazard assessments. Probabilistic Tsunami Hazard Analysis (PTHA) methodology, in particular, is less mature than its seismic counterpart, PSHA. Worldwide recent research efforts of the tsunami science community allowed to start filling this gap, and to define some best practices that are being progressively employed in PTHA for different regions and coasts at threat. In the first part of my talk, I will briefly review some rupture models of recent mega-thrust earthquakes, and highlight some of their surprising features that likely result in bigger error bars associated to PTHA results. More specifically, recent events of unexpected size at a given location, and with unexpected rupture process features, posed first-order open questions which prevent the definition of an heterogeneous rupture probability along a subduction zone, despite of several recent promising results on the subduction zone seismic cycle. In the second part of the talk, I will dig a bit more into a specific ongoing effort for improving PTHA methods, in particular as regards epistemic and aleatory uncertainties determination, and the computational PTHA feasibility when considering the full assumed source variability. Only logic trees are usually explicated in PTHA studies, accounting for different possible assumptions on the source zone properties and behavior. The selection of the earthquakes to be actually modelled is then in general made on a qualitative basis or remains implicit, despite different methods like event trees have been used for different applications. I will define a quite general PTHA framework, based on the mixed use of logic and event trees. I will first discuss a particular class of epistemic uncertainties, i.e. those related to the parametric fault characterization in terms of geometry, kinematics, and assessment of activity rates. A systematic classification in six justification levels of epistemic uncertainty related with the existence and behaviour of fault sources will be presented. Then, a particular branch of the logic tree is chosen in order to discuss just the aleatory variability of earthquake parameters, represented with an event tree. Even so, PTHA based on numerical scenarios is a too demanding computational task, particularly when probabilistic inundation maps are needed. For trying to reduce the computational burden without under-representing the source variability, the event tree is first constructed by taking care of densely (over-)sampling the earthquake parameter space, and then the earthquakes are filtered basing on their associated tsunami impact offshore, before calculating inundation maps. I'll describe this approach by means of a case study in the Mediterranean Sea, namely the PTHA for some locations of Eastern Sicily coasts and Southern Crete coast due to potential subduction earthquakes occurring on the Hellenic Arc.

The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

PubMed

Prosperi, Mattia C F; De Luca, Andrea; Di Giambenedetto, Simona; Bracciale, Laura; Fabbiani, Massimiliano; Cauda, Roberto; Salemi, Marco

2010-10-25

Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation. The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories. TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.

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

PubMed

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

2017-08-16

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

Effects of protection forests on rockfall risks: implementation in the Swiss risk concept

NASA Astrophysics Data System (ADS)

Trappmann, Daniel; Moos, Christine; Fehlmann, Michael; Ernst, Jacqueline; Sandri, Arthur; Dorren, Luuk; Stoffel, Markus

2016-04-01

Forests growing on slopes below active rockfall cliffs can provide effective protection for human lives and infrastructures. The risk-based approach for natural hazards in Switzerland shall take such biological measures just like existing technical protective measures into account, provided that certain criteria regarding condition, maintenance and durability are met. This contribution describes a project in which we are investigating how the effects of protection forests can be considered in rockfall risk analyses in an appropriate way. In principle, protection forests reduce rockfall risks in three different ways: (i) reduction of the event magnitude (energy) due to collisions with tree stems; (ii) reduction of frequency of occurrence of a given scenario (block volume arriving at the damage potential); (iii) reduction of spatial probability of occurrence (spread and runout) of a given scenario in case of multiple fragments during one event. The aim of this work is to develop methods for adequately implementing these three effects of rockfall protection forests in risk calculations. To achieve this, we use rockfall simulations taking collisions with trees into account and detailed field validation. On five test sites, detailed knowledge on past rockfall activity is gathered by combining investigations of impacted trees, analysis of documented historical events, and deposits in the field. Based on this empirical data on past rockfalls, a methodology is developed that allows transferring real past rockfall activity to simulation results obtained with the three-dimensional, process-based model Rockyfor3D. Different ways of quantifying the protective role of forests will be considered by comparing simulation results with and without forest cover. Combining these different research approaches, systematic considerations shall lead to the development of methods for adequate inclusion of the protective effects of forests in risk calculations. The applicability of the developed methods will be tested on the case study slopes in order to ensure practical applicability to a broad range of rockfall situations on forested slopes.

MIRAP, microcomputer reliability analysis program

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

Jehee, J.N.T.

1989-01-01

A program for a microcomputer is outlined that can determine minimal cut sets from a specified fault tree logic. The speed and memory limitations of the microcomputers on which the program is implemented (Atari ST and IBM) are addressed by reducing the fault tree's size and by storing the cut set data on disk. Extensive well proven fault tree restructuring techniques, such as the identification of sibling events and of independent gate events, reduces the fault tree's size but does not alter its logic. New methods are used for the Boolean reduction of the fault tree logic. Special criteria formore » combining events in the 'AND' and 'OR' logic avoid the creation of many subsuming cut sets which all would cancel out due to existing cut sets. Figures and tables illustrates these methods. 4 refs., 5 tabs.« less

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

USDA-ARS?s Scientific Manuscript database

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

Failure mode effect analysis and fault tree analysis as a combined methodology in risk management

NASA Astrophysics Data System (ADS)

Wessiani, N. A.; Yoshio, F.

2018-04-01

There have been many studies reported the implementation of Failure Mode Effect Analysis (FMEA) and Fault Tree Analysis (FTA) as a method in risk management. However, most of the studies usually only choose one of these two methods in their risk management methodology. On the other side, combining these two methods will reduce the drawbacks of each methods when implemented separately. This paper aims to combine the methodology of FMEA and FTA in assessing risk. A case study in the metal company will illustrate how this methodology can be implemented. In the case study, this combined methodology will assess the internal risks that occur in the production process. Further, those internal risks should be mitigated based on their level of risks.

Missing rings in Pinus halepensis – the missing link to relate the tree-ring record to extreme climatic events

Treesearch

Klemen Novak; Martin de Luis; Miguel A. Saz; Luis A. Longares; Roberto Serrano-Notivoli; Josep Raventos; Katarina Cufar; Jozica Gricar; Alfredo Di Filippo; Gianluca Piovesan; Cyrille B.K. Rathgeber; Andreas Papadopoulos; Kevin T. Smith

2016-01-01

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of...

Evidential Networks for Fault Tree Analysis with Imprecise Knowledge

NASA Astrophysics Data System (ADS)

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

2012-06-01

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

A diagnosis system using object-oriented fault tree models

NASA Technical Reports Server (NTRS)

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

1990-01-01

Spaceborne computing systems must provide reliable, continuous operation for extended periods. Due to weight, power, and volume constraints, these systems must manage resources very effectively. A fault diagnosis algorithm is described which enables fast and flexible diagnoses in the dynamic distributed computing environments planned for future space missions. The algorithm uses a knowledge base that is easily changed and updated to reflect current system status. Augmented fault trees represented in an object-oriented form provide deep system knowledge that is easy to access and revise as a system changes. Given such a fault tree, a set of failure events that have occurred, and a set of failure events that have not occurred, this diagnosis system uses forward and backward chaining to propagate causal and temporal information about other failure events in the system being diagnosed. Once the system has established temporal and causal constraints, it reasons backward from heuristically selected failure events to find a set of basic failure events which are a likely cause of the occurrence of the top failure event in the fault tree. The diagnosis system has been implemented in common LISP using Flavors.

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...

Event Classification and Identification Based on the Characteristic Ellipsoid of Phasor Measurement

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

Ma, Jian; Diao, Ruisheng; Makarov, Yuri V.

2011-09-23

In this paper, a method to classify and identify power system events based on the characteristic ellipsoid of phasor measurement is presented. The decision tree technique is used to perform the event classification and identification. Event types, event locations and clearance times are identified by decision trees based on the indices of the characteristic ellipsoid. A sufficiently large number of transient events were simulated on the New England 10-machine 39-bus system based on different system configurations. Transient simulations taking into account different event types, clearance times and various locations are conducted to simulate phasor measurement. Bus voltage magnitudes and recordedmore » reactive and active power flows are used to build the characteristic ellipsoid. The volume, eccentricity, center and projection of the longest axis in the parameter space coordinates of the characteristic ellipsoids are used to classify and identify events. Results demonstrate that the characteristic ellipsoid and the decision tree are capable to detect the event type, location, and clearance time with very high accuracy.« less

[Application of root cause analysis in healthcare].

PubMed

Hsu, Tsung-Fu

2007-12-01

The main purpose of this study was to explore various aspects of root cause analysis (RCA), including its definition, rationale concept, main objective, implementation procedures, most common analysis methodology (fault tree analysis, FTA), and advantages and methodologic limitations in regard to healthcare. Several adverse events that occurred at a certain hospital were also analyzed by the author using FTA as part of this study. RCA is a process employed to identify basic and contributing causal factors underlying performance variations associated with adverse events. The rationale concept of RCA offers a systemic approach to improving patient safety that does not assign blame or liability to individuals. The four-step process involved in conducting an RCA includes: RCA preparation, proximate cause identification, root cause identification, and recommendation generation and implementation. FTA is a logical, structured process that can help identify potential causes of system failure before actual failures occur. Some advantages and significant methodologic limitations of RCA were discussed. Finally, we emphasized that errors stem principally from faults attributable to system design, practice guidelines, work conditions, and other human factors, which induce health professionals to make negligence or mistakes with regard to healthcare. We must explore the root causes of medical errors to eliminate potential RCA system failure factors. Also, a systemic approach is needed to resolve medical errors and move beyond a current culture centered on assigning fault to individuals. In constructing a real environment of patient-centered safety healthcare, we can help encourage clients to accept state-of-the-art healthcare services.

Statistical methodologies for tree-ring research to understand the climate-growth relationships over time and space

EPA Science Inventory

The International Tree-Ring Database is a valuable resource for studying climate change and its effects on terrestrial ecosystems over time and space. We examine the statistical methods in current use in dendroclimatology and dendroecology to process the tree-ring data and make ...

A Black Swan and Sub-continental Scale Dynamics in Humid, Late-Holocene Broadleaf Forests

NASA Astrophysics Data System (ADS)

Pederson, N.; Dyer, J.; McEwan, R.; Hessl, A. E.; Mock, C. J.; Orwig, D.; Rieder, H. E.; Cook, B. I.

2012-12-01

In humid regions with dense broadleaf-dominated forests where gap-dynamics is the prevailing disturbance regime, paleoecological evidence shows regional-scale changes in forest composition associated with climatic change. To investigate the potential for regional events in late-Holocene forests, we use tree-ring data from 76 populations covering 840,000 km2 and 5.3k tree recruitment dates spanning 1.4 million km2 in the eastern US to investigate the occurrence of simultaneous forest dynamics across a humid region. We compare regional forest dynamics with an independent set of annually-resolved tree ring record of hydroclimate to examine whether climate dynamics might drive forest dynamics in this humid region. In forests where light availability is an important limitation for tree recruitment, we document a pulse of tree recruitment during the mid- to late-1600s across the eastern US. This pulse, which can be inferred as large-scale canopy opening, occurred during an era that multiple proxies indicate as extended drought between two intense pluvial. Principal component analysis of the 76 populations indicates a step-change increase in average ring width during the late-1770s resembling a potential canopy accession event over 42,800 km2 of the southeastern US. Growth-release analysis of populations loading strongly on this eigenvector indicates severe canopy disturbance from 1775-1779 that peaked in 1776. The 1776 event follows a period with extended droughts and severe large-scale frost event. We hypothesize these climatic events lead to elevated tree mortality in the late-1770s and canopy accession for understory trees. Superposed epoch analysis reveals that spikes of elevated canopy disturbance from 1685-1850 CE are significantly associated with drought. Extreme value theory statistics indicates the 1776 event lies beyond the 99.9 quantile and nearly 7 sigmas above the 1685-1850 mean rate of disturbance. The time-series of canopy disturbance from 1685-1850 is so poorly described by a Gaussian distribution that it can be considered 'heavy tailed'. Preliminary results show that disturbance events that affect >3-5% of the trees in our dataset occur approximately every 200 years. The most extreme rates (>5%) occur approximately every 500-1000 years. These statistics indicate that the 1775-1779 heavy-tail event can also be considered a 'Black Swan', the rare event that has the potential to alter a system's trajectory further than common events. Our results challenge traditional views regarding characteristic disturbance regime in humid temperate forests, and speak to the importance of punctuated climatic events in shaping forest structure for centuries. Such an understanding is critical given the potential of more frequent extreme climatic events in the future.

Discriminant forest classification method and system

DOEpatents

Chen, Barry Y.; Hanley, William G.; Lemmond, Tracy D.; Hiller, Lawrence J.; Knapp, David A.; Mugge, Marshall J.

2012-11-06

A hybrid machine learning methodology and system for classification that combines classical random forest (RF) methodology with discriminant analysis (DA) techniques to provide enhanced classification capability. A DA technique which uses feature measurements of an object to predict its class membership, such as linear discriminant analysis (LDA) or Andersen-Bahadur linear discriminant technique (AB), is used to split the data at each node in each of its classification trees to train and grow the trees and the forest. When training is finished, a set of n DA-based decision trees of a discriminant forest is produced for use in predicting the classification of new samples of unknown class.

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies.

PubMed

Lanier, Hayley C; Knowles, L Lacey

2015-02-01

Coalescent-based methods for species-tree estimation are becoming a dominant approach for reconstructing species histories from multi-locus data, with most of the studies examining these methodologies focused on recently diverged species. However, deeper phylogenies, such as the datasets that comprise many Tree of Life (ToL) studies, also exhibit gene-tree discordance. This discord may also arise from the stochastic sorting of gene lineages during the speciation process (i.e., reflecting the random coalescence of gene lineages in ancestral populations). It remains unknown whether guidelines regarding methodologies and numbers of loci established by simulation studies at shallow tree depths translate into accurate species relationships for deeper phylogenetic histories. We address this knowledge gap and specifically identify the challenges and limitations of species-tree methods that account for coalescent variance for deeper phylogenies. Using simulated data with characteristics informed by empirical studies, we evaluate both the accuracy of estimated species trees and the characteristics associated with recalcitrant nodes, with a specific focus on whether coalescent variance is generally responsible for the lack of resolution. By determining the proportion of coalescent genealogies that support a particular node, we demonstrate that (1) species-tree methods account for coalescent variance at deep nodes and (2) mutational variance - not gene-tree discord arising from the coalescent - posed the primary challenge for accurate reconstruction across the tree. For example, many nodes were accurately resolved despite predicted discord from the random coalescence of gene lineages and nodes with poor support were distributed across a range of depths (i.e., they were not restricted to a particular recent divergences). Given their broad taxonomic scope and large sampling of taxa, deep level phylogenies pose several potential methodological complications including difficulties with MCMC convergence and estimation of requisite population genetic parameters for coalescent-based approaches. Despite these difficulties, the findings generally support the utility of species-tree analyses for the estimation of species relationships throughout the ToL. We discuss strategies for successful application of species-tree approaches to deep phylogenies. Copyright © 2014 Elsevier Inc. All rights reserved.

Branch-and-Bound algorithm applied to uncertainty quantification of a Boiling Water Reactor Station Blackout

DOE PAGES

Nielsen, Joseph; Tokuhiro, Akira; Hiromoto, Robert; ...

2015-11-13

Evaluation of the impacts of uncertainty and sensitivity in modeling presents a significant set of challenges in particular to high fidelity modeling. Computational costs and validation of models creates a need for cost effective decision making with regards to experiment design. Experiments designed to validate computation models can be used to reduce uncertainty in the physical model. In some cases, large uncertainty in a particular aspect of the model may or may not have a large impact on the final results. For example, modeling of a relief valve may result in large uncertainty, however, the actual effects on final peakmore » clad temperature in a reactor transient may be small and the large uncertainty with respect to valve modeling may be considered acceptable. Additionally, the ability to determine the adequacy of a model and the validation supporting it should be considered within a risk informed framework. Low fidelity modeling with large uncertainty may be considered adequate if the uncertainty is considered acceptable with respect to risk. In other words, models that are used to evaluate the probability of failure should be evaluated more rigorously with the intent of increasing safety margin. Probabilistic risk assessment (PRA) techniques have traditionally been used to identify accident conditions and transients. Traditional classical event tree methods utilize analysts’ knowledge and experience to identify the important timing of events in coordination with thermal-hydraulic modeling. These methods lack the capability to evaluate complex dynamic systems. In these systems, time and energy scales associated with transient events may vary as a function of transition times and energies to arrive at a different physical state. Dynamic PRA (DPRA) methods provide a more rigorous analysis of complex dynamic systems. Unfortunately DPRA methods introduce issues associated with combinatorial explosion of states. This study presents a methodology to address combinatorial explosion using a Branch-and-Bound algorithm applied to Dynamic Event Trees (DET), which utilize LENDIT (L – Length, E – Energy, N – Number, D – Distribution, I – Information, and T – Time) as well as a set theory to describe system, state, resource, and response (S2R2) sets to create bounding functions for the DET. The optimization of the DET in identifying high probability failure branches is extended to create a Phenomenological Identification and Ranking Table (PIRT) methodology to evaluate modeling parameters important to safety of those failure branches that have a high probability of failure. The PIRT can then be used as a tool to identify and evaluate the need for experimental validation of models that have the potential to reduce risk. Finally, in order to demonstrate this methodology, a Boiling Water Reactor (BWR) Station Blackout (SBO) case study is presented.« less

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

PubMed Central

Kamneva, Olga K; Rosenberg, Noah A

2017-01-01

Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species. For recent divergences between hybridizing species, when the influence of ILS is sufficiently high, likelihood methods outperform parsimony and consensus methods, which erroneously identify extra hybridizations. The more sophisticated likelihood methods, however, are affected by gene tree errors to a greater extent than are consensus and parsimony. PMID:28469378

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

Extreme Drought Event and Shrub Invasion Reduce Oak Trees Functioning and Resilience on Water-Limited Ecosystems

NASA Astrophysics Data System (ADS)

Caldeira, M. C.; Lobo-do-Vale, R.; Lecomte, X.; David, T. S.; Pinto, J. G.; Bugalho, M. N.; Werner, C.

2016-12-01

Extreme droughts and plant invasions are major drivers of global change that can critically affect ecosystem functioning. Shrub encroachment is increasing in many regions worldwide and extreme events are projected to increase in frequency and intensity, namely in the Mediterranean region. Nevertheless, little is known about how these drivers may interact and affect ecosystem functioning and resilience Using a manipulative shrub removal experiment and the co-occurrence of an extreme drought event in a Mediterranean oak woodland, we show that the combination of native shrub invasion and extreme drought reduced ecosystem transpiration and the resilience of the key-stone oak tree species. We established six 25 x 25 m paired plots in a shrub (Cistus ladanifer L.) encroached Mediterranean cork-oak (Quercus suber L.) woodland. We measured sapflow and pre-dawn leaf water potential of trees and shrubs and soil water content in all plots during four years. We determined the resilience of tree transpiration to evaluate to what extent trees recovered from the extreme drought event. From February to November 2011 we conducted baseline measurements for plot comparison. In November 2011 all the shrubs from one of all the paired plots were cut and removed. Ecosystem transpiration was dominated by the water use of the invasive shrub, which further increased after the extreme drought. Simultaneously, tree transpiration in invaded plots declined more sharply (67 ± 13 %) than in plots cleared from shrubs (31 ± 11%) relative to the pre-drought year (2011). Trees in invaded plots were not able to recover in the following wetter year showing lower resilience to the extreme drought event. Our results imply that in Mediterranean-type of climates invasion by water spending species coupled with the projected recurrent extreme droughts will cause critical drought tolerance thresholds of trees to be overcome, thus increasing the probability of tree mortality.

Lognormal Approximations of Fault Tree Uncertainty Distributions.

PubMed

El-Shanawany, Ashraf Ben; Ardron, Keith H; Walker, Simon P

2018-01-26

Fault trees are used in reliability modeling to create logical models of fault combinations that can lead to undesirable events. The output of a fault tree analysis (the top event probability) is expressed in terms of the failure probabilities of basic events that are input to the model. Typically, the basic event probabilities are not known exactly, but are modeled as probability distributions: therefore, the top event probability is also represented as an uncertainty distribution. Monte Carlo methods are generally used for evaluating the uncertainty distribution, but such calculations are computationally intensive and do not readily reveal the dominant contributors to the uncertainty. In this article, a closed-form approximation for the fault tree top event uncertainty distribution is developed, which is applicable when the uncertainties in the basic events of the model are lognormally distributed. The results of the approximate method are compared with results from two sampling-based methods: namely, the Monte Carlo method and the Wilks method based on order statistics. It is shown that the closed-form expression can provide a reasonable approximation to results obtained by Monte Carlo sampling, without incurring the computational expense. The Wilks method is found to be a useful means of providing an upper bound for the percentiles of the uncertainty distribution while being computationally inexpensive compared with full Monte Carlo sampling. The lognormal approximation method and Wilks's method appear attractive, practical alternatives for the evaluation of uncertainty in the output of fault trees and similar multilinear models. © 2018 Society for Risk Analysis.

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

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

Stand-structural effects on Heterobasidion abietinum-related mortality following drought events in Abies pinsapo.

PubMed

Linares, Juan Carlos; Camarero, Jesús Julio; Bowker, Matthew A; Ochoa, Victoria; Carreira, José Antonio

2010-12-01

Climate change may affect tree-pathogen interactions. This possibility has important implications for drought-prone forests, where stand dynamics and disease pathogenicity are especially sensitive to climatic stress. In addition, stand structural attributes including density-dependent tree-to-tree competition may modulate the stands' resistance to drought events and pathogen outbreaks. To assess the effects of stand structure on root-rot-related mortality after severe droughts, we focused on Heterobasidion abietinum mortality in relict Spanish stands of Abies pinsapo, a drought-sensitive fir. We compared stand attributes and tree spatial patterns in three plots with H. abietinum root-rot disease and three plots without root-rot. Point-pattern analyses were used to investigate the scale and extent of mortality patterns and to test hypotheses related to the spread of the disease. Dendrochronology was used to date the year of death and to assess the association between droughts and growth decline. We applied a structural equation modelling approach to test if tree mortality occurs more rapidly than predicted by a simple distance model when trees are subjected to high tree-to-tree competition and following drought events. Contrary to expectations of drought mortality, the effect of precipitation on the year of death was strong and negative, indicating that a period of high precipitation induced an earlier tree death. Competition intensity, related to the size and density of neighbour trees, also induced an earlier tree death. The effect of distance to the disease focus was negligible except in combination with intensive competition. Our results indicate that infected trees have decreased ability to withstand drought stress, and demonstrate that tree-to-tree competition and fungal infection act as predisposing factors of forest decline and mortality.

Risk Management in Complex Construction Projects that Apply Renewable Energy Sources: A Case Study of the Realization Phase of the Energis Educational and Research Intelligent Building

NASA Astrophysics Data System (ADS)

Krechowicz, Maria

2017-10-01

Nowadays, one of the characteristic features of construction industry is an increased complexity of a growing number of projects. Almost each construction project is unique, has its project-specific purpose, its own project structural complexity, owner’s expectations, ground conditions unique to a certain location, and its own dynamics. Failure costs and costs resulting from unforeseen problems in complex construction projects are very high. Project complexity drivers pose many vulnerabilities to a successful completion of a number of projects. This paper discusses the process of effective risk management in complex construction projects in which renewable energy sources were used, on the example of the realization phase of the ENERGIS teaching-laboratory building, from the point of view of DORBUD S.A., its general contractor. This paper suggests a new approach to risk management for complex construction projects in which renewable energy sources were applied. The risk management process was divided into six stages: gathering information, identification of the top, critical project risks resulting from the project complexity, construction of the fault tree for each top, critical risks, logical analysis of the fault tree, quantitative risk assessment applying fuzzy logic and development of risk response strategy. A new methodology for the qualitative and quantitative risk assessment for top, critical risks in complex construction projects was developed. Risk assessment was carried out applying Fuzzy Fault Tree analysis on the example of one top critical risk. Application of the Fuzzy sets theory to the proposed model allowed to decrease uncertainty and eliminate problems with gaining the crisp values of the basic events probability, common during expert risk assessment with the objective to give the exact risk score of each unwanted event probability.

Estimating and validating ground-based timber harvesting production through computer simulation

Treesearch

Jingxin Wang; Chris B. LeDoux

2003-01-01

Estimating ground-based timber harvesting systems production with an object oriented methodology was investigated. The estimation model developed generates stands of trees, simulates chain saw, drive-to-tree feller-buncher, swing-to-tree single-grip harvester felling, and grapple skidder and forwarder extraction activities, and analyzes costs and productivity. It also...

A stochastic multiple imputation algorithm for missing covariate data in tree-structured survival analysis.

PubMed

Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati

2010-12-20

Missing covariate data present a challenge to tree-structured methodology due to the fact that a single tree model, as opposed to an estimated parameter value, may be desired for use in a clinical setting. To address this problem, we suggest a multiple imputation algorithm that adds draws of stochastic error to a tree-based single imputation method presented by Conversano and Siciliano (Technical Report, University of Naples, 2003). Unlike previously proposed techniques for accommodating missing covariate data in tree-structured analyses, our methodology allows the modeling of complex and nonlinear covariate structures while still resulting in a single tree model. We perform a simulation study to evaluate our stochastic multiple imputation algorithm when covariate data are missing at random and compare it to other currently used methods. Our algorithm is advantageous for identifying the true underlying covariate structure when complex data and larger percentages of missing covariate observations are present. It is competitive with other current methods with respect to prediction accuracy. To illustrate our algorithm, we create a tree-structured survival model for predicting time to treatment response in older, depressed adults. Copyright © 2010 John Wiley & Sons, Ltd.

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...

Assessment of xylem phenology: a first attempt to verify its accuracy and precision.

PubMed

Lupi, C; Rossi, S; Vieira, J; Morin, H; Deslauriers, A

2014-01-01

This manuscript aims to evaluate the precision and accuracy of current methodology for estimating xylem phenology and tracheid production in trees. Through a simple approach, sampling at two positions on the stem of co-dominant black spruce trees in two sites of the boreal forest of Quebec, we were able to quantify variability among sites, between trees and within a tree for different variables. We demonstrated that current methodology is accurate for the estimation of the onset of xylogenesis, while the accuracy for the evaluation of the ending of xylogenesis may be improved by sampling at multiple positions on the stem. The pattern of variability in different phenological variables and cell production allowed us to advance a novel hypothesis on the shift in the importance of various drivers of xylogenesis, from factors mainly varying at the level of site (e.g., climate) at the beginning of the growing season to factors varying at the level of individual trees (e.g., possibly genetic variability) at the end of the growing season.

The role of hybridization in facilitating tree invasion

USDA-ARS?s Scientific Manuscript database

Hybridization events can generate additional genetic diversity on which natural selection can act and at times enhance invasiveness of the species. Invasive tree species are a growing ecological concern worldwide, and some of these invasions involve hybridization events pre- or post-introduction. Th...

Dynamic travel time estimation using regression trees.

DOT National Transportation Integrated Search

2008-10-01

This report presents a methodology for travel time estimation by using regression trees. The dissemination of travel time information has become crucial for effective traffic management, especially under congested road conditions. In the absence of c...

A review for identification of initiating events in event tree development process on nuclear power plants

NASA Astrophysics Data System (ADS)

Riyadi, Eko H.

2014-09-01

Initiating event is defined as any event either internal or external to the nuclear power plants (NPPs) that perturbs the steady state operation of the plant, if operating, thereby initiating an abnormal event such as transient or loss of coolant accident (LOCA) within the NPPs. These initiating events trigger sequences of events that challenge plant control and safety systems whose failure could potentially lead to core damage or large early release. Selection for initiating events consists of two steps i.e. first step, definition of possible events, such as by evaluating a comprehensive engineering, and by constructing a top level logic model. Then the second step, grouping of identified initiating event's by the safety function to be performed or combinations of systems responses. Therefore, the purpose of this paper is to discuss initiating events identification in event tree development process and to reviews other probabilistic safety assessments (PSA). The identification of initiating events also involves the past operating experience, review of other PSA, failure mode and effect analysis (FMEA), feedback from system modeling, and master logic diagram (special type of fault tree). By using the method of study for the condition of the traditional US PSA categorization in detail, could be obtained the important initiating events that are categorized into LOCA, transients and external events.

Systems Modeling to Implement Integrated System Health Management Capability

NASA Technical Reports Server (NTRS)

Figueroa, Jorge F.; Walker, Mark; Morris, Jonathan; Smith, Harvey; Schmalzel, John

2007-01-01

ISHM capability includes: detection of anomalies, diagnosis of causes of anomalies, prediction of future anomalies, and user interfaces that enable integrated awareness (past, present, and future) by users. This is achieved by focused management of data, information and knowledge (DIaK) that will likely be distributed across networks. Management of DIaK implies storage, sharing (timely availability), maintaining, evolving, and processing. Processing of DIaK encapsulates strategies, methodologies, algorithms, etc. focused on achieving high ISHM Functional Capability Level (FCL). High FCL means a high degree of success in detecting anomalies, diagnosing causes, predicting future anomalies, and enabling health integrated awareness by the user. A model that enables ISHM capability, and hence, DIaK management, is denominated the ISHM Model of the System (IMS). We describe aspects of the IMS that focus on processing of DIaK. Strategies, methodologies, and algorithms require proper context. We describe an approach to define and use contexts, implementation in an object-oriented software environment (G2), and validation using actual test data from a methane thruster test program at NASA SSC. Context is linked to existence of relationships among elements of a system. For example, the context to use a strategy to detect leak is to identify closed subsystems (e.g. bounded by closed valves and by tanks) that include pressure sensors, and check if the pressure is changing. We call these subsystems Pressurizable Subsystems. If pressure changes are detected, then all members of the closed subsystem become suspect of leakage. In this case, the context is defined by identifying a subsystem that is suitable for applying a strategy. Contexts are defined in many ways. Often, a context is defined by relationships of function (e.g. liquid flow, maintaining pressure, etc.), form (e.g. part of the same component, connected to other components, etc.), or space (e.g. physically close, touching the same common element, etc.). The context might be defined dynamically (if conditions for the context appear and disappear dynamically) or statically. Although this approach is akin to case-based reasoning, we are implementing it using a software environment that embodies tools to define and manage relationships (of any nature) among objects in a very intuitive manner. Context for higher level inferences (that use detected anomalies or events), primarily for diagnosis and prognosis, are related to causal relationships. This is useful to develop root-cause analysis trees showing an event linked to its possible causes and effects. The innovation pertaining to RCA trees encompasses use of previously defined subsystems as well as individual elements in the tree. This approach allows more powerful implementations of RCA capability in object-oriented environments. For example, if a pressurizable subsystem is leaking, its root-cause representation within an RCA tree will show that the cause is that all elements of that subsystem are suspect of leak. Such a tree would apply to all instances of leak-events detected and all elements in all pressurizable subsystems in the system. Example subsystems in our environment to build IMS include: Pressurizable Subsystem, Fluid-Fill Subsystem, Flow-Thru-Valve Subsystem, and Fluid Supply Subsystem. The software environment for IMS is designed to potentially allow definition of any relationship suitable to create a context to achieve ISHM capability.

Optimal tree increment models for the Northeastern United Statesq

Treesearch

Don C. Bragg

2003-01-01

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

Optimal Tree Increment Models for the Northeastern United States

Treesearch

Don C. Bragg

2005-01-01

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

Where to plant urban trees? A spatially explicit methodology to explore ecosystem service tradeoffs

Treesearch

E.W. Bodnaruk; C.N. Kroll; Y. Yang; S. Hirabayashi; David Nowak; T.A. Endreny

2017-01-01

Urban trees can help mitigate some of the environmental degradation linked to the rapid urbanization of humanity. Many municipalities are implementing ambitious tree planting programs to help remove air pollution, mitigate urban heat island effects, and provide other ecosystem services and benefits but lack quantitative tools to explore priority planting locations and...

Estimating tree biomass regressions and their error, proceedings of the workshop on tree biomass regression functions and their contribution to the error

Treesearch

Eric H. Wharton; Tiberius Cunia

1987-01-01

Proceedings of a workshop co-sponsored by the USDA Forest Service, the State University of New York, and the Society of American Foresters. Presented were papers on the methodology of sample tree selection, tree biomass measurement, construction of biomass tables and estimation of their error, and combining the error of biomass tables with that of the sample plots or...

RecPhyloXML - a format for reconciled gene trees.

PubMed

Duchemin, Wandrille; Gence, Guillaume; Arigon Chifolleau, Anne-Muriel; Arvestad, Lars; Bansal, Mukul S; Berry, Vincent; Boussau, Bastien; Chevenet, François; Comte, Nicolas; Davín, Adrián A; Dessimoz, Christophe; Dylus, David; Hasic, Damir; Mallo, Diego; Planel, Rémi; Posada, David; Scornavacca, Celine; Szöllosi, Gergely; Zhang, Louxin; Tannier, Éric; Daubin, Vincent

2018-05-14

A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. http://phylariane.univ-lyon1.fr/recphyloxml/. wandrille.duchemin@univ-lyon1.fr. There is no supplementary data associated with this publication.

Large-scale wind disturbances promote tree diversity in a Central Amazon forest.

PubMed

Marra, Daniel Magnabosco; Chambers, Jeffrey Q; Higuchi, Niro; Trumbore, Susan E; Ribeiro, Gabriel H P M; Dos Santos, Joaquim; Negrón-Juárez, Robinson I; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m(2)) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583 ± 46 trees ha(-1)) (mean ± 99% Confidence Interval) and basal area (26.7 ± 2.4 m(2) ha(-1)). Highly impacted areas had tree density and basal area as low as 120 trees ha(-1) and 14.9 m(2) ha(-1), respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m(2)) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

PubMed Central

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; Trumbore, Susan E.; Ribeiro, Gabriel H. P. M.; dos Santos, Joaquim; Negrón-Juárez, Robinson I.; Reu, Björn; Wirth, Christian

2014-01-01

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha−1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m2 ha−1). Highly impacted areas had tree density and basal area as low as 120 trees ha−1 and 14.9 m2 ha−1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level. PMID:25099118

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

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

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

DOE PAGES

Marra, Daniel Magnabosco; Chambers, Jeffrey Q.; Higuchi, Niro; ...

2014-08-06

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m 2) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 tomore » 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha -1) (mean±99% Confidence Interval) and basal area (26.7±2.4 m 2 ha -1). Highly impacted areas had tree density and basal area as low as 120 trees ha -1 and 14.9 m 2 ha -1, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m 2) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.« less

Traversing the tangle: algorithms and applications for cophylogenetic studies.

PubMed

Charleston, Michael A; Perkins, Susan L

2006-02-01

Cophylogenetic analysis supposes that two or more phylogenetic trees for linked groups have been constructed, and explores the relationships the trees have with each other. These types of analyses are most commonly used to assess relationships between hosts and their parasites, however the methodology can also be applied to diverse types of problems such as an examination of the phylogenies of genes with respect to those of organisms or those of geographic areas and the organisms that reside there. The working hypothesis is that the trees are correct, though sometimes attempts are made to take into account their uncertainty. Cophylogeny is computationally hard: that is, there are no known fast methods to compute relationships among such trees for any but the simplest of models. A review of methodology that has been developed to examine cophylogenetic relationships is presented and a brief discussion of some medically relevant examples is given.

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

PubMed Central

Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Soltis, Douglas E.; Wong, Gane Ka-Shu; Carpenter, Eric J.; Zhang, Yong; Chen, Li; Yan, Zhixiang; Xie, Yinlong; Sage, Rowan F.; Covshoff, Sarah; Hibberd, Julian M.; Nelson, Matthew N.; Smith, Stephen A.

2015-01-01

Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups. PMID:25837578

Exposure of trees to drought-induced die-off is defined by a common climatic threshold across different vegetation types

PubMed Central

Mitchell, Patrick J; O'Grady, Anthony P; Hayes, Keith R; Pinkard, Elizabeth A

2014-01-01

Increases in drought and temperature stress in forest and woodland ecosystems are thought to be responsible for the rise in episodic mortality events observed globally. However, key climatic drivers common to mortality events and the impacts of future extreme droughts on tree survival have not been evaluated. Here, we characterize climatic drivers associated with documented tree die-off events across Australia using standardized climatic indices to represent the key dimensions of drought stress for a range of vegetation types. We identify a common probabilistic threshold associated with an increased risk of die-off across all the sites that we examined. We show that observed die-off events occur when water deficits and maximum temperatures are high and exist outside 98% of the observed range in drought intensity; this threshold was evident at all sites regardless of vegetation type and climate. The observed die-off events also coincided with at least one heat wave (three consecutive days above the 90th percentile for maximum temperature), emphasizing a pivotal role of heat stress in amplifying tree die-off and mortality processes. The joint drought intensity and maximum temperature distributions were modeled for each site to describe the co-occurrence of both hot and dry conditions and evaluate future shifts in climatic thresholds associated with the die-off events. Under a relatively dry and moderate warming scenario, the frequency of droughts capable of inducing significant tree die-off across Australia could increase from 1 in 24 years to 1 in 15 years by 2050, accompanied by a doubling in the occurrence of associated heat waves. By defining commonalities in drought conditions capable of inducing tree die-off, we show a strong interactive effect of water and high temperature stress and provide a consistent approach for assessing changes in the exposure of ecosystems to extreme drought events. PMID:24772285

Preventing medical errors by designing benign failures.

PubMed

Grout, John R

2003-07-01

One way to successfully reduce medical errors is to design health care systems that are more resistant to the tendencies of human beings to err. One interdisciplinary approach entails creating design changes, mitigating human errors, and making human error irrelevant to outcomes. This approach is intended to facilitate the creation of benign failures, which have been called mistake-proofing devices and forcing functions elsewhere. USING FAULT TREES TO DESIGN FORCING FUNCTIONS: A fault tree is a graphical tool used to understand the relationships that either directly cause or contribute to the cause of a particular failure. A careful analysis of a fault tree enables the analyst to anticipate how the process will behave after the change. EXAMPLE OF AN APPLICATION: A scenario in which a patient is scalded while bathing can serve as an example of how multiple fault trees can be used to design forcing functions. The first fault tree shows the undesirable event--patient scalded while bathing. The second fault tree has a benign event--no water. Adding a scald valve changes the outcome from the undesirable event ("patient scalded while bathing") to the benign event ("no water") Analysis of fault trees does not ensure or guarantee that changes necessary to eliminate error actually occur. Most mistake-proofing is used to prevent simple errors and to create well-defended processes, but complex errors can also result. The utilization of mistake-proofing or forcing functions can be thought of as changing the logic of a process. Errors that formerly caused undesirable failures can be converted into the causes of benign failures. The use of fault trees can provide a variety of insights into the design of forcing functions that will improve patient safety.

Boolean logic tree of graphene-based chemical system for molecular computation and intelligent molecular search query.

PubMed

Huang, Wei Tao; Luo, Hong Qun; Li, Nian Bing

2014-05-06

The most serious, and yet unsolved, problem of constructing molecular computing devices consists in connecting all of these molecular events into a usable device. This report demonstrates the use of Boolean logic tree for analyzing the chemical event network based on graphene, organic dye, thrombin aptamer, and Fenton reaction, organizing and connecting these basic chemical events. And this chemical event network can be utilized to implement fluorescent combinatorial logic (including basic logic gates and complex integrated logic circuits) and fuzzy logic computing. On the basis of the Boolean logic tree analysis and logic computing, these basic chemical events can be considered as programmable "words" and chemical interactions as "syntax" logic rules to construct molecular search engine for performing intelligent molecular search query. Our approach is helpful in developing the advanced logic program based on molecules for application in biosensing, nanotechnology, and drug delivery.

Widespread Amazon forest tree mortality from a single cross-basin squall line event

NASA Astrophysics Data System (ADS)

Negrón-Juárez, Robinson I.; Chambers, Jeffrey Q.; Guimaraes, Giuliano; Zeng, Hongcheng; Raupp, Carlos F. M.; Marra, Daniel M.; Ribeiro, Gabriel H. P. M.; Saatchi, Sassan S.; Nelson, Bruce W.; Higuchi, Niro

2010-08-01

Climate change is expected to increase the intensity of extreme precipitation events in Amazonia that in turn might produce more forest blowdowns associated with convective storms. Yet quantitative tree mortality associated with convective storms has never been reported across Amazonia, representing an important additional source of carbon to the atmosphere. Here we demonstrate that a single squall line (aligned cluster of convective storm cells) propagating across Amazonia in January, 2005, caused widespread forest tree mortality and may have contributed to the elevated mortality observed that year. Forest plot data demonstrated that the same year represented the second highest mortality rate over a 15-year annual monitoring interval. Over the Manaus region, disturbed forest patches generated by the squall followed a power-law distribution (scaling exponent α = 1.48) and produced a mortality of 0.3-0.5 million trees, equivalent to 30% of the observed annual deforestation reported in 2005 over the same area. Basin-wide, potential tree mortality from this one event was estimated at 542 ± 121 million trees, equivalent to 23% of the mean annual biomass accumulation estimated for these forests. Our results highlight the vulnerability of Amazon trees to wind-driven mortality associated with convective storms. Storm intensity is expected to increase with a warming climate, which would result in additional tree mortality and carbon release to the atmosphere, with the potential to further warm the climate system.

Technology transfer by means of fault tree synthesis

NASA Astrophysics Data System (ADS)

Batzias, Dimitris F.

2012-12-01

Since Fault Tree Analysis (FTA) attempts to model and analyze failure processes of engineering, it forms a common technique for good industrial practice. On the contrary, fault tree synthesis (FTS) refers to the methodology of constructing complex trees either from dentritic modules built ad hoc or from fault tress already used and stored in a Knowledge Base. In both cases, technology transfer takes place in a quasi-inductive mode, from partial to holistic knowledge. In this work, an algorithmic procedure, including 9 activity steps and 3 decision nodes is developed for performing effectively this transfer when the fault under investigation occurs within one of the latter stages of an industrial procedure with several stages in series. The main parts of the algorithmic procedure are: (i) the construction of a local fault tree within the corresponding production stage, where the fault has been detected, (ii) the formation of an interface made of input faults that might occur upstream, (iii) the fuzzy (to count for uncertainty) multicriteria ranking of these faults according to their significance, and (iv) the synthesis of an extended fault tree based on the construction of part (i) and on the local fault tree of the first-ranked fault in part (iii). An implementation is presented, referring to 'uneven sealing of Al anodic film', thus proving the functionality of the developed methodology.

Stomatal oscillations in olive trees: analysis and methodological implications.

PubMed

López-Bernal, Alvaro; García-Tejera, Omar; Testi, Luca; Orgaz, Francisco; Villalobos, Francisco J

2018-04-01

Stomatal oscillations have long been disregarded in the literature despite the fact that the phenomenon has been described for a variety of plant species. This study aims to characterize the occurrence of oscillations in olive trees (Olea europaea L.) under different growing conditions and its methodological implications. Three experiments with young potted olives and one with large field-grown trees were performed. Sap flow measurements were always used to monitor the occurrence of oscillations, with additional determinations of trunk diameter variations and leaf-level stomatal conductance, photosynthesis and water potential also conducted in some cases. Strong oscillations with periods of 30-60 min were generally observed for young trees, while large field trees rarely showed significant oscillations. Severe water stress led to the disappearance of oscillations, but moderate water deficits occasionally promoted them. Simultaneous oscillations were also found for leaf stomatal conductance, leaf photosynthesis and trunk diameter, with the former presenting the highest amplitudes. The strong oscillations found in young potted olive trees preclude the use of infrequent measurements of stomatal conductance and related variables to characterize differences between trees of different cultivars or subjected to different experimental treatments. Under these circumstances, our results suggest that reliable estimates could be obtained using measurement intervals below 15 min.

Methodology Investigation Characterization of Test Environment.

DTIC Science & Technology

1979-08-01

canopy trees may be briefly deciduous, especially when flowering . Number of tree species is very large. Canopy: Trees 145 to 180 feet (45 to 55 m) tall...rooted palms are abundant. Shrub layer: Dwarf palms 5 to 8 feet (1.5 to 2.5 m) tall with undi- vided leaves usually abundant. Giant herbs with banana ...forest cover for agricultural purposes, corn and banana culture. These sites are now either abandoned or poorly maintained; in either case, tree

An object-based approach for tree species extraction from digital orthophoto maps

NASA Astrophysics Data System (ADS)

Jamil, Akhtar; Bayram, Bulent

2018-05-01

Tree segmentation is an active and ongoing research area in the field of photogrammetry and remote sensing. It is more challenging due to both intra-class and inter-class similarities among various tree species. In this study, we exploited various statistical features for extraction of hazelnut trees from 1 : 5000 scaled digital orthophoto maps. Initially, the non-vegetation areas were eliminated using traditional normalized difference vegetation index (NDVI) followed by application of mean shift segmentation for transforming the pixels into meaningful homogeneous objects. In order to eliminate false positives, morphological opening and closing was employed on candidate objects. A number of heuristics were also derived to eliminate unwanted effects such as shadow and bounding box aspect ratios, before passing them into the classification stage. Finally, a knowledge based decision tree was constructed to distinguish the hazelnut trees from rest of objects which include manmade objects and other type of vegetation. We evaluated the proposed methodology on 10 sample orthophoto maps obtained from Giresun province in Turkey. The manually digitized hazelnut tree boundaries were taken as reference data for accuracy assessment. Both manually digitized and segmented tree borders were converted into binary images and the differences were calculated. According to the obtained results, the proposed methodology obtained an overall accuracy of more than 85 % for all sample images.

New methods, algorithms, and software for rapid mapping of tree positions in coordinate forest plots

Treesearch

A. Dan Wilson

2000-01-01

The theories and methodologies for two new tree mapping methods, the Sequential-target method and the Plot-origin radial method, are described. The methods accommodate the use of any conventional distance measuring device and compass to collect horizontal distance and azimuth data between source or reference positions (origins) and target trees. Conversion equations...

Synergy of extreme drought and shrub invasion reduce ecosystem functioning and resilience in water-limited climates

PubMed Central

Caldeira, Maria C.; Lecomte, Xavier; David, Teresa S.; Pinto, Joaquim G.; Bugalho, Miguel N.; Werner, Christiane

2015-01-01

Extreme drought events and plant invasions are major drivers of global change that can critically affect ecosystem functioning and alter ecosystem-atmosphere exchange. Invaders are expanding worldwide and extreme drought events are projected to increase in frequency and intensity. However, very little is known on how these drivers may interact to affect the functioning and resilience of ecosystems to extreme events. Using a manipulative shrub removal experiment and the co-occurrence of an extreme drought event (2011/2012) in a Mediterranean woodland, we show that native shrub invasion and extreme drought synergistically reduced ecosystem transpiration and the resilience of key-stone oak tree species. Ecosystem transpiration was dominated by the water use of the invasive shrub Cistus ladanifer, which further increased after the extreme drought event. Meanwhile, the transpiration of key-stone tree species decreased, indicating a competitive advantage in favour of the invader. Our results suggest that in Mediterranean-type climates the invasion of water spending species and projected recurrent extreme drought events may synergistically cause critical drought tolerance thresholds of key-stone tree species to be surpassed, corroborating observed higher tree mortality in the invaded ecosystems. Ultimately, this may shift seasonally water limited ecosystems into less desirable alternative states dominated by water spending invasive shrubs. PMID:26461978

Synergy of extreme drought and shrub invasion reduce ecosystem functioning and resilience in water-limited climates.

PubMed

Caldeira, Maria C; Lecomte, Xavier; David, Teresa S; Pinto, Joaquim G; Bugalho, Miguel N; Werner, Christiane

2015-10-13

Extreme drought events and plant invasions are major drivers of global change that can critically affect ecosystem functioning and alter ecosystem-atmosphere exchange. Invaders are expanding worldwide and extreme drought events are projected to increase in frequency and intensity. However, very little is known on how these drivers may interact to affect the functioning and resilience of ecosystems to extreme events. Using a manipulative shrub removal experiment and the co-occurrence of an extreme drought event (2011/2012) in a Mediterranean woodland, we show that native shrub invasion and extreme drought synergistically reduced ecosystem transpiration and the resilience of key-stone oak tree species. Ecosystem transpiration was dominated by the water use of the invasive shrub Cistus ladanifer, which further increased after the extreme drought event. Meanwhile, the transpiration of key-stone tree species decreased, indicating a competitive advantage in favour of the invader. Our results suggest that in Mediterranean-type climates the invasion of water spending species and projected recurrent extreme drought events may synergistically cause critical drought tolerance thresholds of key-stone tree species to be surpassed, corroborating observed higher tree mortality in the invaded ecosystems. Ultimately, this may shift seasonally water limited ecosystems into less desirable alternative states dominated by water spending invasive shrubs.

Synergy of extreme drought and shrub invasion reduce ecosystem functioning and resilience in water-limited climates

NASA Astrophysics Data System (ADS)

Caldeira, Maria C.; Lecomte, Xavier; David, Teresa S.; Pinto, Joaquim G.; Bugalho, Miguel N.; Werner, Christiane

2015-10-01

Extreme drought events and plant invasions are major drivers of global change that can critically affect ecosystem functioning and alter ecosystem-atmosphere exchange. Invaders are expanding worldwide and extreme drought events are projected to increase in frequency and intensity. However, very little is known on how these drivers may interact to affect the functioning and resilience of ecosystems to extreme events. Using a manipulative shrub removal experiment and the co-occurrence of an extreme drought event (2011/2012) in a Mediterranean woodland, we show that native shrub invasion and extreme drought synergistically reduced ecosystem transpiration and the resilience of key-stone oak tree species. Ecosystem transpiration was dominated by the water use of the invasive shrub Cistus ladanifer, which further increased after the extreme drought event. Meanwhile, the transpiration of key-stone tree species decreased, indicating a competitive advantage in favour of the invader. Our results suggest that in Mediterranean-type climates the invasion of water spending species and projected recurrent extreme drought events may synergistically cause critical drought tolerance thresholds of key-stone tree species to be surpassed, corroborating observed higher tree mortality in the invaded ecosystems. Ultimately, this may shift seasonally water limited ecosystems into less desirable alternative states dominated by water spending invasive shrubs.

Methodology for the Incorporation of Passive Component Aging Modeling into the RAVEN/ RELAP-7 Environment

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

Mandelli, Diego; Rabiti, Cristian; Cogliati, Joshua

2014-11-01

Passive system, structure and components (SSCs) will degrade over their operation life and this degradation may cause to reduction in the safety margins of a nuclear power plant. In traditional probabilistic risk assessment (PRA) using the event-tree/fault-tree methodology, passive SSC failure rates are generally based on generic plant failure data and the true state of a specific plant is not reflected realistically. To address aging effects of passive SSCs in the traditional PRA methodology [1] does consider physics based models that account for the operating conditions in the plant, however, [1] does not include effects of surveillance/inspection. This paper representsmore » an overall methodology for the incorporation of aging modeling of passive components into the RAVEN/RELAP-7 environment which provides a framework for performing dynamic PRA. Dynamic PRA allows consideration of both epistemic and aleatory uncertainties (including those associated with maintenance activities) in a consistent phenomenological and probabilistic framework and is often needed when there is complex process/hardware/software/firmware/ human interaction [2]. Dynamic PRA has gained attention recently due to difficulties in the traditional PRA modeling of aging effects of passive components using physics based models and also in the modeling of digital instrumentation and control systems. RAVEN (Reactor Analysis and Virtual control Environment) [3] is a software package under development at the Idaho National Laboratory (INL) as an online control logic driver and post-processing tool. It is coupled to the plant transient code RELAP-7 (Reactor Excursion and Leak Analysis Program) also currently under development at INL [3], as well as RELAP 5 [4]. The overall methodology aims to: • Address multiple aging mechanisms involving large number of components in a computational feasible manner where sequencing of events is conditioned on the physical conditions predicted in a simulation environment such as RELAP-7. • Identify the risk-significant passive components, their failure modes and anticipated rates of degradation • Incorporate surveillance and maintenance activities and their effects into the plant state and into component aging progress. • Asses aging affects in a dynamic simulation environment 1. C. L. SMITH, V. N. SHAH, T. KAO, G. APOSTOLAKIS, “Incorporating Ageing Effects into Probabilistic Risk Assessment –A Feasibility Study Utilizing Reliability Physics Models,” NUREG/CR-5632, USNRC, (2001). 2. T. ALDEMIR, “A Survey of Dynamic Methodologies for Probabilistic Safety Assessment of Nuclear Power Plants, Annals of Nuclear Energy, 52, 113-124, (2013). 3. C. RABITI, A. ALFONSI, J. COGLIATI, D. MANDELLI and R. KINOSHITA “Reactor Analysis and Virtual Control Environment (RAVEN) FY12 Report,” INL/EXT-12-27351, (2012). 4. D. ANDERS et.al, "RELAP-7 Level 2 Milestone Report: Demonstration of a Steady State Single Phase PWR Simulation with RELAP-7," INL/EXT-12-25924, (2012).« less

A review for identification of initiating events in event tree development process on nuclear power plants

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

Riyadi, Eko H., E-mail: e.riyadi@bapeten.go.id

2014-09-30

Initiating event is defined as any event either internal or external to the nuclear power plants (NPPs) that perturbs the steady state operation of the plant, if operating, thereby initiating an abnormal event such as transient or loss of coolant accident (LOCA) within the NPPs. These initiating events trigger sequences of events that challenge plant control and safety systems whose failure could potentially lead to core damage or large early release. Selection for initiating events consists of two steps i.e. first step, definition of possible events, such as by evaluating a comprehensive engineering, and by constructing a top level logicmore » model. Then the second step, grouping of identified initiating event's by the safety function to be performed or combinations of systems responses. Therefore, the purpose of this paper is to discuss initiating events identification in event tree development process and to reviews other probabilistic safety assessments (PSA). The identification of initiating events also involves the past operating experience, review of other PSA, failure mode and effect analysis (FMEA), feedback from system modeling, and master logic diagram (special type of fault tree). By using the method of study for the condition of the traditional US PSA categorization in detail, could be obtained the important initiating events that are categorized into LOCA, transients and external events.« less

Patterns of drought tolerance in major European temperate forest trees: climatic drivers and levels of variability.

PubMed

Zang, Christian; Hartl-Meier, Claudia; Dittmar, Christoph; Rothe, Andreas; Menzel, Annette

2014-12-01

The future performance of native tree species under climate change conditions is frequently discussed, since increasingly severe and more frequent drought events are expected to become a major risk for forest ecosystems. To improve our understanding of the drought tolerance of the three common European temperate forest tree species Norway spruce, silver fir and common beech, we tested the influence of climate and tree-specific traits on the inter and intrasite variability in drought responses of these species. Basal area increment data from a large tree-ring network in Southern Germany and Alpine Austria along a climatic cline from warm-dry to cool-wet conditions were used to calculate indices of tolerance to drought events and their variability at the level of individual trees and populations. General patterns of tolerance indicated a high vulnerability of Norway spruce in comparison to fir and beech and a strong influence of bioclimatic conditions on drought response for all species. On the level of individual trees, low-growth rates prior to drought events, high competitive status and low age favored resilience in growth response to drought. Consequently, drought events led to heterogeneous and variable response patterns in forests stands. These findings may support the idea of deliberately using spontaneous selection and adaption effects as a passive strategy of forest management under climate change conditions, especially a strong directional selection for more tolerant individuals when frequency and intensity of summer droughts will increase in the course of global climate change. © 2014 John Wiley & Sons Ltd.

Structural system reliability calculation using a probabilistic fault tree analysis method

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

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

PubMed

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

2018-01-01

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

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

PubMed Central

Lindenbergh, Roderik; Rodríguez-Gonzálvez, Pablo

2018-01-01

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

Context-sensitive extraction of tree crown objects in urban areas using VHR satellite images

NASA Astrophysics Data System (ADS)

Ardila, Juan P.; Bijker, Wietske; Tolpekin, Valentyn A.; Stein, Alfred

2012-04-01

Municipalities need accurate and updated inventories of urban vegetation in order to manage green resources and estimate their return on investment in urban forestry activities. Earlier studies have shown that semi-automatic tree detection using remote sensing is a challenging task. This study aims to develop a reproducible geographic object-based image analysis (GEOBIA) methodology to locate and delineate tree crowns in urban areas using high resolution imagery. We propose a GEOBIA approach that considers the spectral, spatial and contextual characteristics of tree objects in the urban space. The study presents classification rules that exploit object features at multiple segmentation scales modifying the labeling and shape of image-objects. The GEOBIA methodology was implemented on QuickBird images acquired over the cities of Enschede and Delft (The Netherlands), resulting in an identification rate of 70% and 82% respectively. False negative errors concentrated on small trees and false positive errors in private gardens. The quality of crown boundaries was acceptable, with an overall delineation error <0.24 outside of gardens and backyards.

When are pathogen genome sequences informative of transmission events?

PubMed Central

Ferguson, Neil; Jombart, Thibaut

2018-01-01

Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data. PMID:29420641

Secure Embedded System Design Methodologies for Military Cryptographic Systems

DTIC Science & Technology

2016-03-31

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

Simple Methodologies to Estimate the Energy Amount Stored in a Tree Due to an Explosive Seed Dispersal Mechanism

ERIC Educational Resources Information Center

do Carmo, Eduardo; Hönnicke, Marcelo Goncalves

2018-01-01

There are different forms to introduce/illustrate the energy concepts for the basic physics students. The explosive seed dispersal mechanism found in a variety of trees could be one of them. Sibipiruna trees carry out fruits (pods) who show such an explosive mechanism. During the explosion, the pods throw out seeds several meters away. In this…

Reliability analysis of repairable systems using Petri nets and vague Lambda-Tau methodology.

PubMed

Garg, Harish

2013-01-01

The main objective of the paper is to developed a methodology, named as vague Lambda-Tau, for reliability analysis of repairable systems. Petri net tool is applied to represent the asynchronous and concurrent processing of the system instead of fault tree analysis. To enhance the relevance of the reliability study, vague set theory is used for representing the failure rate and repair times instead of classical(crisp) or fuzzy set theory because vague sets are characterized by a truth membership function and false membership functions (non-membership functions) so that sum of both values is less than 1. The proposed methodology involves qualitative modeling using PN and quantitative analysis using Lambda-Tau method of solution with the basic events represented by intuitionistic fuzzy numbers of triangular membership functions. Sensitivity analysis has also been performed and the effects on system MTBF are addressed. The methodology improves the shortcomings of the existing probabilistic approaches and gives a better understanding of the system behavior through its graphical representation. The washing unit of a paper mill situated in a northern part of India, producing approximately 200 ton of paper per day, has been considered to demonstrate the proposed approach. The results may be helpful for the plant personnel for analyzing the systems' behavior and to improve their performance by adopting suitable maintenance strategies. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

On Forests and Trees: A Response to Klingner.

ERIC Educational Resources Information Center

Neuman, Susan B.; Koskinen, Patricia

1993-01-01

Responds to criticisms raised in another article in this issue concerning a study of incidental word learning among second-language learners viewing captioned television. Suggests that the criticisms fail to "see the forest for the trees." Responds to specific methodological criticisms. (RS)

Selective Tree-ring Models: A Novel Method for Reconstructing Streamflow Using Tree Rings

NASA Astrophysics Data System (ADS)

Foard, M. B.; Nelson, A. S.; Harley, G. L.

2017-12-01

Surface water is among the most instrumental and vulnerable resources in the Northwest United States (NW). Recent observations show that overall water quantity is declining in streams across the region, while extreme flooding events occur more frequently. Historical streamflow models inform probabilities of extreme flow events (flood or drought) by describing frequency and duration of past events. There are numerous examples of tree-rings being utilized to reconstruct streamflow in the NW. These models confirm that tree-rings are highly accurate at predicting streamflow, however there are many nuances that limit their applicability through time and space. For example, most models predict streamflow from hydrologically altered rivers (e.g. dammed, channelized) which may hinder our ability to predict natural prehistoric flow. They also have a tendency to over/under-predict extreme flow events. Moreover, they often neglect to capture the changing relationships between tree-growth and streamflow over time and space. To address these limitations, we utilized national tree-ring and streamflow archives to investigate the relationships between the growth of multiple coniferous species and free-flowing streams across the NW using novel species-and site-specific streamflow models - a term we coined"selective tree-ring models." Correlation function analysis and regression modeling were used to evaluate the strengths and directions of the flow-growth relationships. Species with significant relationships in the same direction were identified as strong candidates for selective models. Temporal and spatial patterns of these relationships were examined using running correlations and inverse distance weighting interpolation, respectively. Our early results indicate that (1) species adapted to extreme climates (e.g. hot-dry, cold-wet) exhibit the most consistent relationships across space, (2) these relationships weaken in locations with mild climatic variability, and (3) some species appear to be strong candidates for predicting high flow events, while others may be better at pridicting drought. These findings indicate that selective models may outperform traditional models when reconstructing distinctive aspects of streamflow.

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

NASA Astrophysics Data System (ADS)

Šilhán, Karel; Stoffel, Markus

2015-05-01

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

Triggered surface slips in the Coachella Valley area associated with the 1992 Joshua Tree and Landers, California, Earthquakes

USGS Publications Warehouse

Rymer, M.J.

2000-01-01

The Coachella Valley area was strongly shaken by the 1992 Joshua Tree (23 April) and Landers (28 June) earthquakes, and both events caused triggered slip on active faults within the area. Triggered slip associated with the Joshua Tree earthquake was on a newly recognized fault, the East Wide Canyon fault, near the southwestern edge of the Little San Bernardino Mountains. Slip associated with the Landers earthquake formed along the San Andreas fault in the southeastern Coachella Valley. Surface fractures formed along the East Wide Canyon fault in association with the Joshua Tree earthquake. The fractures extended discontinuously over a 1.5-km stretch of the fault, near its southern end. Sense of slip was consistently right-oblique, west side down, similar to the long-term style of faulting. Measured offset values were small, with right-lateral and vertical components of slip ranging from 1 to 6 mm and 1 to 4 mm, respectively. This is the first documented historic slip on the East Wide Canyon fault, which was first mapped only months before the Joshua Tree earthquake. Surface slip associated with the Joshua Tree earthquake most likely developed as triggered slip given its 5 km distance from the Joshua Tree epicenter and aftershocks. As revealed in a trench investigation, slip formed in an area with only a thin (<3 m thick) veneer of alluvium in contrast to earlier documented triggered slip events in this region, all in the deep basins of the Salton Trough. A paleoseismic trench study in an area of 1992 surface slip revealed evidence of two and possibly three surface faulting events on the East Wide Canyon fault during the late Quaternary, probably latest Pleistocene (first event) and mid- to late Holocene (second two events). About two months after the Joshua Tree earthquake, the Landers earthquake then triggered slip on many faults, including the San Andreas fault in the southeastern Coachella Valley. Surface fractures associated with this event formed discontinuous breaks over a 54-km-long stretch of the fault, from the Indio Hills southeastward to Durmid Hill. Sense of slip was right-lateral; only locally was there a minor (~1 mm) vertical component of slip. Measured dextral displacement values ranged from 1 to 20 mm, with the largest amounts found in the Mecca Hills where large slip values have been measured following past triggered-slip events.

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

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

Extreme drought event and shrub invasion combine to reduce ecosystem functioning and resilience in water-limited climates

NASA Astrophysics Data System (ADS)

Caldeira, Maria; Lecomte, Xavier; David, Teresa; Pinto, Joaquim; Bugalho, Miguel; Werner, Christiane

2016-04-01

Extreme droughts and plant invasions are major drivers of global change that can critically affect ecosystem functioning. Shrub encroachment is increasing in many regions worldwide and extreme events are projected to increase in frequency and intensity, namely in the Mediterranean region. Nevertheless, little is known about how these drivers may interact and affect ecosystem functioning and resilience to extreme droughts. Using a manipulative shrub removal experiment and the co-occurrence of an extreme drought event (2011/2012) in a Mediterranean woodland, we show that the native shrub invasion and extreme drought combined to reduce ecosystem transpiration and the resilience of the key-stone oak tree species. We established six 25 x 25 m paired plots in a shrub (Cistus ladanifer L.) encroached Mediterranean cork-oak (Quercus suber L.) woodland. We measured sapflow and pre-dawn leaf water potential of trees and shrubs and soil water content in all plots during three years. We determined the resilience of tree transpiration to evaluate to what extent trees recovered from the extreme drought event. From February to November 2011 we conducted baseline measurements for plot comparison. In November 2011 all the shrubs from one of all the paired plots were cut and removed. Ecosystem transpiration was dominated by the water use of the invasive shrub, which further increased after the extreme drought. Simultaneously, tree transpiration in invaded plots declined much stronger (67 ± 13 %) than in plots cleared from shrubs (31 ± 11%) relative to the pre-drought year. Trees in invaded plots were not able to recover in the following wetter year showing lower resilience to the extreme drought event. Our results imply that in Mediterranean-type of climates invasion by water spending species can combine with projected recurrent extreme droughts causing critical drought tolerance thresholds of trees to be overcome increasing the probability of tree mortality (Caldeira et.al. 2015). Caldeira M.C., Lecomte X., David T.S., Pinto J.G., Bugalho M.N. & Werner C. (2015). Synergy of extreme drought and shrub invasion reduce ecosystem functioning and resilience in water-limited climates. Scientific Reports, 5, 15110.

Knowledge Representation Standards and Interchange Formats for Causal Graphs

NASA Technical Reports Server (NTRS)

Throop, David R.; Malin, Jane T.; Fleming, Land

2005-01-01

In many domains, automated reasoning tools must represent graphs of causally linked events. These include fault-tree analysis, probabilistic risk assessment (PRA), planning, procedures, medical reasoning about disease progression, and functional architectures. Each of these fields has its own requirements for the representation of causation, events, actors and conditions. The representations include ontologies of function and cause, data dictionaries for causal dependency, failure and hazard, and interchange formats between some existing tools. In none of the domains has a generally accepted interchange format emerged. The paper makes progress towards interoperability across the wide range of causal analysis methodologies. We survey existing practice and emerging interchange formats in each of these fields. Setting forth a set of terms and concepts that are broadly shared across the domains, we examine the several ways in which current practice represents them. Some phenomena are difficult to represent or to analyze in several domains. These include mode transitions, reachability analysis, positive and negative feedback loops, conditions correlated but not causally linked and bimodal probability distributions. We work through examples and contrast the differing methods for addressing them. We detail recent work in knowledge interchange formats for causal trees in aerospace analysis applications in early design, safety and reliability. Several examples are discussed, with a particular focus on reachability analysis and mode transitions. We generalize the aerospace analysis work across the several other domains. We also recommend features and capabilities for the next generation of causal knowledge representation standards.

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

PubMed Central

2010-01-01

Background Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. Results We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. Conclusions GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events. PMID:20534164

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

PubMed

Thomas, Paul D

2010-06-09

Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the tree of life, and knowledge of the complete complement of genes in a species' genome. The algorithm, called GIGA, constructs trees agglomeratively from a distance matrix representation of sequences, using simple rules to incorporate this genomic age information. GIGA makes use of a novel conceptualization of gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary events such as gene duplication or horizontal gene transfer. An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it. Remarkably, GIGA performs well even when using a very simple distance metric (pairwise sequence differences) and no distance averaging over clades during the tree construction process. GIGA is efficient, allowing phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is exceptionally robust to adding more gene sequences, opening up the possibility of creating stable identifiers for referring to not only extant genes, but also their common ancestors. We compared trees produced by GIGA to those in the TreeFam database, and they were very similar in general, with most differences likely due to poor alignment quality. However, some remaining differences are algorithmic, and can be explained by the fact that GIGA tends to put a larger emphasis on minimizing gene duplication and deletion events.

A CFD study on the effectiveness of trees to disperse road traffic emissions at a city scale

NASA Astrophysics Data System (ADS)

Jeanjean, A. P. R.; Hinchliffe, G.; McMullan, W. A.; Monks, P. S.; Leigh, R. J.

2015-11-01

This paper focuses on the effectiveness of trees at dispersing road traffic emissions on a city scale. CFD simulations of air-pollutant concentrations were performed using the OpenFOAM software platform using the k-ε model. Results were validated against the CODASC wind tunnel database before being applied to a LIDAR database of buildings and trees representing the City of Leicester (UK). Most other CFD models in the literature typically use idealised buildings to model wind flow and pollution dispersion. However, the methodology used in this study uses real buildings and trees data from LIDAR to reconstruct a 3D representation of Leicester City Centre. It focuses on a 2 × 2 km area which is on a scale larger than those usually used in other CFD studies. Furthermore, the primary focus of this study is on the interaction of trees with wind flow dynamics. It was found that in effect, trees have a regionally beneficial impact on road traffic emissions by increasing turbulence and reducing ambient concentrations of road traffic emissions by 7% at pedestrian height on average. This was an important result given that previous studies generally concluded that trees trapped pollution by obstructing wind flow in street canyons. Therefore, this study is novel both in its methodology and subsequent results, highlighting the importance of combining local and regional scale models for assessing the impact of trees in urban planning.

SCAP: a new methodology for safety management based on feedback from credible accident-probabilistic fault tree analysis system.

PubMed

Khan, F I; Iqbal, A; Ramesh, N; Abbasi, S A

2001-10-12

As it is conventionally done, strategies for incorporating accident--prevention measures in any hazardous chemical process industry are developed on the basis of input from risk assessment. However, the two steps-- risk assessment and hazard reduction (or safety) measures--are not linked interactively in the existing methodologies. This prevents a quantitative assessment of the impacts of safety measures on risk control. We have made an attempt to develop a methodology in which risk assessment steps are interactively linked with implementation of safety measures. The resultant system tells us the extent of reduction of risk by each successive safety measure. It also tells based on sophisticated maximum credible accident analysis (MCAA) and probabilistic fault tree analysis (PFTA) whether a given unit can ever be made 'safe'. The application of the methodology has been illustrated with a case study.

Object-oriented fault tree evaluation program for quantitative analyses

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1988-01-01

Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

Assessing School Readiness for a Practice Arrangement Using Decision Tree Methodology.

ERIC Educational Resources Information Center

Barger, Sara E.

1998-01-01

Questions in a decision-tree address mission, faculty interest, administrative support, and practice plan as a way of assessing arrangements for nursing faculty's clinical practice. Decisions should be based on congruence between the human resource allocation and the reward systems. (SK)

Fault Tree Analysis: An Emerging Methodology for Instructional Science.

ERIC Educational Resources Information Center

Wood, R. Kent; And Others

1979-01-01

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

Use of the "Tree" Analogy in Evolution Teaching by Biology Teachers

NASA Astrophysics Data System (ADS)

Marcelos, Maria Fátima; Nagem, Ronaldo Luiz

2012-04-01

This work discusses the use of Darwin's `Tree of Life' as a didactic analogy and metaphor in teaching evolution. It investigates whether biology teachers of pupils from 17 to 18 years old know Darwin's text `Tree of Life'. In addition, it examines whether those teachers systematically employ either the analogies present in that text or other analogies between the tree and evolution, and whether they adopt a specific methodology for teaching with analogies and metaphors (A&M). The academic training of teachers regarding use of A&M is review briefly. A diagnostic study was carried out with biology teachers in a public school in the town of Contagem in the state of Minas Gerais in Brazil. The data were obtained through direct observation, questionnaires and a focus group. The teachers pointed out in the questionnaires that some details of Darwin's analogy are utilized as a resource. However, analysis of the data indicates that the `Tree of Life' text is not known or utilized in class. At the same time, the teachers state that they use aspects of the tree as a didactic resource to teach evolution and that its use facilitates the learning of content. The teachers have little knowledge of specific methodologies of teaching with analogies and metaphors, revealing that their training is incomplete in this area.

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

PubMed

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

2014-09-01

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

Remote Detection and Modeling of Abrupt and Gradual Tree Mortality in the Southwestern USA

NASA Astrophysics Data System (ADS)

Muss, J. D.; Xu, C.; McDowell, N. G.

2014-12-01

Current climate models predict a warming and drying trend that has a high probability of increasing the frequency and spatial extent of tree mortality events. Field surveys can be used to identify, date, and attribute a cause of mortality to specific trees, but monetary and time constraints prevent broad-scale surveys, which are necessary to establish regional or global trends in tree mortality. This is significant because widespread forest mortality will likely lead to radical changes in evapotranspiration and surface albedo, which could compound climate change. While understanding the causes and mechanisms of tree mortality events is crucial, it is equally important to be able to detect and monitor mortality and subsequent changes to the ecosystem at broad spatial- and temporal-scales. Over the past five years our ability to remotely detect abrupt forest mortality events has improved greatly, but gradual events—such as those caused by drought or certain types of insects—are still difficult to identify. Moreover, it is virtually impossible to quantify the amount of mortality that has occurred within a mixed pixel. We have developed a system that fuses climate and satellite-derived spectral data to identify both the date and the agent of forest mortality events. This system has been used with Landsat time series data to detect both abrupt and general trends in tree loss that have occurred during the past quarter-century in northern New Mexico. It has also been used with MODIS data to identify pixels with a high likelihood of drought-caused tree mortality in the Southwestern US. These candidate pixels were then fed to ED-FRT, a coupled forest dynamics-radiative transfer model, to generate estimates of drought-induced. We demonstrate a multi-scale approach that can produce results that will be instrumental in advancing our understanding of tree mortality-climate feedbacks, and improve our ability to predict what forests could look like in the future.

Survey of critical failure events in on-chip interconnect by fault tree analysis

NASA Astrophysics Data System (ADS)

Yokogawa, Shinji; Kunii, Kyousuke

2018-07-01

In this paper, a framework based on reliability physics is proposed for adopting fault tree analysis (FTA) to the on-chip interconnect system of a semiconductor. By integrating expert knowledge and experience regarding the possibilities of failure on basic events, critical issues of on-chip interconnect reliability will be evaluated by FTA. In particular, FTA is used to identify the minimal cut sets with high risk priority. Critical events affecting the on-chip interconnect reliability are identified and discussed from the viewpoint of long-term reliability assessment. The moisture impact is evaluated as an external event.

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.

Vegetation optical depth measured by microwave radiometry as an indicator of tree mortality risk

NASA Astrophysics Data System (ADS)

Rao, K.; Anderegg, W.; Sala, A.; Martínez-Vilalta, J.; Konings, A. G.

2017-12-01

Increased drought-related tree mortality has been observed across several regions in recent years. Vast spatial extent and high temporal variability makes field monitoring of tree mortality cumbersome and expensive. With global coverage and high temporal revisit, satellite remote sensing offers an unprecedented tool to monitor terrestrial ecosystems and identify areas at risk of large drought-driven tree mortality events. To date, studies that use remote sensing data to monitor tree mortality have focused on external climatic thresholds such as temperature and evapotranspiration. However, this approach fails to consider internal water stress in vegetation - which can vary across trees even for similar climatic conditions due to differences in hydraulic behavior, soil type, etc - and may therefore be a poor basis for measuring mortality events. There is a consensus that xylem hydraulic failure often precedes drought-induced mortality, suggesting depleted canopy water content shortly before onset of mortality. Observations of vegetation optical depth (VOD) derived from passive microwave are proportional to canopy water content. In this study, we propose to use variations in VOD as an indicator of potential tree mortality. Since VOD accounts for intrinsic water stress undergone by vegetation, it is expected to be more accurate than external climatic stress indicators. Analysis of tree mortality events in California, USA observed by airborne detection shows a consistent relationship between mortality and the proposed VOD metric. Although this approach is limited by the kilometer-scale resolution of passive microwave radiometry, our results nevertheless demonstrate that microwave-derived estimates of vegetation water content can be used to study drought-driven tree mortality, and may be a valuable tool for mortality predictions if they can be combined with higher-resolution variables.

Fault-Tree Compiler

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Boerschlein, David P.

1993-01-01

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

Model-Based Economic Evaluation of Treatments for Depression: A Systematic Literature Review.

PubMed

Kolovos, Spyros; Bosmans, Judith E; Riper, Heleen; Chevreul, Karine; Coupé, Veerle M H; van Tulder, Maurits W

2017-09-01

An increasing number of model-based studies that evaluate the cost effectiveness of treatments for depression are being published. These studies have different characteristics and use different simulation methods. We aimed to systematically review model-based studies evaluating the cost effectiveness of treatments for depression and examine which modelling technique is most appropriate for simulating the natural course of depression. The literature search was conducted in the databases PubMed, EMBASE and PsycInfo between 1 January 2002 and 1 October 2016. Studies were eligible if they used a health economic model with quality-adjusted life-years or disability-adjusted life-years as an outcome measure. Data related to various methodological characteristics were extracted from the included studies. The available modelling techniques were evaluated based on 11 predefined criteria. This methodological review included 41 model-based studies, of which 21 used decision trees (DTs), 15 used cohort-based state-transition Markov models (CMMs), two used individual-based state-transition models (ISMs), and three used discrete-event simulation (DES) models. Just over half of the studies (54%) evaluated antidepressants compared with a control condition. The data sources, time horizons, cycle lengths, perspectives adopted and number of health states/events all varied widely between the included studies. DTs scored positively in four of the 11 criteria, CMMs in five, ISMs in six, and DES models in seven. There were substantial methodological differences between the studies. Since the individual history of each patient is important for the prognosis of depression, DES and ISM simulation methods may be more appropriate than the others for a pragmatic representation of the course of depression. However, direct comparisons between the available modelling techniques are necessary to yield firm conclusions.

Fault-Tree Compiler Program

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1992-01-01

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

Design and implementation of the tree-based fuzzy logic controller.

PubMed

Liu, B D; Huang, C Y

1997-01-01

In this paper, a tree-based approach is proposed to design the fuzzy logic controller. Based on the proposed methodology, the fuzzy logic controller has the following merits: the fuzzy control rule can be extracted automatically from the input-output data of the system and the extraction process can be done in one-pass; owing to the fuzzy tree inference structure, the search spaces of the fuzzy inference process are largely reduced; the operation of the inference process can be simplified as a one-dimensional matrix operation because of the fuzzy tree approach; and the controller has regular and modular properties, so it is easy to be implemented by hardware. Furthermore, the proposed fuzzy tree approach has been applied to design the color reproduction system for verifying the proposed methodology. The color reproduction system is mainly used to obtain a color image through the printer that is identical to the original one. In addition to the software simulation, an FPGA is used to implement the prototype hardware system for real-time application. Experimental results show that the effect of color correction is quite good and that the prototype hardware system can operate correctly under the condition of 30 MHz clock rate.

Risk Analysis of Return Support Material on Gas Compressor Platform Project

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Mines Systems Safety Improvement Using an Integrated Event Tree and Fault Tree Analysis

NASA Astrophysics Data System (ADS)

Kumar, Ranjan; Ghosh, Achyuta Krishna

2017-04-01

Mines systems such as ventilation system, strata support system, flame proof safety equipment, are exposed to dynamic operational conditions such as stress, humidity, dust, temperature, etc., and safety improvement of such systems can be done preferably during planning and design stage. However, the existing safety analysis methods do not handle the accident initiation and progression of mine systems explicitly. To bridge this gap, this paper presents an integrated Event Tree (ET) and Fault Tree (FT) approach for safety analysis and improvement of mine systems design. This approach includes ET and FT modeling coupled with redundancy allocation technique. In this method, a concept of top hazard probability is introduced for identifying system failure probability and redundancy is allocated to the system either at component or system level. A case study on mine methane explosion safety with two initiating events is performed. The results demonstrate that the presented method can reveal the accident scenarios and improve the safety of complex mine systems simultaneously.

Improving the flash flood frequency analysis applying dendrogeomorphological evidences

NASA Astrophysics Data System (ADS)

Ruiz-Villanueva, V.; Ballesteros, J. A.; Bodoque, J. M.; Stoffel, M.; Bollschweiler, M.; Díez-Herrero, A.

2009-09-01

Flash floods are one of the natural hazards that cause major damages worldwide. Especially in Mediterranean areas they provoke high economic losses every year. In mountain areas with high stream gradients, floods events are characterized by extremely high flow and debris transport rates. Flash flood analysis in mountain areas presents specific scientific challenges. On one hand, there is a lack of information on precipitation and discharge due to a lack of spatially well distributed gauge stations with long records. On the other hand, gauge stations may not record correctly during extreme events when they are damaged or the discharge exceeds the recordable level. In this case, no systematic data allows improvement of the understanding of the spatial and temporal occurrence of the process. Since historic documentation is normally scarce or even completely missing in mountain areas, tree-ring analysis can provide an alternative approach. Flash floods may influence trees in different ways: (1) tilting of the stem through the unilateral pressure of the flowing mass or individual boulders; (2) root exposure through erosion of the banks; (3) injuries and scars caused by boulders and wood transported in the flow; (4) decapitation of the stem and resulting candelabra growth through the severe impact of boulders; (5) stem burial through deposition of material. The trees react to these disturbances with specific growth changes such as abrupt change of the yearly increment and anatomical changes like reaction wood or callus tissue. In this study, we sampled 90 cross sections and 265 increment cores of trees heavily affected by past flash floods in order to date past events and to reconstruct recurrence intervals in two torrent channels located in the Spanish Central System. The first study site is located along the Pelayo River, a torrent in natural conditions. Based on the external disturbances of trees and their geomorphological position, 114 Pinus pinaster (Ait.) influenced by flash flood events were sampled using an increment borer. For each tree sampled, additional information were recorded including the geographical position (GPS measure), the geomorphological situation based on a detailed geomorphological map, the social position within neighbouring trees, a description of the external disturbances and information on tree diameter, tree height and the position of the cores extracted. 265 cores were collected. In the laboratory, the 265 samples were analyzed using the standard methods: surface preparation, counting of tree rings as well as measuring of ring widths using a digital LINTAB positioning table and TSAP 4.6 software. Increment curves of the disturbed trees were then crossdated with a reference chronology in order to correct faulty tree-ring series derived from disturbed samples and to determine initiation of abrupt growth suppression or release. The age of the trees in this field site is between 50 and 100 years old. In the field most of the trees were tilted (93 %) and showed exposed roots (64 %). In the laboratory, growth suppressions were detected in 165 samples. Based on the number of trees showing disturbances, the intensity of the disturbance and the spatial distribution of the trees in the field, seven well represented events were dated for the last 50 years: 2005, 2000, 1996, 1976, 1973, 1966 and 1963. The second field site was a reach of 2 km length along the Arenal River, where the stream is channelized. Here stumps from previously felled trees could be analyzed directly in the field. 100 Alnus glutinosa (L.) Gaertn. and Fraxinus angustifolia (Vahl.) cross sections were investigated in order to date internal wounds. Different carpenter tools, sanding paper and magnifying glasses were used to count tree rings and to date the wounds in the field. In addition to the dating in the field, 22 cross sections were sampled and analyzed in the laboratory using the standard methods. The age of the trees ranges between 30 and 50 years. Based on the injuries dated in the field and in the laboratory, and based on the location of the trees, 8 main events were dated for the last 30 years: 2005, 2003, 2000, 1998, 1997, 1995, 1993 and 1978. Additional results are in progress, such as the amount of rainfall responsible for the triggering of the events, estimation of the magnitude, and the influence of the channelization in the case of the Arenal River. The strength of Dendrogeomorphology in flood analysis has been demonstrated, especially in areas where the lack of historical documents, rainfall and flow data limits the use of traditional methods.

Priority Queues for Computer Simulations

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S. (Inventor)

1998-01-01

The present invention is embodied in new priority queue data structures for event list management of computer simulations, and includes a new priority queue data structure and an improved event horizon applied to priority queue data structures. ne new priority queue data structure is a Qheap and is made out of linked lists for robust, fast, reliable, and stable event list management and uses a temporary unsorted list to store all items until one of the items is needed. Then the list is sorted, next, the highest priority item is removed, and then the rest of the list is inserted in the Qheap. Also, an event horizon is applied to binary tree and splay tree priority queue data structures to form the improved event horizon for event management.

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

ERIC Educational Resources Information Center

Spitzer, Dean

1980-01-01

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

Pedologic and geomorphic impacts of a tornado blowdown event in a mixed pine-hardwood forest

Treesearch

Jonathan D. Phillips; Daniel A. Marion; Alice V. Turkington

2008-01-01

Biomechanical effects of trees on soils and surface processes may be extensive in forest environments. Two blowdown sites caused by a November 2005 tornado in the Ouachita National Forest, Arkansas allowed a case study examination of bioturbation associated with a specific forest blowdown event, as well as detailed examination of relationships between tree root systems...

A fast bottom-up algorithm for computing the cut sets of noncoherent fault trees

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

Corynen, G.C.

1987-11-01

An efficient procedure for finding the cut sets of large fault trees has been developed. Designed to address coherent or noncoherent systems, dependent events, shared or common-cause events, the method - called SHORTCUT - is based on a fast algorithm for transforming a noncoherent tree into a quasi-coherent tree (COHERE), and on a new algorithm for reducing cut sets (SUBSET). To assure sufficient clarity and precision, the procedure is discussed in the language of simple sets, which is also developed in this report. Although the new method has not yet been fully implemented on the computer, we report theoretical worst-casemore » estimates of its computational complexity. 12 refs., 10 figs.« less

Modeling ground-based timber harvesting systems using computer simulation

Treesearch

Jingxin Wang; Chris B. LeDoux

2001-01-01

Modeling ground-based timber harvesting systems with an object-oriented methodology was investigated. Object-oriented modeling and design promote a better understanding of requirements, cleaner designs, and better maintainability of the harvesting simulation system. The model developed simulates chainsaw felling, drive-to-tree feller-buncher, swing-to-tree single-grip...

Research frontiers for improving our understanding of drought‐induced tree and forest mortality

USGS Publications Warehouse

Hartmann, Henrik; Moura, Catarina; Anderegg, William R. L.; Ruehr, Nadine; Salmon, Yann; Allen, Craig D.; Arndt, Stefan K.; Breshears, David D.; Davi, Hendrik; Galbraith, David; Ruthrof, Katinka X.; Wunder, Jan; Adams, Henry D.; Bloemen, Jasper; Cailleret, Maxime; Cobb, Richard; Gessler, Arthur; Grams, Thorsten E. E.; Jansen, Steven; Kautz, Markus; Lloret, Francisco; O’Brien, Michael

2018-01-01

Accumulating evidence highlights increased mortality risks for trees during severe drought, particularly under warmer temperatures and increasing vapour pressure deficit (VPD). Resulting forest die‐off events have severe consequences for ecosystem services, biophysical and biogeochemical land–atmosphere processes. Despite advances in monitoring, modelling and experimental studies of the causes and consequences of tree death from individual tree to ecosystem and global scale, a general mechanistic understanding and realistic predictions of drought mortality under future climate conditions are still lacking. We update a global tree mortality map and present a roadmap to a more holistic understanding of forest mortality across scales. We highlight priority research frontiers that promote: (1) new avenues for research on key tree ecophysiological responses to drought; (2) scaling from the tree/plot level to the ecosystem and region; (3) improvements of mortality risk predictions based on both empirical and mechanistic insights; and (4) a global monitoring network of forest mortality. In light of recent and anticipated large forest die‐off events such a research agenda is timely and needed to achieve scientific understanding for realistic predictions of drought‐induced tree mortality. The implementation of a sustainable network will require support by stakeholders and political authorities at the international level.

Transaction based approach

NASA Astrophysics Data System (ADS)

Hunka, Frantisek; Matula, Jiri

2017-07-01

Transaction based approach is utilized in some methodologies in business process modeling. Essential parts of these transactions are human beings. The notion of agent or actor role is usually used for them. The paper on a particular example describes possibilities of Design Engineering Methodology for Organizations (DEMO) and Resource-Event-Agent (REA) methodology. Whereas the DEMO methodology can be regarded as a generic methodology having its foundation in the theory of Enterprise Ontology the REA methodology is regarded as the domain specific methodology and has its origin in accountancy systems. The results of these approaches is that the DEMO methodology captures everything that happens in the reality with a good empirical evidence whereas the REA methodology captures only changes connected with economic events. Economic events represent either change of the property rights to economic resource or consumption or production of economic resources. This results from the essence of economic events and their connection to economic resources.

A new Bayesian Event Tree tool to track and quantify volcanic unrest and its application to Kawah Ijen volcano

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Sandri, Laura; Rouwet, Dmitri; Caudron, Corentin; Marzocchi, Warner; Suparjan

2016-07-01

Although most of volcanic hazard studies focus on magmatic eruptions, volcanic hazardous events can also occur when no migration of magma can be recognized. Examples are tectonic and hydrothermal unrest that may lead to phreatic eruptions. Recent events (e.g., Ontake eruption on September 2014) have demonstrated that phreatic eruptions are still hard to forecast, despite being potentially very hazardous. For these reasons, it is of paramount importance to identify indicators that define the condition of nonmagmatic unrest, in particular for hydrothermal systems. Often, this type of unrest is driven by movement of fluids, requiring alternative monitoring setups, beyond the classical seismic-geodetic-geochemical architectures. Here we present a new version of the probabilistic BET (Bayesian Event Tree) model, specifically developed to include the forecasting of nonmagmatic unrest and related hazards. The structure of the new event tree differs from the previous schemes by adding a specific branch to detail nonmagmatic unrest outcomes. A further goal of this work consists in providing a user-friendly, open-access, and straightforward tool to handle the probabilistic forecast and visualize the results as possible support during a volcanic crisis. The new event tree and tool are here applied to Kawah Ijen stratovolcano, Indonesia, as exemplificative application. In particular, the tool is set on the basis of monitoring data for the learning period 2000-2010, and is then blindly applied to the test period 2010-2012, during which significant unrest phases occurred.

The fundamental theorem of asset pricing under default and collateral in finite discrete time

NASA Astrophysics Data System (ADS)

Alvarez-Samaniego, Borys; Orrillo, Jaime

2006-08-01

We consider a financial market where time and uncertainty are modeled by a finite event-tree. The event-tree has a length of N, a unique initial node at the initial date, and a continuum of branches at each node of the tree. Prices and returns of J assets are modeled, respectively, by a R2JxR2J-valued stochastic process . In this framework we prove a version of the Fundamental Theorem of Asset Pricing which applies to defaultable securities backed by exogenous collateral suffering a contingent linear depreciation.

Risk Analysis of a Fuel Storage Terminal Using HAZOP and FTA

PubMed Central

Baixauli-Pérez, Mª Piedad

2017-01-01

The size and complexity of industrial chemical plants, together with the nature of the products handled, means that an analysis and control of the risks involved is required. This paper presents a methodology for risk analysis in chemical and allied industries that is based on a combination of HAZard and OPerability analysis (HAZOP) and a quantitative analysis of the most relevant risks through the development of fault trees, fault tree analysis (FTA). Results from FTA allow prioritizing the preventive and corrective measures to minimize the probability of failure. An analysis of a case study is performed; it consists in the terminal for unloading chemical and petroleum products, and the fuel storage facilities of two companies, in the port of Valencia (Spain). HAZOP analysis shows that loading and unloading areas are the most sensitive areas of the plant and where the most significant danger is a fuel spill. FTA analysis indicates that the most likely event is a fuel spill in tank truck loading area. A sensitivity analysis from the FTA results show the importance of the human factor in all sequences of the possible accidents, so it should be mandatory to improve the training of the staff of the plants. PMID:28665325

Risk Analysis of a Fuel Storage Terminal Using HAZOP and FTA.

PubMed

Fuentes-Bargues, José Luis; González-Cruz, Mª Carmen; González-Gaya, Cristina; Baixauli-Pérez, Mª Piedad

2017-06-30

The size and complexity of industrial chemical plants, together with the nature of the products handled, means that an analysis and control of the risks involved is required. This paper presents a methodology for risk analysis in chemical and allied industries that is based on a combination of HAZard and OPerability analysis (HAZOP) and a quantitative analysis of the most relevant risks through the development of fault trees, fault tree analysis (FTA). Results from FTA allow prioritizing the preventive and corrective measures to minimize the probability of failure. An analysis of a case study is performed; it consists in the terminal for unloading chemical and petroleum products, and the fuel storage facilities of two companies, in the port of Valencia (Spain). HAZOP analysis shows that loading and unloading areas are the most sensitive areas of the plant and where the most significant danger is a fuel spill. FTA analysis indicates that the most likely event is a fuel spill in tank truck loading area. A sensitivity analysis from the FTA results show the importance of the human factor in all sequences of the possible accidents, so it should be mandatory to improve the training of the staff of the plants.

A Statistical Methodology for Detecting and Monitoring Change in Forest Ecosystems Using Remotely Sensed Imagery

NASA Astrophysics Data System (ADS)

Mills, R. T.; Kumar, J.; Hoffman, F. M.; Hargrove, W. W.; Spruce, J.

2011-12-01

Variations in vegetation phenology, the annual temporal pattern of leaf growth and senescence, can be a strong indicator of ecological change or disturbance. However, phenology is also strongly influenced by seasonal, interannual, and long-term trends in climate, making identification of changes in forest ecosystems a challenge. Forest ecosystems are vulnerable to extreme weather events, insect and disease attacks, wildfire, harvesting, and other land use change. Normalized difference vegetation index (NDVI), a remotely sensed measure of greenness, provides a proxy for phenology. NDVI for the conterminous United States (CONUS) derived from the Moderate Resolution Spectroradiometer (MODIS) at 250 m resolution was used in this study to develop phenological signatures of ecological regimes called phenoregions. By applying a quantitative data mining technique to the NDVI measurements for every eight days over the entire MODIS record, annual maps of phenoregions were developed. This geospatiotemporal cluster analysis technique employs high performance computing resources, enabling analysis of such very large data sets. This technique produces a prescribed number of prototypical phenological states to which every location belongs in any year. Analysis of the shifts among phenological states yields information about responses to interannual climate variability and, more importantly, changes in ecosystem health due to disturbances. Moreover, a large change in the phenological states occupied by a single location over time indicates a significant disturbance or ecological shift. This methodology has been applied for identification of various forest disturbance events, including wildfire, tree mortality due to Mountain Pine Beetle, and other insect infestation and diseases, as well as extreme events like storms and hurricanes in the U.S. Presented will be results from analysis of phenological state dynamics, along with disturbance and validation data.

Effects of biotic and abiotic factors on resistance versus resilience of Douglas fir to drought.

PubMed

Carnwath, Gunnar; Nelson, Cara

2017-01-01

Significant increases in tree mortality due to drought-induced physiological stress have been documented worldwide. This trend is likely to continue with increased frequency and severity of extreme drought events in the future. Therefore, understanding the factors that influence variability in drought responses among trees will be critical to predicting ecosystem responses to climate change and developing effective management actions. In this study, we used hierarchical mixed-effects models to analyze drought responses of Pseudotsuga menziesii in 20 unmanaged forests stands across a broad range of environmental conditions in northeastern Washington, USA. We aimed to 1) identify the biotic and abiotic attributes most closely associated with the responses of individual trees to drought and 2) quantify the variability in drought responses at different spatial scales. We found that growth rates and competition for resources significantly affected resistance to a severe drought event in 2001: slow-growing trees and trees growing in subordinate canopy positions and/or with more neighbors suffered greater declines in radial growth during the drought event. In contrast, the ability of a tree to return to normal growth when climatic conditions improved (resilience) was unaffected by competition or relative growth rates. Drought responses were significantly influenced by tree age: older trees were more resistant but less resilient than younger trees. Finally, we found differences between resistance and resilience in spatial scale: a significant proportion (approximately 50%) of the variability in drought resistance across the study area was at broad spatial scales (i.e. among different forest types), most likely due to differences in the total amount of precipitation received at different elevations; in contrast, variation in resilience was overwhelmingly (82%) at the level of individual trees within stands and there was no difference in drought resilience among forest types. Our results suggest that for Pseudotsuga menziesii resistance and resilience to drought are driven by different factors and vary at different spatial scales.

A synthesis of radial growth patterns preceding tree mortality

USGS Publications Warehouse

Cailleret, Maxime; Jansen, Steven; Robert, Elisabeth M.R.; Desoto, Lucia; Aakala, Tuomas; Antos, Joseph A.; Beikircher, Barbara; Bigler, Christof; Bugmann, Harald; Caccianiga, Marco; Cada, Vojtech; Camarero, Jesus J.; Cherubini, Paolo; Cochard, Herve; Coyea, Marie R.; Cufar, Katarina; Das, Adrian J.; Davi, Hendrik; Delzon, Sylvain; Dorman, Michael; Gea-Izquierdo, Guillermo; Gillner, Sten; Haavik, Laurel J.; Hartmann, Henrik; Heres, Ana-Maria; Hultine, Kevin R.; Janda, Pavel; Kane, Jeffrey M.; Kharuk, Vyacheslav I.; Kitzberger, Thomas; Klein, Tamir; Kramer, Koen; Lens, Frederic; Levanic, Tom; Calderon, Juan C. Linares; Lloret, Francisco; Lobo-Do-Vale, Raquel; Lombardi, Fabio; Lopez Rodriguez, Rosana; Makinen, Harri; Mayr, Stefan; Meszaros, IIona; Metsaranta, Juha M.; Minunno, Francesco; Oberhuber, Walter; Papadopoulos, Andreas; Peltoniemi, Mikko; Petritan, Any M.; Rohner, Brigitte; Sanguesa-Barreda, Gabriel; Sarris, Dimitrios; Smith, Jeremy M.; Stan, Amanda B.; Sterck, Frank; Stojanovic, Dejan B.; Suarez, Maria L.; Svoboda, Miroslav; Tognetti, Roberto; Torres-Ruiz, Jose M.; Trotsiuk, Volodymyr; Villalba, Ricardo; Vodde, Floor; Westwood, Alana R.; Wyckoff, Peter H.; Zafirov, Nikolay; Martinez-Vilalta, Jordi

2017-01-01

Tree mortality is a key factor influencing forest functions and dynamics, but our understanding of the mechanisms leading to mortality and the associated changes in tree growth rates are still limited. We compiled a new pan-continental tree-ring width database from sites where both dead and living trees were sampled (2970 dead and 4224 living trees from 190 sites, including 36 species), and compared early and recent growth rates between trees that died and those that survived a given mortality event. We observed a decrease in radial growth before death in ca. 84% of the mortality events. The extent and duration of these reductions were highly variable (1–100 years in 96% of events) due to the complex interactions among study species and the source(s) of mortality. Strong and long-lasting declines were found for gymnosperms, shade- and drought-tolerant species, and trees that died from competition. Angiosperms and trees that died due to biotic attacks (especially bark-beetles) typically showed relatively small and short-term growth reductions. Our analysis did not highlight any universal trade-off between early growth and tree longevity within a species, although this result may also reflect high variability in sampling design among sites. The intersite and interspecific variability in growth patterns before mortality provides valuable information on the nature of the mortality process, which is consistent with our understanding of the physiological mechanisms leading to mortality. Abrupt changes in growth immediately before death can be associated with generalized hydraulic failure and/or bark-beetle attack, while long-term decrease in growth may be associated with a gradual decline in hydraulic performance coupled with depletion in carbon reserves. Our results imply that growth-based mortality algorithms may be a powerful tool for predicting gymnosperm mortality induced by chronic stress, but not necessarily so for angiosperms and in case of intense drought or bark-beetle outbreaks.

A synthesis of radial growth patterns preceding tree mortality.

PubMed

Cailleret, Maxime; Jansen, Steven; Robert, Elisabeth M R; Desoto, Lucía; Aakala, Tuomas; Antos, Joseph A; Beikircher, Barbara; Bigler, Christof; Bugmann, Harald; Caccianiga, Marco; Čada, Vojtěch; Camarero, Jesus J; Cherubini, Paolo; Cochard, Hervé; Coyea, Marie R; Čufar, Katarina; Das, Adrian J; Davi, Hendrik; Delzon, Sylvain; Dorman, Michael; Gea-Izquierdo, Guillermo; Gillner, Sten; Haavik, Laurel J; Hartmann, Henrik; Hereş, Ana-Maria; Hultine, Kevin R; Janda, Pavel; Kane, Jeffrey M; Kharuk, Vyacheslav I; Kitzberger, Thomas; Klein, Tamir; Kramer, Koen; Lens, Frederic; Levanic, Tom; Linares Calderon, Juan C; Lloret, Francisco; Lobo-Do-Vale, Raquel; Lombardi, Fabio; López Rodríguez, Rosana; Mäkinen, Harri; Mayr, Stefan; Mészáros, Ilona; Metsaranta, Juha M; Minunno, Francesco; Oberhuber, Walter; Papadopoulos, Andreas; Peltoniemi, Mikko; Petritan, Any M; Rohner, Brigitte; Sangüesa-Barreda, Gabriel; Sarris, Dimitrios; Smith, Jeremy M; Stan, Amanda B; Sterck, Frank; Stojanović, Dejan B; Suarez, Maria L; Svoboda, Miroslav; Tognetti, Roberto; Torres-Ruiz, José M; Trotsiuk, Volodymyr; Villalba, Ricardo; Vodde, Floor; Westwood, Alana R; Wyckoff, Peter H; Zafirov, Nikolay; Martínez-Vilalta, Jordi

2017-04-01

Tree mortality is a key factor influencing forest functions and dynamics, but our understanding of the mechanisms leading to mortality and the associated changes in tree growth rates are still limited. We compiled a new pan-continental tree-ring width database from sites where both dead and living trees were sampled (2970 dead and 4224 living trees from 190 sites, including 36 species), and compared early and recent growth rates between trees that died and those that survived a given mortality event. We observed a decrease in radial growth before death in ca. 84% of the mortality events. The extent and duration of these reductions were highly variable (1-100 years in 96% of events) due to the complex interactions among study species and the source(s) of mortality. Strong and long-lasting declines were found for gymnosperms, shade- and drought-tolerant species, and trees that died from competition. Angiosperms and trees that died due to biotic attacks (especially bark-beetles) typically showed relatively small and short-term growth reductions. Our analysis did not highlight any universal trade-off between early growth and tree longevity within a species, although this result may also reflect high variability in sampling design among sites. The intersite and interspecific variability in growth patterns before mortality provides valuable information on the nature of the mortality process, which is consistent with our understanding of the physiological mechanisms leading to mortality. Abrupt changes in growth immediately before death can be associated with generalized hydraulic failure and/or bark-beetle attack, while long-term decrease in growth may be associated with a gradual decline in hydraulic performance coupled with depletion in carbon reserves. Our results imply that growth-based mortality algorithms may be a powerful tool for predicting gymnosperm mortality induced by chronic stress, but not necessarily so for angiosperms and in case of intense drought or bark-beetle outbreaks. © 2016 John Wiley & Sons Ltd.

Effects of biotic and abiotic factors on resistance versus resilience of Douglas fir to drought

PubMed Central

Nelson, Cara

2017-01-01

Significant increases in tree mortality due to drought-induced physiological stress have been documented worldwide. This trend is likely to continue with increased frequency and severity of extreme drought events in the future. Therefore, understanding the factors that influence variability in drought responses among trees will be critical to predicting ecosystem responses to climate change and developing effective management actions. In this study, we used hierarchical mixed-effects models to analyze drought responses of Pseudotsuga menziesii in 20 unmanaged forests stands across a broad range of environmental conditions in northeastern Washington, USA. We aimed to 1) identify the biotic and abiotic attributes most closely associated with the responses of individual trees to drought and 2) quantify the variability in drought responses at different spatial scales. We found that growth rates and competition for resources significantly affected resistance to a severe drought event in 2001: slow-growing trees and trees growing in subordinate canopy positions and/or with more neighbors suffered greater declines in radial growth during the drought event. In contrast, the ability of a tree to return to normal growth when climatic conditions improved (resilience) was unaffected by competition or relative growth rates. Drought responses were significantly influenced by tree age: older trees were more resistant but less resilient than younger trees. Finally, we found differences between resistance and resilience in spatial scale: a significant proportion (approximately 50%) of the variability in drought resistance across the study area was at broad spatial scales (i.e. among different forest types), most likely due to differences in the total amount of precipitation received at different elevations; in contrast, variation in resilience was overwhelmingly (82%) at the level of individual trees within stands and there was no difference in drought resilience among forest types. Our results suggest that for Pseudotsuga menziesii resistance and resilience to drought are driven by different factors and vary at different spatial scales. PMID:28973008

Windthrown trees on the Kings River Ranger District, Sierra National Forest: meteorological aspects

Treesearch

Michael A. Fosberg

1986-01-01

Blowdown in shelterwood, sanitation cuts, and other partial cuts on the Kings River Ranger District, Sierra National Forest, are due to Mono winds. Both winter storm and Mono winds were considered as causes of winter blowdown. All evidence, e.g., direction of tree-fall and occurrence of high wind events, point to Mono wind events as the cause of blowdown. Only 12...

Object-Oriented Algorithm For Evaluation Of Fault Trees

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1992-01-01

Algorithm for direct evaluation of fault trees incorporates techniques of object-oriented programming. Reduces number of calls needed to solve trees with repeated events. Provides significantly improved software environment for such computations as quantitative analyses of safety and reliability of complicated systems of equipment (e.g., spacecraft or factories).

The Imprint of Extreme Climate Events in Century-Long Time Series of Wood Anatomical Traits in High-Elevation Conifers

PubMed Central

Carrer, Marco; Brunetti, Michele; Castagneri, Daniele

2016-01-01

Extreme climate events are of key importance for forest ecosystems. However, both the inherent infrequency, stochasticity and multiplicity of extreme climate events, and the array of biological responses, challenges investigations. To cope with the long life cycle of trees and the paucity of the extreme events themselves, our inferences should be based on long-term observations. In this context, tree rings and the related xylem anatomical traits represent promising sources of information, due to the wide time perspective and quality of the information they can provide. Here we test, on two high-elevation conifers (Larix decidua and Picea abies sampled at 2100 m a.s.l. in the Eastern Alps), the associations among temperature extremes during the growing season and xylem anatomical traits, specifically the number of cells per ring (CN), cell wall thickness (CWT), and cell diameter (CD). To better track the effect of extreme events over the growing season, tree rings were partitioned in 10 sectors. Climate variability has been reconstructed, for 1800–2011 at monthly resolution and for 1926–2011 at daily resolution, by exploiting the excellent availability of very long and high quality instrumental records available for the surrounding area, and taking into account the relationship between meteorological variables and site topographical settings. Summer temperature influenced anatomical traits of both species, and tree-ring anatomical profiles resulted as being associated to temperature extremes. Most of the extreme values in anatomical traits occurred with warm (positive extremes) or cold (negative) conditions. However, 0–34% of occurrences did not match a temperature extreme event. Specifically, CWT and CN extremes were more clearly associated to climate than CD, which presented a bias to track cold extremes. Dendroanatomical analysis, coupled to high-quality daily-resolved climate records, seems a promising approach to study the effects of extreme events on trees, but further investigations are needed to improve our comprehension of the critical role of such elusive events in forest ecosystems. PMID:27242880

Fuel treatment effects on tree mortality following wildfire in dry mixed conifer forests, Washington State, USA

Treesearch

Susan J. Prichard; Maureen C. Kennedy

2012-01-01

Fuel reduction treatments are increasingly used to mitigate future wildfire severity in dry forests, but few opportunities exist to assess their effectiveness. We evaluated the influence of fuel treatment, tree size and species on tree mortality following a large wildfire event in recent thin-only, thin and prescribed burn (thin-Rx) units. Of the trees that died within...

Precipitation thresholds and drought-induced tree die-off: Insights from patterns of Pinus edulis mortality along an environmental stress gradient

Treesearch

Michael J. Clifford; Patrick D. Royer; Neil S. Cobb; David D. Breshears; Paulette L. Ford

2013-01-01

Recent regional tree die-off events appear to have been triggered by a combination of drought and heat - referred to as 'global-change-type drought'. To complement experiments focused on resolving mechanisms of drought-induced tree mortality, an evaluation of how patterns of tree die-off relate to highly spatially variable precipitation is needed....

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

PubMed

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

2017-11-01

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

Using Classification Trees to Predict Alumni Giving for Higher Education

ERIC Educational Resources Information Center

Weerts, David J.; Ronca, Justin M.

2009-01-01

As the relative level of public support for higher education declines, colleges and universities aim to maximize alumni-giving to keep their programs competitive. Anchored in a utility maximization framework, this study employs the classification and regression tree methodology to examine characteristics of alumni donors and non-donors at a…

Evaluation of three electronic noses for detecting incipient wood decay

Treesearch

Manuela Baietto; Alphus D. Wilson; Daniele Bassi; Francesco Ferrini

2010-01-01

Tree assessment methodologies, currently used to evaluate the structural stability of individual urban trees, usually involve a visual analysis followed by measurements of the internal soundness of wood using various instruments that are often invasive, expensive, or inadequate for use within the urban environment. Moreover, most conventional instruments do not provide...

Agroforestry systems and valuation methodologies

Treesearch

Janaki R.R. Alavalapati; D. Evan Mercer; Jensen R. Montambault

2004-01-01

Agroforestry, the deliberate integration of trees with agricultural crops andor livestock either simultaneously or sequentially on the same unit of land, has been an established practice for centuries. Throughout the tropics and, to some extent, temperate zones, farmers have a long tradition of retaining trees on their fields and pastures, as well as growing crops or...

Using classification tree analysis to predict oak wilt distribution in Minnesota and Texas

Treesearch

Marla c. Downing; Vernon L. Thomas; Jennifer Juzwik; David N. Appel; Robin M. Reich; Kim Camilli

2008-01-01

We developed a methodology and compared results for predicting the potential distribution of Ceratocystis fagacearum (causal agent of oak wilt), in both Anoka County, MN, and Fort Hood, TX. The Potential Distribution of Oak Wilt (PDOW) utilizes a binary classification tree statistical technique that incorporates: geographical information systems (GIS...

Optimal Diameter Growth Equations for Major Tree Species of the Midsouth

Treesearch

Don C. Bragg

2003-01-01

Optimal diameter growth equations for 60 major tree species were fit using the potential relative increment (PRI) methodology. Almost 175,000 individuals from the Midsouth (Arkansas, Louisiana, Missouri, Oklahoma, and Texas) were selected from the USDA Forest Service's Eastwide Forest Inventory Database (EFIDB). These records were then reduced to the individuals...

A Sustainability Initiative to Quantify Carbon Sequestration by Campus Trees

ERIC Educational Resources Information Center

Cox, Helen M.

2012-01-01

Over 3,900 trees on a university campus were inventoried by an instructor-led team of geography undergraduates in order to quantify the carbon sequestration associated with biomass growth. The setting of the project is described, together with its logistics, methodology, outcomes, and benefits. This hands-on project provided a team of students…

"Tree Investigators": Supporting Families' Scientific Talk in an Arboretum with Mobile Computers

ERIC Educational Resources Information Center

Zimmerman, Heather Toomey; Land, Susan M.; McClain, Lucy R.; Mohney, Michael R.; Choi, Gi Woong; Salman, Fariha H.

2015-01-01

This research examines the "Tree Investigators" project to support science learning with mobile devices during family public programmes in an arboretum. Using a case study methodology, researchers analysed video records of 10 families (25 people) using mobile technologies with naturalists at an arboretum to understand how mobile devices…

Tree mortality in the eastern Mediterranean, causes and implications under climatic change

NASA Astrophysics Data System (ADS)

Sarris, Dimitrios; Iacovou, Valentina; Hoch, Guenter; Vennetier, Michel; Siegwolf, Rolf; Christodoulakis, Dimitrios; Koerner, Christian

2015-04-01

The eastern Mediterranean has experienced repeated incidents of forest mortality related to drought in recent decades. Such events may become more frequent in the future as drought conditions are projected to further intensify due to global warming. We have been investigating the causes behind such forest mortality events in Pinus halepensis, (the most drought tolerant pine in the Mediterranean). We cored tree stems and sampled various tissue types from dry habitats close to sea level and explored growth responses, stable isotope signals and non-structural carbohydrate (NSC) concentrations. Under intense drought that coincided with pine desiccation events in natural populations our result indicate a significant reduction in tree growth, the most significant in more than a century despite the increase in atmospheric CO2 concentrations in recent decades. This has been accompanied by a lengthening in the integration periods of rainfall needed for pine growth, reaching even 5-6 years before and including the year of mortality occurrence. Oxygen stable isotopes indicate that these signals were associated with a shift in tree water utilization from deeper moisture pools related to past rainfall events. Furthermore, where the driest conditions occur, pine carbon reserves were found to increase in stem tissue, indicating that mortality in these pines cannot be explained by carbon starvation. Our findings suggest that for pine populations that are already water limited (i) a further atmospheric CO2 increase will not compensate for the reduction in growth because of a drier climate, (ii) hydraulic failure appears as the most likely cause of pine desiccation, as no shortage occurs in tree carbon reserves, (iii) a further increase in mortality events may cause these systems to become carbon sources.

Towards generating ECSS-compliant fault tree analysis results via ConcertoFLA

NASA Astrophysics Data System (ADS)

Gallina, B.; Haider, Z.; Carlsson, A.

2018-05-01

Attitude Control Systems (ACSs) maintain the orientation of the satellite in three-dimensional space. ACSs need to be engineered in compliance with ECSS standards and need to ensure a certain degree of dependability. Thus, dependability analysis is conducted at various levels and by using ECSS-compliant techniques. Fault Tree Analysis (FTA) is one of these techniques. FTA is being automated within various Model Driven Engineering (MDE)-based methodologies. The tool-supported CHESS-methodology is one of them. This methodology incorporates ConcertoFLA, a dependability analysis technique enabling failure behavior analysis and thus FTA-results generation. ConcertoFLA, however, similarly to other techniques, still belongs to the academic research niche. To promote this technique within the space industry, we apply it on an ACS and discuss about its multi-faceted potentialities in the context of ECSS-compliant engineering.

Development of a methodology for assessing the safety of embedded software systems

NASA Technical Reports Server (NTRS)

Garrett, C. J.; Guarro, S. B.; Apostolakis, G. E.

1993-01-01

A Dynamic Flowgraph Methodology (DFM) based on an integrated approach to modeling and analyzing the behavior of software-driven embedded systems for assessing and verifying reliability and safety is discussed. DFM is based on an extension of the Logic Flowgraph Methodology to incorporate state transition models. System models which express the logic of the system in terms of causal relationships between physical variables and temporal characteristics of software modules are analyzed to determine how a certain state can be reached. This is done by developing timed fault trees which take the form of logical combinations of static trees relating the system parameters at different point in time. The resulting information concerning the hardware and software states can be used to eliminate unsafe execution paths and identify testing criteria for safety critical software functions.

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

PubMed

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

An analysis of dinosaurian biogeography: evidence for the existence of vicariance and dispersal patterns caused by geological events.

PubMed

Upchurch, Paul; Hunn, Craig A; Norman, David B

2002-03-22

As the supercontinent Pangaea fragmented during the Mesozoic era, dinosaur faunas were divided into isolated populations living on separate continents. It has been predicted, therefore, that dinosaur distributions should display a branching ('vicariance') pattern that corresponds with the sequence and timing of continental break-up. Several recent studies, however, minimize the importance of plate tectonics and instead suggest that dispersal and regional extinction were the main controls on dinosaur biogeography. Here, in order to test the vicariance hypothesis, we apply a cladistic biogeographical method to a large dataset on dinosaur relationships and distributions. We also introduce a methodological refinement termed 'time-slicing', which is shown to be a key step in the detection of ancient biogeographical patterns. These analyses reveal biogeographical patterns that closely correlate with palaeogeography. The results provide the first statistically robust evidence that, from Middle Jurassic to mid-Cretaceous times, tectonic events had a major role in determining where and when particular dinosaur groups flourished. The fact that evolutionary trees for extinct organisms preserve such distribution patterns opens up a new and fruitful direction for palaeobiogeographical research.

The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae).

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Alexander, Patrick J; Bailey, C Donovan

2011-12-01

The evolutionary history of Leucaena has been impacted by polyploidy, hybridization, and divergent allopatric species diversification, suggesting that this is an ideal group to investigate the evolutionary tempo of polyploidy and the complexities of reticulation and divergence in plant diversification. Parsimony- and ML-based phylogenetic approaches were applied to 105 accessions sequenced for six sequence characterized amplified region-based nuclear encoded loci, nrDNA ITS, and four cpDNA regions. Hypotheses for the origin of tetraploid species were inferred using results derived from a novel species tree and established gene tree methods and from data on genome sizes and geographic distributions. The combination of comprehensively sampled multilocus DNA sequence data sets and a novel methodology provide strong resolution and support for the origins of all five tetraploid species. A minimum of four allopolyploidization events are required to explain the origins of these species. The origin(s) of one tetraploid pair (L. involucrata/L. pallida) can be equally explained by two unique allopolyploidizations or a single event followed by divergent speciation. Alongside other recent findings, a comprehensive picture of the complex evolutionary dynamics of polyploidy in Leucaena is emerging that includes paleotetraploidization, diploidization of the last common ancestor to Leucaena, allopatric divergence among diploids, and recent allopolyploid origins for tetraploid species likely associated with human translocation of seed. These results provide insights into the role of divergence and reticulation in a well-characterized angiosperm lineage and into traits of diploid parents and derived tetraploids (particularly self-compatibility and year-round flowering) favoring the formation and establishment of novel tetraploids combinations.

Growth and reproduction respond differently to climate in three Neotropical tree species.

PubMed

Alfaro-Sánchez, Raquel; Muller-Landau, Helene C; Wright, S Joseph; Camarero, J Julio

2017-06-01

The response of tropical forests to anthropogenic climate change is critically important to future global carbon budgets, yet remains highly uncertain. Here, we investigate how precipitation, temperature, solar radiation and dry- and wet-season lengths are related to annual tree growth, flower production, and fruit production in three moist tropical forest tree species using long-term datasets from tree rings and litter traps in central Panama. We also evaluated how growth, flower, and fruit production were interrelated. We found that growth was positively correlated with wet-season precipitation in all three species: Jacaranda copaia (r = 0.63), Tetragastris panamensis (r = 0.39) and Trichilia tuberculata (r = 0.39). Flowering and fruiting in Jacaranda were negatively related to current-year dry-season rainfall and positively related to prior-year dry-season rainfall. Flowering in Tetragastris was negatively related to current-year annual mean temperature while Trichilia showed no significant relationships of reproduction with climate. Growth was significantly related to reproduction only in Tetragastris, where it was positively related to previous year fruiting. Our results suggest that tree growth in moist tropical forest tree species is generally reduced by drought events such as those associated with strong El Niño events. In contrast, interannual variation in reproduction is not generally associated with growth and has distinct and species-specific climate responses, with positive effects of El Niño events in some species. Understanding these contrasting climate effects on tree growth and reproduction is critical to predicting changes in tropical forest dynamics and species composition under climate change.

Arenal-type pyroclastic flows: A probabilistic event tree risk analysis

NASA Astrophysics Data System (ADS)

Meloy, Anthony F.

2006-09-01

A quantitative hazard-specific scenario-modelling risk analysis is performed at Arenal volcano, Costa Rica for the newly recognised Arenal-type pyroclastic flow (ATPF) phenomenon using an event tree framework. These flows are generated by the sudden depressurisation and fragmentation of an active basaltic andesite lava pool as a result of a partial collapse of the crater wall. The deposits of this type of flow include angular blocks and juvenile clasts, which are rarely found in other types of pyroclastic flow. An event tree analysis (ETA) is a useful tool and framework in which to analyse and graphically present the probabilities of the occurrence of many possible events in a complex system. Four event trees are created in the analysis, three of which are extended to investigate the varying individual risk faced by three generic representatives of the surrounding community: a resident, a worker, and a tourist. The raw numerical risk estimates determined by the ETA are converted into a set of linguistic expressions (i.e. VERY HIGH, HIGH, MODERATE etc.) using an established risk classification scale. Three individually tailored semi-quantitative risk maps are then created from a set of risk conversion tables to show how the risk varies for each individual in different areas around the volcano. In some cases, by relocating from the north to the south, the level of risk can be reduced by up to three classes. While the individual risk maps may be broadly applicable, and therefore of interest to the general community, the risk maps and associated probability values generated in the ETA are intended to be used by trained professionals and government agencies to evaluate the risk and effectively manage the long-term development of infrastructure and habitation. With the addition of fresh monitoring data, the combination of both long- and short-term event trees would provide a comprehensive and consistent method of risk analysis (both during and pre-crisis), and as such, an ETA is considered to be a valuable quantitative decision support tool.

Tree mortality from a short-duration freezing event and global-change-type drought in a Southwestern piñon-juniper woodland, USA

PubMed Central

2014-01-01

This study documents tree mortality in Big Bend National Park in Texas in response to the most acute one-year drought on record, which occurred following a five-day winter freeze. I estimated changes in forest stand structure and species composition due to freezing and drought in the Chisos Mountains of Big Bend National Park using permanent monitoring plot data. The drought killed over half (63%) of the sampled trees over the entire elevation gradient. Significant mortality occurred in trees up to 20 cm diameter (P < 0.05). Pinus cembroides Zucc. experienced the highest seedling and tree mortality (P < 0.0001) (55% of piñon pines died), and over five times as many standing dead pines were observed in 2012 than in 2009. Juniperus deppeana vonSteudal and Quercus emoryi Leibmann also experienced significant declines in tree density (P < 0.02) (30.9% and 20.7%, respectively). Subsequent droughts under climate change will likely cause even greater damage to trees that survived this record drought, especially if such events follow freezes. The results from this study highlight the vulnerability of trees in the Southwest to climatic change and that future shifts in forest structure can have large-scale community consequences. PMID:24949231

Modelling Single Tree Structure with Terrestrial Laser Scanner

NASA Astrophysics Data System (ADS)

Yurtseven, H.; Akgül, M.; Gülci, S.

2017-11-01

Recent technological developments, which has reliable accuracy and quality for all engineering works, such as remote sensing tools have wide range use in forestry applications. Last decade, sustainable use and management opportunities of forest resources are favorite topics. Thus, precision of obtained data plays an important role in evaluation of current status of forests' value. The use of aerial and terrestrial laser technology has more reliable and effective models to advance the appropriate natural resource management. This study investigates the use of terrestrial laser scanner (TLS) technology in forestry, and also the methodological data processing stages for tree volume extraction is explained. Z+F Imager 5010C TLS system was used for measure single tree information such as tree height, diameter of breast height, branch volume and canopy closure. In this context more detailed and accurate data can be obtained than conventional inventory sampling in forestry by using TLS systems. However the accuracy of obtained data is up to the experiences of TLS operator in the field. Number of scan stations and its positions are other important factors to reduce noise effect and accurate 3D modelling. The results indicated that the use of point cloud data to extract tree information for forestry applications are promising methodology for precision forestry.

78 FR 66762 - Notice of Public Meeting and Request for Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-06

... of request for public meeting and public comments on the planning of the National Christmas Tree... and suggestions on the planning of the 2013 National Christmas Tree Lighting and the subsequent 26-day... on the planning of the 2013 National Christmas Tree Lighting and the subsequent 26-day event, which...

76 FR 66082 - Notice of Public Meeting and Request for Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-25

... for Public Meeting and Public Comments--The National Christmas Tree Lighting and the subsequent 31 day... the 2011 National Christmas Tree Lighting and the subsequent 31 day event. DATES: The meeting will be... and suggestions on the planning of the 2011 National Christmas Tree Lighting and the subsequent 31 day...

Tasting the Tree of Life: Development of a Collaborative, Cross-Campus, Science Outreach Meal Event.

PubMed

Clement, Wendy L; Elliott, Kathryn T; Cordova-Hoyos, Okxana; Distefano, Isabel; Kearns, Kate; Kumar, Raagni; Leto, Ashley; Tumaliuan, Janis; Franchetti, Lauren; Kulesza, Evelyn; Tineo, Nicole; Mendes, Patrice; Roth, Karen; Osborn, Jeffrey M

2018-01-01

Communicating about science with the public can present a number of challenges, from participation to engagement to impact. In an effort to broadly communicate messages regarding biodiversity, evolution, and tree-thinking with the campus community at The College of New Jersey (TCNJ), a public, primarily undergraduate institution, we created a campus-wide, science-themed meal, "Tasting the Tree of Life: Exploring Biodiversity through Cuisine." We created nine meals that incorporated 149 species/ingredients across the Tree of Life. Each meal illustrated a scientific message communicated through interactions with undergraduate biology students, informational signs, and an interactive website. To promote tree-thinking, we reconstructed a phylogeny of all 149 ingredients. In total, 3,262 people attended the meal, and evaluations indicated that participants left with greater appreciation for the biodiversity and evolutionary relatedness of their food. A keynote lecture and a coordinated social media campaign enhanced the scientific messages, and media coverage extended the reach of this event. "Tasting the Tree of Life" highlights the potential of cuisine as a valuable science communication tool.

Tropical forest carbon balance: effects of field- and satellite-based mortality regimes on the dynamics and the spatial structure of Central Amazon forest biomass

NASA Astrophysics Data System (ADS)

Di Vittorio, Alan V.; Negrón-Juárez, Robinson I.; Higuchi, Niro; Chambers, Jeffrey Q.

2014-03-01

Debate continues over the adequacy of existing field plots to sufficiently capture Amazon forest dynamics to estimate regional forest carbon balance. Tree mortality dynamics are particularly uncertain due to the difficulty of observing large, infrequent disturbances. A recent paper (Chambers et al 2013 Proc. Natl Acad. Sci. 110 3949-54) reported that Central Amazon plots missed 9-17% of tree mortality, and here we address ‘why’ by elucidating two distinct mortality components: (1) variation in annual landscape-scale average mortality and (2) the frequency distribution of the size of clustered mortality events. Using a stochastic-empirical tree growth model we show that a power law distribution of event size (based on merged plot and satellite data) is required to generate spatial clustering of mortality that is consistent with forest gap observations. We conclude that existing plots do not sufficiently capture losses because their placement, size, and longevity assume spatially random mortality, while mortality is actually distributed among differently sized events (clusters of dead trees) that determine the spatial structure of forest canopies.

A method for investigating relative timing information on phylogenetic trees.

PubMed

Ford, Daniel; Matsen, Frederick A; Stadler, Tanja

2009-04-01

In this paper, we present a new way to describe the timing of branching events in phylogenetic trees. Our description is in terms of the relative timing of diversification events between sister clades; as such it is complementary to existing methods using lineages-through-time plots which consider diversification in aggregate. The method can be applied to look for evidence of diversification happening in lineage-specific "bursts", or the opposite, where diversification between 2 clades happens in an unusually regular fashion. In order to be able to distinguish interesting events from stochasticity, we discuss 2 classes of neutral models on trees with relative timing information and develop a statistical framework for testing these models. These model classes include both the coalescent with ancestral population size variation and global rate speciation-extinction models. We end the paper with 2 example applications: first, we show that the evolution of the hepatitis C virus deviates from the coalescent with arbitrary population size. Second, we analyze a large tree of ants, demonstrating that a period of elevated diversification rates does not appear to have occurred in a bursting manner.

Responses of tree species to heat waves and extreme heat events.

PubMed

Teskey, Robert; Wertin, Timothy; Bauweraerts, Ingvar; Ameye, Maarten; McGuire, Mary Anne; Steppe, Kathy

2015-09-01

The number and intensity of heat waves has increased, and this trend is likely to continue throughout the 21st century. Often, heat waves are accompanied by drought conditions. It is projected that the global land area experiencing heat waves will double by 2020, and quadruple by 2040. Extreme heat events can impact a wide variety of tree functions. At the leaf level, photosynthesis is reduced, photooxidative stress increases, leaves abscise and the growth rate of remaining leaves decreases. In some species, stomatal conductance increases at high temperatures, which may be a mechanism for leaf cooling. At the whole plant level, heat stress can decrease growth and shift biomass allocation. When drought stress accompanies heat waves, the negative effects of heat stress are exacerbated and can lead to tree mortality. However, some species exhibit remarkable tolerance to thermal stress. Responses include changes that minimize stress on photosynthesis and reductions in dark respiration. Although there have been few studies to date, there is evidence of within-species genetic variation in thermal tolerance, which could be important to exploit in production forestry systems. Understanding the mechanisms of differing tree responses to extreme temperature events may be critically important for understanding how tree species will be affected by climate change. © 2014 John Wiley & Sons Ltd.

The Strong Wind event of 24th January 2009 in Catalonia: a social impact analysis

NASA Astrophysics Data System (ADS)

Amaro, J.; Aran, M.; Barberia, L.; Llasat, M. C.

2009-09-01

Although strong winds are frequent in Catalonia, one of the events with the strongest impact in recent years was on January 24th 2009. An explosive cyclogenesis process took place in the Atlantic: pressure fell 30 hPa in less than 24 hours. The strong wind storm pounded the northern of Spain and the south of France with some fatalities and important economic losses in these regions. Several automatic weather stations recorded wind gusts higher than 100 km/h in Catalonia. Emergency services received more than 20.000 calls in 24 hours and there were 497 interventions in only 12 hours. As a consequence of fallen and uprooted trees railway and road infrastructures got damages and more than 30.000 customers had no electricity during 24 hours. Unfortunately there were a total of 6 fatalities, two of them because of fallen trees and the other ones when a sports centre collapsed over a group of children. In Spain, insurance policies cover damages due to strong winds when fixed thresholds are overcome and, according to the Royal Decree 300/2004 of 20th February, extraordinary risk are assumed by the Consorcio de Compensación de Seguros. Subsequently, Public Weather Services (PWS) had an increased on the number of requests received from people affected by this event and from insurance companies, for the corresponding indemnity or not. As an example, during the first month after the event, in the Servei Meteorològic de Catalunya (SMC) more than 600 requests were received only related to these damages (as an average PWS of SMC received a total of 400 requests per month). Following the research started by the Social Impact Research Group of MEDEX project, a good vulnerability indicator of a meteorological risk can be the number of requests reported. This study uses the information received in the PWS of the SMC during the six months after the event, according the criteria and methodology established in Gayà et al (2008). The objective is to compare the vulnerability with the hazard intensity and to analyze elements at risk. In order to do this, data about population density, land uses, type of damages and media information are also considered. The first results show that the major number of requests corresponds to areas densely populated, with vulnerable urban materials, and to residential areas, where fallen trees caused damages on buildings. However, the highest wind gusts were recorded in rural areas where a minor number of requests have been reported in spite of the ecological damages. Finally, the different risk perception of the population played an important role in their reaction to the warnings received.

An estimate of the number of tropical tree species.

PubMed

Slik, J W Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L; Bellingham, Peter J; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L M; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K; Chazdon, Robin L; Robin, Chazdon L; Clark, Connie; Clark, David B; Clark, Deborah A; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A O; Eisenlohr, Pedro V; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A; Joly, Carlos A; de Jong, Bernardus H J; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F; Lawes, Michael J; Amaral, Ieda Leao do; Letcher, Susan G; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H; Meilby, Henrik; Melo, Felipe P L; Metcalfe, Daniel J; Medjibe, Vincent P; Metzger, Jean Paul; Millet, Jerome; Mohandass, D; Montero, Juan C; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T F; Pitman, Nigel C A; Poorter, Lourens; Poulsen, Axel D; Poulsen, John; Powers, Jennifer; Prasad, Rama C; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; Dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A; Santos, Fernanda; Sarker, Swapan K; Satdichanh, Manichanh; Schmitt, Christine B; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I-Fang; Sunderland, Terry; Sunderand, Terry; Suresh, H S; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L C H; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A; Webb, Campbell O; Whitfeld, Timothy; Wich, Serge A; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C Yves; Yap, Sandra L; Yoneda, Tsuyoshi; Zahawi, Rakan A; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L; Garcia Luize, Bruno; Venticinque, Eduardo M

2015-06-16

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

Mistletoe infection alters the transpiration flow path and suppresses water regulation of host trees during extreme events

NASA Astrophysics Data System (ADS)

Griebel, A.; Maier, C.; Barton, C. V.; Metzen, D.; Renchon, A.; Boer, M. M.; Pendall, E.

2017-12-01

Mistletoe is a globally distributed group of parasitic plants that infiltrates the vascular tissue of its host trees to acquire water, carbon and nutrients, making it a leading agent of biotic disturbance. Many mistletoes occur in water-limited ecosystems, thus mistletoe infection in combination with increased climatic stress may exacerbate water stress and potentially accelerate mortality rates of infected trees during extreme events. This is an emerging problem in Australia, as mistletoe distribution is increasing and clear links between mistletoe infection and mortality have been established. However, direct observations about how mistletoes alter host physiological processes during extreme events are rare, which impedes our understanding of mechanisms underlying increased tree mortality rates. We addressed this gap by continuously monitoring stem and branch sap flow and a range of leaf traits of infected and uninfected trees of two co-occurring eucalypt species during a severe heatwave in south-eastern Australia. We demonstrate that mistletoes' leaf water potentials were maintained 30% lower than hosts' to redirect the trees' transpiration flow path towards mistletoe leaves. Eucalypt leaves reduced water loss through stomatal regulation when atmospheric dryness exceeded 2 kPa, but the magnitude of stomatal regulation in non-infected eucalypts differed by species (between 40-80%). Remarkably, when infected, sap flow rates of stems and branches of both eucalypt species remained unregulated even under extreme atmospheric dryness (>8 kPa). Our observations indicate that excessive water use of mistletoes likely increases xylem cavitation rates in hosts during prolonged droughts and supports that hydraulic failure contributes to increased mortality of infected trees. Hence, in order to accurately model the contribution of biotic disturbances to tree mortality under a changing climate, it will be crucial to increase our process-based understanding of the interaction between biotic and abiotic dynamics, especially to establish thresholds of critical cavitation rates of infected trees.

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

PubMed

McTavish, Emily Jane; Steel, Mike; Holder, Mark T

2015-12-01

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree - though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of the 2015/16 ENSO event on tropical trees in regrowing secondary forests in Central Panama

NASA Astrophysics Data System (ADS)

Bretfeld, M.; Ewers, B. E.; Hall, J. S.; Ogden, F. L.

2016-12-01

The 2015/16 El Niño-Southern Oscillation (ENSO) event ranks amongst the driest and hottest periods on record in Panama, with severe drought conditions reported for over 90% of the country. A predicted long-term transition into a drier climatic period makes this event an ideal opportunity to study the effects of drought on tropical tree species in secondary forests of central Panama. These forests are associated with desirable hydrological ecosystem services, characterized by reduced peak runoff during high precipitation events in the rainy season and increased base flow during the dry season ("sponge-effect"), making these forest invaluable for water provisioning for the Panama Canal's $2 billion business and Panama's thriving capital city. Starting in February 2015, we installed heat-ratio sap flow sensors in 76 trees (representing 42 different species) in secondary forests of three different ages (8, 25, and 80+ years) in the 15 km2 Agua Salud study area, located in the Panama Canal Watershed. Within each site, trees were selected to represent local tree size distribution. Additional sensors were installed on the roots of a subset of trees. Sap flow data were logged every 30 minutes and soil moisture was measured every 3 minutes at 10, 30, 50, and 100 cm depth. Pre-dawn, mid-day, and pre-dusk leaf water potentials were measured during the dry season (March 2016) and rainy season (July 2016). Meteorological data were taken from a nearby met-station ("Celestino"). Primary drivers of transpiration were vapor pressure deficit and solar radiation. Trees of the 25 and 80+ year old forests appear not water limited during the dry season following ENSO while reduced sap flow rates of trees in the 8 year old forest are indicative of a regulatory response to the drought. Younger understory trees in the 80+ year old forest showed no signs of a drought response. Throughout most of the dry season, volumetric water content at 30 and 50 cm depths was 8% lower in the 8 year old forest than in the 80+ year old forest. Our data indicate higher resilience to drought in older forest and support that hydrological properties improve as secondary forests mature in central Panama.

Which Types of Leadership Styles Do Followers Prefer? A Decision Tree Approach

ERIC Educational Resources Information Center

Salehzadeh, Reza

2017-01-01

Purpose: The purpose of this paper is to propose a new method to find the appropriate leadership styles based on the followers' preferences using the decision tree technique. Design/methodology/approach: Statistical population includes the students of the University of Isfahan. In total, 750 questionnaires were distributed; out of which, 680…

Early crop-tree release in even-aged stands of Appalachian hardwoods

Treesearch

George R., Jr. Trimble; George R. Trimble

1971-01-01

Now that even-aged silviculture is well established as a successful method of growing Appalachian hardwoods, a pressing need exists for guidelines for precommercial operations. We started research several years ago on the Fernow Experimental Forest near Parsons, West Virginia, to learn more about the cost and methodology of early crop-tree release in mountain hardwood...

Discovering Decision Knowledge from Web Log Portfolio for Managing Classroom Processes by Applying Decision Tree and Data Cube Technology.

ERIC Educational Resources Information Center

Chen, Gwo-Dong; Liu, Chen-Chung; Ou, Kuo-Liang; Liu, Baw-Jhiune

2000-01-01

Discusses the use of Web logs to record student behavior that can assist teachers in assessing performance and making curriculum decisions for distance learning students who are using Web-based learning systems. Adopts decision tree and data cube information processing methodologies for developing more effective pedagogical strategies. (LRW)

Impacts of short-term heatwaves on sun-induced chlorophyll fluorescence(SiF) in temperate tree species

NASA Astrophysics Data System (ADS)

Wang, F.; Gu, L.; Guha, A.; Han, J.; Warren, J.

2017-12-01

The current projections for global climate change forecast an increase in the intensity and frequency of extreme climatic events, such as droughts and short-term heat waves. Understanding the effects of short-term heat wave on photosynthesis process is of critical importance to predict global impacts of extreme weather event on vegetation. The diurnal and seasonal characteristics of SIF emitted from natural vegetation, e.g., forest and crop, have been studied at the ecosystem-scale, regional-scale and global-scale. However, the detailed response of SIF from different plant species under extremely weather event, especially short-term heat wave, have not been reported. The purpose of this study was to study the response of solar-induced chlorophyll fluorescence, gas exchange and continuous fluorescence at leaf scale for different temperate tree species. The short-term heatwave experiment was conducted using plant growth chamber (CMP6050, Conviron Inc., Canada). We developed an advanced spectral fitting method to obtain the plant SIF in the plant growth chamber. We compared SIF variation among different wavelength and chlorophyll difference among four temperate tree species. The diurnal variation of SIF signals at leaf-scales for temperate tree species are different under heat stress. The SIF response at leaf-scales and their difference for four temperate tree species are different during a cycle of short-term heatwave stress. We infer that SIF be used as a measure of heat tolerance for temperate tree species.

Assessment of Methods to Determine Tree Ring Response to Large Magnitude Mississippi River Floods

NASA Astrophysics Data System (ADS)

Therrell, M. D.; Meko, M. D.; Bialecki, M.; Remo, J. W.

2017-12-01

Riparian trees that experience prolonged inundation can record major flood events as inter-and intra-annual variability in size, shape and arrangement of vessels in the annual xylem growth increment. As part of an NSF-funded project to develop tree-ring records of past flooding, we have made collections of several oak species (e.g., Quercus lyrata, Q. macrocarpa) at six sites in the Mississippi River Basin. At each of these sites sampled trees exhibit notably anomalous anatomy of growth increments formed in years coinciding with major recorded floods. We have used these "flood rings" to develop individual site chronologies as well as a regional chronology of spring flood events in the basin for the past several hundred years. We have also analyzed earlywood vessel diameter as a proxy for flooding and find that although this variable reflects only a fraction of the annual-growth increment it strongly reflects tree response to flooding at all the sites so far examined. We compare both these chronologies with the instrumental and historical record of flooding and find that our chronologies are recording nearly all large observed Mississippi River floods in the 20th century, and provide a new record of similar events in the 18th and 19th centuries. These results suggest that tree-rings can be effectively used to develop and improve pre-instrumental flood records throughout the basin and potentially other similar systems.

Decision tree methods: applications for classification and prediction.

PubMed

Song, Yan-Yan; Lu, Ying

2015-04-25

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

Allometric scaling theory applied to FIA biomass estimation

Treesearch

David C. Chojnacky

2002-01-01

Tree biomass estimates in the Forest Inventory and Analysis (FIA) database are derived from numerous methodologies whose abundance and complexity raise questions about consistent results throughout the U.S. A new model based on allometric scaling theory ("WBE") offers simplified methodology and a theoretically sound basis for improving the reliability and...

Divergence in strategies for coping with winter embolism among co-occurring temperate tree species: the role of positive xylem pressure, wood type and tree stature

Treesearch

Cun-Yang Niu; Frederick C. Meinzer; Guang-You Hao

2017-01-01

1. In temperate ecosystems, freeze-thaw events are an important environmental stress that can induce severe xylem embolism (i.e. clogging of conduits by air bubbles) in overwintering organs of trees. However, no comparative studies of different adaptive strategies among sympatric tree species for coping with winter embolism have examined the potential role of the...

Structural Equation Model Trees

PubMed Central

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

2015-01-01

In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree structures that separate a data set recursively into subsets with significantly different parameter estimates in a SEM. SEM Trees provide means for finding covariates and covariate interactions that predict differences in structural parameters in observed as well as in latent space and facilitate theory-guided exploration of empirical data. We describe the methodology, discuss theoretical and practical implications, and demonstrate applications to a factor model and a linear growth curve model. PMID:22984789

Strip-Bark Morphology and Radial Growth Trends in Ancient Pinus sibirica Trees From Central Mongolia

NASA Astrophysics Data System (ADS)

Leland, Caroline; Cook, Edward R.; Andreu-Hayles, Laia; Pederson, Neil; Hessl, Amy; Anchukaitis, Kevin J.; Byambasuren, Oyunsanaa; Nachin, Baatarbileg; Davi, Nicole; D'Arrigo, Rosanne; Griffin, Kevin; Bishop, Daniel A.; Rao, Mukund Palat

2018-03-01

Some of the oldest and most important trees used for dendroclimatic reconstructions develop strip-bark morphology, in which only a portion of the stem contains living tissue. Yet the ecophysiological factors initiating strip bark and the potential effect of cambial dieback on annual ring widths and tree-ring estimates of past climate remain poorly understood. Using a combination of field observations and tree-ring data, we investigate the causes and timing of cambial dieback events in Pinus sibirica strip-bark trees from central Mongolia and compare the radial growth rates and trends of strip-bark and whole-bark trees over the past 515 years. Results indicate that strip bark is more common on the southern aspect of trees, and dieback events were most prevalent in the 19th century, a cold and dry period. Further, strip-bark and whole-bark trees have differing centennial trends, with strip-bark trees exhibiting notably large increases in ring widths at the beginning of the 20th century. We find a steeper positive trend in the strip-bark chronology relative to the whole-bark chronology when standardizing with age-dependent splines. We hypothesize that localized warming on the southern side of stems due to solar irradiance results in physiological damage and dieback and leads to increasing tree-ring increment along the living portion of strip-bark trees. Because the impact of cambial dieback on ring widths likely varies depending on species and site, we suggest conducting a comparison of strip-bark and whole-bark ring widths before statistically treating ring-width data for climate reconstructions.

The use of minimal spanning trees in particle physics

DOE PAGES

Rainbolt, J. Lovelace; Schmitt, M.

2017-02-14

Minimal spanning trees (MSTs) have been used in cosmology and astronomy to distinguish distributions of points in a multi-dimensional space. They are essentially unknown in particle physics, however. We briefly define MSTs and illustrate their properties through a series of examples. We show how they might be applied to study a typical event sample from a collider experiment and conclude that MSTs may prove useful in distinguishing different classes of events.

The use of minimal spanning trees in particle physics

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

Rainbolt, J. Lovelace; Schmitt, M.

Minimal spanning trees (MSTs) have been used in cosmology and astronomy to distinguish distributions of points in a multi-dimensional space. They are essentially unknown in particle physics, however. We briefly define MSTs and illustrate their properties through a series of examples. We show how they might be applied to study a typical event sample from a collider experiment and conclude that MSTs may prove useful in distinguishing different classes of events.

Temporal Association Between Nonfatal Self-Directed Violence and Tree and Grass Pollen Counts.

PubMed

Jeon-Slaughter, Haekyung; Claassen, Cynthia A; Khan, David A; Mihalakos, Perry; Lee, Kevin B; Brown, E Sherwood

2016-09-01

Prior research suggests a possible association between pollen and suicide. No studies have examined the relationship between pollen and attempted suicide. This study examines the temporal association between airborne pollen counts and nonfatal suicidal and nonsuicidal self-directed violence (SDV) requiring an emergency department visit. Data on daily emergency department visits due to nonfatal SDV as identified by ICD-9 diagnosis criteria were extracted from emergency department medical records of Parkland Memorial Hospital in Dallas, Texas, between January 2000 and December 2003. Concurrent daily airborne tree, grass, and ragweed pollen data from the city of Dallas were extracted from the National Allergy Bureau online database. The data were analyzed using the time series method of generalized autoregressive conditional heteroskedasticity. There were statistically significant and positive temporal associations between tree pollen counts and the number of nonfatal SDV events among women (P = .04) and between grass pollen counts and number of nonfatal SDV events among both men (P = .03) and women (P < .0001). There was no significant temporal association found between ragweed pollen counts and number of nonfatal SDV events. The study findings suggest that an increase in nonfatal SDV is associated with changes in tree and grass pollen counts. This is the first study that has examined an association between seasonal variation in tree and grass pollen levels and nonfatal SDV event data. The study also used a narrowly defined geographic area and temporal window. The findings suggest that pollen count may be a factor influencing seasonal patterns in suicidal behavior. © Copyright 2016 Physicians Postgraduate Press, Inc.

Can Religious Beliefs be a Protective Factor for Suicidal Behavior? A Decision Tree Analysis in a Mid-Sized City in Iran, 2013.

PubMed

Baneshi, Mohammad Reza; Haghdoost, Ali Akbar; Zolala, Farzaneh; Nakhaee, Nouzar; Jalali, Maryam; Tabrizi, Reza; Akbari, Maryam

2017-04-01

This study aimed to assess using tree-based models the impact of different dimensions of religion and other risk factors on suicide attempts in the Islamic Republic of Iran. Three hundred patients who attempted suicide and 300 age- and sex-matched patient attendants with other types of disease who referred to Kerman Afzalipour Hospital were recruited for this study following a convenience sampling. Religiosity was assessed by the Duke University Religion Index. A tree-based model was constructed using the Gini Index as the homogeneity criterion. A complementary discrimination analysis was also applied. Variables contributing to the construction of the tree were stressful life events, mental disorder, family support, and religious belief. Strong religious belief was a protective factor for those with a low number of stressful life events and those with a high mental disorder score; 72 % of those who formed these two groups had not attempted suicide. Moreover, 63 % of those with a high number of stressful life events, strong family support, strong problem-solving skills, and a low mental disorder score were less likely to attempt suicide. The significance of four other variables, GHQ, problem-coping skills, friend support, and neuroticism, was revealed in the discrimination analysis. Religious beliefs seem to be an independent factor that can predict risk for suicidal behavior. Based on the decision tree, religious beliefs among people with a high number of stressful life events might not be a dissuading factor. Such subjects need more family support and problem-solving skills.

Historical vegetation change in Oakland and its implications for urban forest management

Treesearch

David J. Nowak

1993-01-01

The history of Oakland, California's urban forest was researched to determine events that could influence future urban forests. Vegetation in Oakland has changed drastically from a preurbanized area with approximately 2% tree cover to a present tree cover of 19%. Species composition of trees was previously dominated by coast live oak (Quercus agrifolia...

Patterns of conifer tree regeneration following an autumn wildfire event in the western Oregon Cascade Range, USA.

Treesearch

Andrew J. Larson; Jerry F. Franklin

2005-01-01

We investigated the effect of fire severity and environmental conditions on conifer tree regeneration 11 years after an autumn wildfire in the western Oregon Cascade Range. Conifer tree seedlings, including those of Pseudotsuga menziesii, established promptly and at high densities following fire, in contrast to long establishment periods documented...

Reliability computation using fault tree analysis

NASA Technical Reports Server (NTRS)

Chelson, P. O.

1971-01-01

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

A framework for adapting urban forests to climate change

Treesearch

Leslie Brandt; Abigail Derby Lewis; Robert Fahey; Lydia Scott; Lindsay Darling; Chris Swanston

2016-01-01

Planting urban trees and expanding urban forest canopy cover are often considered key strategies for reducing climate change impacts in urban areas. However, urban trees and forests can also be vulnerable to climate change through shifts in tree habitat suitability, changes in pests and diseases, and changes in extreme weather events. We developed a three-step...

Survival and ecophysiology of tree seedlings during El Nino drought in a tropical moist forest in Panama

Treesearch

Betinna M.J. Engelbrecht; S. Joseph Wright; Diane De Steven

2002-01-01

In tropical forests, severe droughts caused by El Nino events may strongly influence the water relations of tree seedlings and thereby increase their mortality. Data on known-aged seedlings of three common shade-tolerant canopy tree species (Trichilia tuberculata, Tetragastris panamensis and Quararibea asterolepis) in a Panamanian...

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.

Evaluation of growth disturbances of Picea abies (L.) Karst. to disturbances caused by landslide movements

NASA Astrophysics Data System (ADS)

Šilhán, Karel

2017-01-01

Dendrogeomorphic methods are frequently used in landslide analyses. Although methods of landslide dating based on tree rings are well developed, they still indicated many questions. The aim of this study was to evaluate the frequently used theoretical scheme based on the event-response relationship. Seventy-four individuals of Norway spruce (Picea abies (L.) Karst.) exhibiting visible external disturbance, were sampled on the Girová landslide (the largest historical flow-like landslide in the Czech Republic). This landslide reactivated in May 2010, and post-landslide tree growth responses were studied in detail. These growth responses were compared with the intensity and occurrence of visible external tree disturbance: tilted stems, damaged root systems, and decapitation. Twenty-nine trees (39.2%) died within one to four years following the 2010 landslide movement. The trees that died following the landslide movement were significantly younger and displayed significantly greater stem tilting than the live trees. Abrupt growth suppression was a more-frequent response among the dead trees, whereas growth release dominated among the live trees. Only two trees (2.7%) created no reaction wood in response to the landslide movement. Forty-four percent of the trees started to produce reaction wood structure after a delay, which generally spanned one year. Some eccentric growth was evident in the tree rings of the landslide year and was significant in the first years following the landslide movement. Missing rings were observed only on the upper sides of the stems, and no false tree rings were observed. The results confirm the general validity of event-response relationship, nevertheless this study points out the limitations and uncertainties of this generally accepted working scheme.

Drought-induced changes in Amazon forest structure from repeat airborne lidar

NASA Astrophysics Data System (ADS)

Morton, D. C.; Leitold, V.; Longo, M.; Keller, M.; dos-Santos, M. N.; Scaranello, M. A., Sr.

2017-12-01

Drought events in tropical forests, including the 2015-2016 El Niño, may reduce net primary productivity and increase canopy tree mortality, thereby altering the short and long-term net carbon balance of tropical forests. Given the broad extent of drought impacts, forest inventory plots or eddy flux towers may not capture regional variability in forest response to drought. Here, we analyzed repeat airborne lidar data to evaluate canopy turnover from branch and tree fall before (2013-2014) and during (2014-2016) the recent El Niño drought in the eastern and central Brazilian Amazon. Coincident field surveys for a 16-ha subset of the lidar coverage provided complementary information to classify turnover areas by mechanism (branch, multiple branch, tree fall, multiple tree fall) and estimate the total coarse woody debris volume from canopy and understory tree mortality. Annualized rates of canopy turnover increased by 50%, on average, during the drought period in both intact and fragmented forests near Santarém, Pará. Turnover increased uniformly across all size classes, and there was limited evidence that taller trees contributed a greater proportion of turnover events in any size class in 2014-2016 compared to 2013-2014. This short-term increase in canopy turnover differs from findings in multi-year rainfall exclusion experiments that large trees were more sensitive to drought impacts. Field measurements confirmed the separability of the smallest (single branch) and largest damage classes (multiple tree falls), but single tree and multiple branch fall events generated similar coarse woody debris production and lidar-derived changes in canopy volume. Large-scale sampling possible with repeat airborne lidar data also captured strong local and regional gradients in canopy turnover. Differences in slope partially explained the north-south gradient in canopy turnover dynamics near Santarém, with larger increases in turnover on flatter terrain. Regional variability in canopy turnover in response to drought conditions highlights the need for a mechanistic representation of branch and tree fall dynamics in ecosystem models to resolve changes in net carbon balance from the increase in coarse woody debris production and reorganization of canopy light environments during drought years.

Modeling flash floods in ungauged mountain catchments of China: A decision tree learning approach for parameter regionalization

NASA Astrophysics Data System (ADS)

Ragettli, S.; Zhou, J.; Wang, H.; Liu, C.

2017-12-01

Flash floods in small mountain catchments are one of the most frequent causes of loss of life and property from natural hazards in China. Hydrological models can be a useful tool for the anticipation of these events and the issuing of timely warnings. Since sub-daily streamflow information is unavailable for most small basins in China, one of the main challenges is finding appropriate parameter values for simulating flash floods in ungauged catchments. In this study, we use decision tree learning to explore parameter set transferability between different catchments. For this purpose, the physically-based, semi-distributed rainfall-runoff model PRMS-OMS is set up for 35 catchments in ten Chinese provinces. Hourly data from more than 800 storm runoff events are used to calibrate the model and evaluate the performance of parameter set transfers between catchments. For each catchment, 58 catchment attributes are extracted from several data sets available for whole China. We then use a data mining technique (decision tree learning) to identify catchment similarities that can be related to good transfer performance. Finally, we use the splitting rules of decision trees for finding suitable donor catchments for ungauged target catchments. We show that decision tree learning allows to optimally utilize the information content of available catchment descriptors and outperforms regionalization based on a conventional measure of physiographic-climatic similarity by 15%-20%. Similar performance can be achieved with a regionalization method based on spatial proximity, but decision trees offer flexible rules for selecting suitable donor catchments, not relying on the vicinity of gauged catchments. This flexibility makes the method particularly suitable for implementation in sparsely gauged environments. We evaluate the probability to detect flood events exceeding a given return period, considering measured discharge and PRMS-OMS simulated flows with regionalized parameters. Overall, the probability of detection of an event with a return period of 10 years is 62%. 44% of all 10-year flood peaks can be detected with a timing error of 2 hours or less. These results indicate that the modeling system can provide useful information about the timing and magnitude of flood events at ungauged sites.

Drought frequency in central California since 101 B.C. recordered in giant sequoia tree rings

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

Hughes, M.K.; Brown, P.M.

1992-01-01

Well replicated tree-ring width index chronologies have been developed for giant sequoia at three sites in the Sierra Nevada, California. Extreme low-growth events in these chronologies correspond with regional drought events in the twentieth century in the San Joaquin drainage, in which the giant sequoia sites are located. This relationship is based upon comparison of tree-ring indices with August Palmer Drought Severity Indices for California Climate Division 5. Ring-width indices in the lowest decile from each site were compared. The frequency of low-growth events which occurred at all three sites in the same year is reconstructed from 101 B.C. tomore » A.D. 1988. The inferred frequency of severe drought events changes through time, sometimes suddenly. The period from roughly 1850 to 1950 had one of the lowest frequencies of drought of any one hundred year period in the 2089 year record. The twentieth century so far has had a below-average frequency of extreme droughts. 26 refs., 6 figs., 1 tab.« less

Fault tree analysis for urban flooding.

PubMed

ten Veldhuis, J A E; Clemens, F H L R; van Gelder, P H A J M

2009-01-01

Traditional methods to evaluate flood risk generally focus on heavy storm events as the principal cause of flooding. Conversely, fault tree analysis is a technique that aims at modelling all potential causes of flooding. It quantifies both overall flood probability and relative contributions of individual causes of flooding. This paper presents a fault model for urban flooding and an application to the case of Haarlem, a city of 147,000 inhabitants. Data from a complaint register, rainfall gauges and hydrodynamic model calculations are used to quantify probabilities of basic events in the fault tree. This results in a flood probability of 0.78/week for Haarlem. It is shown that gully pot blockages contribute to 79% of flood incidents, whereas storm events contribute only 5%. This implies that for this case more efficient gully pot cleaning is a more effective strategy to reduce flood probability than enlarging drainage system capacity. Whether this is also the most cost-effective strategy can only be decided after risk assessment has been complemented with a quantification of consequences of both types of events. To do this will be the next step in this study.

Using Boosting Decision Trees in Gravitational Wave Searches triggered by Gamma-ray Bursts

NASA Astrophysics Data System (ADS)

Zuraw, Sarah; LIGO Collaboration

2015-04-01

The search for gravitational wave bursts requires the ability to distinguish weak signals from background detector noise. Gravitational wave bursts are characterized by their transient nature, making them particularly difficult to detect as they are similar to non-Gaussian noise fluctuations in the detector. The Boosted Decision Tree method is a powerful machine learning algorithm which uses Multivariate Analysis techniques to explore high-dimensional data sets in order to distinguish between gravitational wave signal and background detector noise. It does so by training with known noise events and simulated gravitational wave events. The method is tested using waveform models and compared with the performance of the standard gravitational wave burst search pipeline for Gamma-ray Bursts. It is shown that the method is able to effectively distinguish between signal and background events under a variety of conditions and over multiple Gamma-ray Burst events. This example demonstrates the usefulness and robustness of the Boosted Decision Tree and Multivariate Analysis techniques as a detection method for gravitational wave bursts. LIGO, UMass, PREP, NEGAP.

Vulnerability of Amazon forests to storm-driven tree mortality

NASA Astrophysics Data System (ADS)

Negrón-Juárez, Robinson I.; Holm, Jennifer A.; Magnabosco Marra, Daniel; Rifai, Sami W.; Riley, William J.; Chambers, Jeffrey Q.; Koven, Charles D.; Knox, Ryan G.; McGroddy, Megan E.; Di Vittorio, Alan V.; Urquiza-Muñoz, Jose; Tello-Espinoza, Rodil; Alegria Muñoz, Waldemar; Ribeiro, Gabriel H. P. M.; Higuchi, Niro

2018-05-01

Tree mortality is a key driver of forest community composition and carbon dynamics. Strong winds associated with severe convective storms are dominant natural drivers of tree mortality in the Amazon. Why forests vary with respect to their vulnerability to wind events and how the predicted increase in storm events might affect forest ecosystems within the Amazon are not well understood. We found that windthrows are common in the Amazon region extending from northwest (Peru, Colombia, Venezuela, and west Brazil) to central Brazil, with the highest occurrence of windthrows in the northwest Amazon. More frequent winds, produced by more frequent severe convective systems, in combination with well-known processes that limit the anchoring of trees in the soil, help to explain the higher vulnerability of the northwest Amazon forests to winds. Projected increases in the frequency and intensity of convective storms in the Amazon have the potential to increase wind-related tree mortality. A forest demographic model calibrated for the northwestern and the central Amazon showed that northwestern forests are more resilient to increased wind-related tree mortality than forests in the central Amazon. Our study emphasizes the importance of including wind-related tree mortality in model simulations for reliable predictions of the future of tropical forests and their effects on the Earth’ system.

A spatio-temporal model for probabilistic seismic hazard zonation of Tehran

NASA Astrophysics Data System (ADS)

Hashemi, Mahdi; Alesheikh, Ali Asghar; Zolfaghari, Mohammad Reza

2013-08-01

A precondition for all disaster management steps, building damage prediction, and construction code developments is a hazard assessment that shows the exceedance probabilities of different ground motion levels at a site considering different near- and far-field earthquake sources. The seismic sources are usually categorized as time-independent area sources and time-dependent fault sources. While the earlier incorporates the small and medium events, the later takes into account only the large characteristic earthquakes. In this article, a probabilistic approach is proposed to aggregate the effects of time-dependent and time-independent sources on seismic hazard. The methodology is then applied to generate three probabilistic seismic hazard maps of Tehran for 10%, 5%, and 2% exceedance probabilities in 50 years. The results indicate an increase in peak ground acceleration (PGA) values toward the southeastern part of the study area and the PGA variations are mostly controlled by the shear wave velocities across the city. In addition, the implementation of the methodology takes advantage of GIS capabilities especially raster-based analyses and representations. During the estimation of the PGA exceedance rates, the emphasis has been placed on incorporating the effects of different attenuation relationships and seismic source models by using a logic tree.

Evaluation of the diagnostic feasibility of the electronic nose in detecting incipient decay of artificially inoculated wood

Treesearch

Manuela Baietto; A. Dan Wilson; Daniele Bassi; Francesco Ferrini

2008-01-01

The tree stability-assessment methodology currently used in Italian cities initially follows a visual analysis of individual trees, followed by an evaluation of the internal state using different instruments that are often invasive, expensive, or cannot be effectively used in the urban environment. Moreover, many of these instruments do not provide an adequate...

Development of a standardized methodology for quantifying total chlorophyll and carotenoids from foliage of hardwood and conifer tree species

Treesearch

Rakesh Minocha; Gabriela Martinez; Benjamin Lyons; Stephanie Long

2009-01-01

Despite the availability of several protocols for the extraction of chlorophylls and carotenoids from foliage of forest trees, information regarding their respective extraction efficiencies is scarce. We compared the efficiencies of acetone, ethanol, dimethyl sulfoxide (DMSO), and N, N-dimethylformamide (DMF) over a range of incubation times for the extraction of...

Joint proceedings, Second Genetics Workshop of the Society of American Foresters and Seventh Lake States Forest Tree Improvement Conference, October 21-23, 1965.

Treesearch

NCFES

1966-01-01

Included are (1) 22 technical papers (by researchers from many sections of the United States and Canada) pertaining to selection and progeny testing, radiation genetics, intraspecific variation, natural and artificial hybridization, breeding systems, breeding methodology and specialized tree breeding techniques, and applied breeding and allied fields; (2) concise...

D.B.H. and Survival Analysis: A New Methodology for Assessing Forest Inventory Mortality

Treesearch

Christopher W. Woodall; Patricia L. Grambsch; William Thomas

2005-01-01

Tree mortality has typically been assessed in Forest Inventory and Analysis (FIA) studies through summaries of mortality by location, species, and causal agents. Although these methods have historically been used for most of FIA's tree mortality analyses, they are inadequate for robust assessment of mortality trends and dynamics. To offer a new method of analyzing...

Comparing Methodologies for Developing an Early Warning System: Classification and Regression Tree Model versus Logistic Regression. REL 2015-077

ERIC Educational Resources Information Center

Koon, Sharon; Petscher, Yaacov

2015-01-01

The purpose of this report was to explicate the use of logistic regression and classification and regression tree (CART) analysis in the development of early warning systems. It was motivated by state education leaders' interest in maintaining high classification accuracy while simultaneously improving practitioner understanding of the rules by…

Theoretical implications for the estimation of dinitrogen fixation by large perennial plant species using isotope dilution

Treesearch

Dwight D. Baker; Maurice Fried; John A. Parrotta

1995-01-01

Estimation of symbiotic N2 fixation associated with large perennial plant species, especially trees, poses special problems because the process must be followed over a potentially long period of time to integrate the total amount of fixation. Estimations using isotope dilution methodology have begun to be used for trees in field studies. Because...

3D reconstruction of a tree stem using video images and pulse distances

Treesearch

N. E. Clark

2002-01-01

This paper demonstrates how a 3D tree stem model can be reconstructed using video imagery combined with laser pulse distance measurements. Perspective projection is used to place the data collected with the portable video laser-rangefinding device into a real world coordinate system. This hybrid methodology uses a relatively small number of range measurements (compared...

How Much Water Trees Access and How It Determines Forest Response to Drought

NASA Astrophysics Data System (ADS)

Berdanier, A. B.; Clark, J. S.

2015-12-01

Forests are transformed by drought as water availability drops below levels where trees of different sizes and species can maintain productivity and survive. Physiological studies have provided detailed understanding of how species differences affect drought vulnerability but they offer almost no insights about the amount of water different trees can access beyond general statements about rooting depth. While canopy architecture provides strong evidence for light availability aboveground, belowground moisture availability remains essentially unknown. For example, do larger trees always have greater access to soil moisture? In temperate mixed forests, the ability to access a large soil moisture pool could minimize damage during drought events and facilitate post-drought recovery, potentially at the expense of neighboring trees. We show that the pool of accessible soil moisture can be estimated for trees with data on whole-plant transpiration and that this data can be used to predict water availability for forest stands. We estimate soil water availability with a Bayesian state-space model based on a simple water balance, where cumulative depressions in water use below potential transpiration indicate soil resource depletion. We compare trees of different sizes and species, extend these findings to the entire stand, and connect them to our recent research showing that tree survival after drought depends on post-drought growth recovery and local moisture availability. These results can be used to predict competitive abilities for soil water, understand ecohydrological variation within stands, and identify trees that are at risk of damage from future drought events.

Temporal Dynamics in the Concentration, Flux, and Optical Properties of Tree-derived Dissolved Organic Matter (Tree-DOM) in an Epiphyte-laden Oak-cedar Forest.

NASA Astrophysics Data System (ADS)

Whitetree, A.; Van Stan, J. T., II; Wagner, S.; Guillemette, F.; Lewis, J.; Silva, L.; Stubbins, A.

2017-12-01

Studies on the fate and transport of dissolved organic matter (DOM) along the rainfall-to-discharge flow pathway typically begin in streams or soils, neglecting the initial enrichment of rainfall with DOM during contact with plant canopies. However, rain water can gather significant amounts of tree-derived DOM (tree-DOM) when it drains from the canopy, as throughfall, and down the stem, as stemflow. We examined the temporal variability of event-scale tree-DOM concentrations, yield, and optical (light absorbance and fluorescence) characteristics from an epiphyte-laden Quercus virginiana-Juniperus virginiana forest on Skidaway Island, Savannah, Georgia (USA). All tree-DOM fluxes were highly enriched compared to rainfall and epiphytes further increased concentrations. Stemflow DOC concentrations were greater than throughfall across study species, yet larger throughfall water yields produced greater DOC yields versus stemflow. Tree-DOM optical characteristics indicate it is aromatic-rich with FDOM dominated by humic-like fluorescence, containing 10-20% protein-like (tryptophan-like) fluorescence. Storm size was the only storm condition that strongly correlated with tree-DOM concentration and flux; however, throughfall and stemflow optical characteristics varied little across a wide range of storm conditions (from low magnitude events to intense tropical storms). Annual tree-DOM yields from the study forest (0.8-46 g-C m-2 yr-1) compared well to other yields along the rainfall-to- discharge flow pathway, exceeding DOM yields from some river watersheds.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees.

PubMed

Martínez-Aquino, Andrés

2016-08-01

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

PubMed Central

2016-01-01

Abstract Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host–parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a “compass” when “walking” through jungles of tangled phylogenetic trees. PMID:29491928

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.

PubMed

Bogdanowicz, Damian; Giaro, Krzysztof

2017-05-01

Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.

Tree rings reveal a major episode of forest mortality in the late 18th century on the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Fang, Ouya; Alfaro, René I.; Zhang, Qi-Bin

2018-04-01

There is a growing research interest on studying forest mortality in relation to ongoing climate warming, but little is known about such events in past history. The study of past forest mortality provides valuable information for determining baselines that establish the normal parameters of functioning in forest ecosystems. Here we report a major episode of previously undocumented forest mortality in the late 18th century on the northern Tibetan Plateau, China. The event was not spatially uniform, in which a more severe mortality happened in dryer sites. We used dendrochronology to compare radial growth trajectories of individual trees from 11 sites in the region, and found that many trees showed positive growth trend, or growth release, during 1796-1800 CE. Growth releases are a proxy indicator of stand thinning caused by tree mortality. The growth release was preceded by an almost two-decade long growth reduction. Long-term drought related to weakened North Atlantic Oscillation and frequent El Niño events are the likely factors causing the tree mortality in a large area of the plateau. Our findings suggest that, besides the effect of drought in the late 18th century, large-scale forest mortality may be an additional factor that further deteriorated the environment and increased the intensity of dust storms.

Updated precipitation reconstruction (AD 1482-2012) for Huashan, north-central China

NASA Astrophysics Data System (ADS)

Chen, Feng; Zhang, Ruibo; Wang, Huiqin; Qin, Li; Yuan, Yujiang

2016-02-01

We developed a tree-ring width chronology from pine trees ( Pinus tabulaeformis and Pinus armandii) stand near the peaks of Huashan, Shaanxi, north-central China. Growth-climate response analyses showed that the radial growth of pine trees is mainly influenced by April-June precipitation. A model to reconstruct precipitation based on tree widths was constructed, accounting for 55 % of the instrumental variance during the period 1953-2012. Spatial correlation analyses between the reconstruction and observed gridded precipitation data shows that the seasonal precipitation reconstruction captures regional climatic variations over north China. Compared with the historical archives and other tree-ring records in north China, many large-scale drought events, linked to the El Niño-Southern Oscillation (ENSO), were found. Many of these events have had profound impacts on the people of north China over the past several centuries. Composite maps of sea surface temperatures and 500 hPa geopotential heights for selected extremely dry and wet years in Huashan show characteristics similar to those related to the ENSO patterns, particularly with regard to ocean and atmospheric conditions in the equatorial and north Pacific. Our 531-year precipitation reconstruction for Huashan provides a long-term perspective on current and 20th century wet and dry events in north China, and is useful to guide expectations of future variability, and helps us to address climate change.

Assessing the stability of tree ranges and influence of disturbance in eastern US forests

Treesearch

C.W. Woodall; K. Zhu; J.A. Westfall; C.M. Oswalt; A.W. D' Amato; B.F. Walters; H.E. Lintz

2013-01-01

Shifts in tree species ranges may occur due to global climate change, which in turn may be exacerbated by natural disturbance events. Within the context of global climate change, developing techniques to monitor tree range dynamics as affected by natural disturbances may enable mitigation/adaptation of projected impacts. Using a forest inventory across the eastern U.S...

Biological control reduces growth, and alters water relations of the saltcedar tree (Tamarix spp.) in western Nevada, USA

Treesearch

R.R. Pattison; C.M. D' Antonio; T.L. Dudley

2011-01-01

We monitored the impacts of a biological control agent, the saltcedar leaf beetle (Diorhabda carinulata), on the saltcedar tree (Tamarix spp.) at two sites (Humboldt and Walker rivers) in Nevada, USA. At the Humboldt site trees that had experienced three to four defoliation events had more negative water potentials and lower...

Vernal freeze damage and genetic variation alter tree growth, chemistry, and insect interactions.

PubMed

Rubert-Nason, Kennedy F; Couture, John J; Gryzmala, Elizabeth A; Townsend, Philip A; Lindroth, Richard L

2017-11-01

Anticipated consequences of climate change in temperate regions include early spring warmup punctuated by intermittent hard freezes. Warm weather accelerates leaf flush in perennial woody species, potentially exposing vulnerable young tissues to damaging frosts. We employed a 2 × 6 randomized factorial design to examine how the interplay of vernal (springtime) freeze damage and genetic variation in a hardwood species (Populus tremuloides) influences tree growth, phytochemistry, and interactions with an insect herbivore (Chaitophorus stevensis). Acute effects of freezing included defoliation and mortality. Surviving trees exhibited reduced growth and altered biomass distribution. Reflushed leaves on these trees had lower mass per area, lower lignin concentrations, and higher nitrogen concentrations, altered chemical defence profiles, and supported faster aphid population growth. Many effects varied among plant genotypes and were related with herbivore performance. This study suggests that a single damaging vernal freeze event can alter tree-insect interactions through effects on plant growth and chemistry. Differential responses of various genotypes to freeze damage suggest that more frequent vernal freeze events could also influence natural selection, favouring trees with greater freeze hardiness, and more resistance or tolerance to herbivores following damage. © 2017 John Wiley & Sons Ltd.

The role of hybridization in facilitating tree invasion

PubMed Central

2017-01-01

Abstract Hybridization events can generate additional genetic diversity upon which natural selection can act and at times enhance invasiveness of the species. Invasive tree species are a growing ecological concern worldwide, and some of these invasions involve hybridization events pre- or post-introduction. There are 20 hybrid invasive tree taxa in 15 genera (11 plant families) discussed here. When reported, abundance of hybrids comprised 10–100 % of an invasion, the remainder being parental taxa. In seven hybrid taxa, researchers identified phenotypes that may make hybrids better invaders. Twelve hybrid tree taxa involved introgression and more hybrids involved all non-native taxa than native × non-native taxa. Three hybrid tree taxa were the result of intentional crosses, and all hybrid taxa involved intentional introduction of either one or more parental taxon or the hybrid itself. The knowledge gaps present in some hybrid tree taxa can weaken our effectiveness in predicting and controlling invasions, as hybrids can add a level of complexity to an invasion by being morphologically cryptic, causing genetic pollution of a native parental taxon, presenting novel genotypes for which there may not be coevolved biological control agents, or evolving adaptive traits through increased genetic variation. PMID:28028055

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

A global reference database from very high resolution commercial satellite data and methodology for application to Landsat derived 30 m continuous field tree cover data

USGS Publications Warehouse

Pengra, Bruce; Long, Jordan; Dahal, Devendra; Stehman, Stephen V.; Loveland, Thomas R.

2015-01-01

The methodology for selection, creation, and application of a global remote sensing validation dataset using high resolution commercial satellite data is presented. High resolution data are obtained for a stratified random sample of 500 primary sampling units (5 km  ×  5 km sample blocks), where the stratification based on Köppen climate classes is used to distribute the sample globally among biomes. The high resolution data are classified to categorical land cover maps using an analyst mediated classification workflow. Our initial application of these data is to evaluate a global 30 m Landsat-derived, continuous field tree cover product. For this application, the categorical reference classification produced at 2 m resolution is converted to percent tree cover per 30 m pixel (secondary sampling unit)for comparison to Landsat-derived estimates of tree cover. We provide example results (based on a subsample of 25 sample blocks in South America) illustrating basic analyses of agreement that can be produced from these reference data. Commercial high resolution data availability and data quality are shown to provide a viable means of validating continuous field tree cover. When completed, the reference classifications for the full sample of 500 blocks will be released for public use.

PhySIC_IST: cleaning source trees to infer more informative supertrees

PubMed Central

Scornavacca, Celine; Berry, Vincent; Lefort, Vincent; Douzery, Emmanuel JP; Ranwez, Vincent

2008-01-01

Background Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees. Results To overcome this problem, we propose to infer non-plenary supertrees, i.e. supertrees that do not necessarily contain all the taxa present in the source trees, discarding those whose position greatly differs among source trees or for which insufficient information is provided. We detail a variant of the PhySIC veto method called PhySIC_IST that can infer non-plenary supertrees. PhySIC_IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is estimated using a variation of the CIC (Cladistic Information Content) criterion, that takes into account both the presence of multifurcations and the absence of some taxa. Additionally, we propose a statistical preprocessing step called STC (Source Trees Correction) to correct the source trees prior to the supertree inference. STC is a liberal step that removes the parts of each source tree that significantly conflict with other source trees. Combining STC with a veto method allows an explicit trade-off between veto and liberal approaches, tuned by a single parameter. Performing large-scale simulations, we observe that STC+PhySIC_IST infers much more informative supertrees than PhySIC, while preserving low type I error compared to the well-known MRP method. Two biological case studies on animals confirm that the STC preprocess successfully detects anomalies in the source trees while STC+PhySIC_IST provides well-resolved supertrees agreeing with current knowledge in systematics. Conclusion The paper introduces and tests two new methodologies, PhySIC_IST and STC, that demonstrate the interest in inferring non-plenary supertrees as well as preprocessing the source trees. An implementation of the methods is available at: . PMID:18834542

PhySIC_IST: cleaning source trees to infer more informative supertrees.

PubMed

Scornavacca, Celine; Berry, Vincent; Lefort, Vincent; Douzery, Emmanuel J P; Ranwez, Vincent

2008-10-04

Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees. To overcome this problem, we propose to infer non-plenary supertrees, i.e. supertrees that do not necessarily contain all the taxa present in the source trees, discarding those whose position greatly differs among source trees or for which insufficient information is provided. We detail a variant of the PhySIC veto method called PhySIC_IST that can infer non-plenary supertrees. PhySIC_IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is estimated using a variation of the CIC (Cladistic Information Content) criterion, that takes into account both the presence of multifurcations and the absence of some taxa. Additionally, we propose a statistical preprocessing step called STC (Source Trees Correction) to correct the source trees prior to the supertree inference. STC is a liberal step that removes the parts of each source tree that significantly conflict with other source trees. Combining STC with a veto method allows an explicit trade-off between veto and liberal approaches, tuned by a single parameter.Performing large-scale simulations, we observe that STC+PhySIC_IST infers much more informative supertrees than PhySIC, while preserving low type I error compared to the well-known MRP method. Two biological case studies on animals confirm that the STC preprocess successfully detects anomalies in the source trees while STC+PhySIC_IST provides well-resolved supertrees agreeing with current knowledge in systematics. The paper introduces and tests two new methodologies, PhySIC_IST and STC, that demonstrate the interest in inferring non-plenary supertrees as well as preprocessing the source trees. An implementation of the methods is available at: http://www.atgc-montpellier.fr/physic_ist/.

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.

Simulation of olive grove gross primary production by the combination of ground and multi-sensor satellite data

NASA Astrophysics Data System (ADS)

Brilli, L.; Chiesi, M.; Maselli, F.; Moriondo, M.; Gioli, B.; Toscano, P.; Zaldei, A.; Bindi, M.

2013-08-01

We developed and tested a methodology to estimate olive (Olea europaea L.) gross primary production (GPP) combining ground and multi-sensor satellite data. An eddy-covariance station placed in an olive grove in central Italy provided carbon and water fluxes over two years (2010-2011), which were used as reference to evaluate the performance of a GPP estimation methodology based on a Monteith type model (modified C-Fix) and driven by meteorological and satellite (NDVI) data. A major issue was related to the consideration of the two main olive grove components, i.e. olive trees and inter-tree ground vegetation: this issue was addressed by the separate simulation of carbon fluxes within the two ecosystem layers, followed by their recombination. In this way the eddy covariance GPP measurements were successfully reproduced, with the exception of two periods that followed tillage operations. For these periods measured GPP could be approximated by considering synthetic NDVI values which simulated the expected response of inter-tree ground vegetation to tillages.

An estimate of the number of tropical tree species

PubMed Central

Slik, J. W. Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F.; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L.; Bellingham, Peter J.; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q.; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L. M.; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K.; Chazdon, Robin L.; Clark, Connie; Clark, David B.; Clark, Deborah A.; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S.; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J.; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A. O.; Eisenlohr, Pedro V.; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J.; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T.; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M.; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A.; Joly, Carlos A.; de Jong, Bernardus H. J.; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L.; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F.; Lawes, Michael J.; do Amaral, Ieda Leao; Letcher, Susan G.; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H.; Meilby, Henrik; Melo, Felipe P. L.; Metcalfe, Daniel J.; Medjibe, Vincent P.; Metzger, Jean Paul; Millet, Jerome; Mohandass, D.; Montero, Juan C.; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T. F.; Pitman, Nigel C. A.; Poorter, Lourens; Poulsen, Axel D.; Poulsen, John; Powers, Jennifer; Prasad, Rama C.; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A.; Santos, Fernanda; Sarker, Swapan K.; Satdichanh, Manichanh; Schmitt, Christine B.; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S.; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I.-Fang; Sunderland, Terry; Suresh, H. S.; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W.; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L. C. H.; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A.; Webb, Campbell O.; Whitfeld, Timothy; Wich, Serge A.; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C. Yves; Yap, Sandra L.; Yoneda, Tsuyoshi; Zahawi, Rakan A.; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L.; Garcia Luize, Bruno; Venticinque, Eduardo M.

2015-01-01

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa. PMID:26034279

Environmental controls in the water use patterns of a tropical cloud forest tree species, Drimys brasiliensis (Winteraceae).

PubMed

Eller, Cleiton B; Burgess, Stephen S O; Oliveira, Rafael S

2015-04-01

Trees from tropical montane cloud forest (TMCF) display very dynamic patterns of water use. They are capable of downwards water transport towards the soil during leaf-wetting events, likely a consequence of foliar water uptake (FWU), as well as high rates of night-time transpiration (Enight) during drier nights. These two processes might represent important sources of water losses and gains to the plant, but little is known about the environmental factors controlling these water fluxes. We evaluated how contrasting atmospheric and soil water conditions control diurnal, nocturnal and seasonal dynamics of sap flow in Drimys brasiliensis (Miers), a common Neotropical cloud forest species. We monitored the seasonal variation of soil water content, micrometeorological conditions and sap flow of D. brasiliensis trees in the field during wet and dry seasons. We also conducted a greenhouse experiment exposing D. brasiliensis saplings under contrasting soil water conditions to deuterium-labelled fog water. We found that during the night D. brasiliensis possesses heightened stomatal sensitivity to soil drought and vapour pressure deficit, which reduces night-time water loss. Leaf-wetting events had a strong suppressive effect on tree transpiration (E). Foliar water uptake increased in magnitude with drier soil and during longer leaf-wetting events. The difference between diurnal and nocturnal stomatal behaviour in D. brasiliensis could be attributed to an optimization of carbon gain when leaves are dry, as well as minimization of nocturnal water loss. The leaf-wetting events on the other hand seem important to D. brasiliensis water balance, especially during soil droughts, both by suppressing tree transpiration (E) and as a small additional water supply through FWU. Our results suggest that decreases in leaf-wetting events in TMCF might increase D. brasiliensis water loss and decrease its water gains, which could compromise its ecophysiological performance and survival during dry periods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Fire safety in transit systems fault tree analysis

DOT National Transportation Integrated Search

1981-09-01

Fire safety countermeasures applicable to transit vehicles are identified and evaluated. This document contains fault trees which illustrate the sequences of events which may lead to a transit-fire related casualty. A description of the basis for the...

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

PubMed Central

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

2016-01-01

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

Beyond the extreme: Recovery dynamics following heat and drought stress in trees

NASA Astrophysics Data System (ADS)

Ruehr, N.; Duarte, A. G.; Arneth, A.

2016-12-01

Plant recovery processes following extreme events can have profound impacts on forest carbon and water cycling. However, large knowledge gaps persist on recovery dynamics of tree physiological processes following heat and drought stress. To date, few experimental studies exist that include recovery responses in stress research. We synthesized recent research on tree recovery processes related to carbon and water exchange following heat and drought stress, and show that the intensity of stress can affect the pace of recovery with large variations among tree species and processes. Following stress release, leaf water potential recovers instantaneously upon rewatering as found in most studies. Transpiration (T), stomatal conductance (gs) and photosynthesis (A) often lag behind, with lowest recovery following severe stress. Interestingly, the patterns in heat and drought stress recovery apparently differ. While A recovers generally more quickly than gs following drought, which increases water-use-efficiency, both gs and A tend to remain reduced following heat events. The pace of recovery following heat events likely depends on water availability during stress and temperature maxima reached (photosynthetic impairment at temperatures > 40°C). Slow recovery during the initial post-stress days might result from hydraulic limitation and elevated levels of abscisic acid. The mechanisms resulting in a continued impairment of T and gs during a later stage of the recovery period (from weeks up to months) are still elusive. Feedback loops from the photosynthetic machinery, reduced mesophyll conductance or leaf morphological changes may play an important role. In summary, post-stress recovery can substantially affect tree carbon and water cycling. Thus, in order to estimate the impacts of extreme climate events on forest ecosystems in the long-term, we need a better understanding of recovery dynamics and their limitations in terms of stress timing, intensity and duration.

A Multi-stakeholder Approach to Moving Beyond Tree Mortality in the Sierra Nevada

NASA Astrophysics Data System (ADS)

Balachowski, J.; Buluc, L.; Fischer, C.; Ko, J.; Ostoja, S.

2017-12-01

The US Forest Service has estimated that 102 million trees have died in California since 2010. This die off event has been attributed to the combined effects of historical land management practices, fire suppression, insect outbreaks, and climate-related stressors. This tree mortality event represents the largest and most significant ecological disturbance in California in centuries, if not longer. Both scientists and managers recognize the need to rethink our approach to forest management in the face of a changing climate and increasingly frequent, uncharacteristically large wildfires, while budgets and staffing capacity continue to decrease. Addressing the uncertainly in managing under climate change with fewer financial resources will require multiple partners and stakeholders—including federal and state agencies, local governments, and non-governmental organizations—to work together to identify common goals and paths moving forward. The USDA California Climate Hub and USFS Region 5 convened a symposium on drought and tree mortality in July 2017. With nearly 170 attendees across a wide range of sectors, the event provided a meaningful opportunity for reflection, analysis, and consideration of next steps. Among the outcomes of this symposium was the identification of areas in which our capacity for individual and synergistic action is stronger, and those in which it is lacking that will thus require additional attention and effort. From this symposium, which included a series of smaller, stakeholder and partner working groups, we collectively identified research and information needs, possible policy adjustments, future management actions, and funding needs and opportunities. Here, we present these findings and suggest approaches for addressing the current tree mortality event based on the shared interests of multiple, diverse stakeholder groups.

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

Sarrack, A.G.

The purpose of this report is to document fault tree analyses which have been completed for the Defense Waste Processing Facility (DWPF) safety analysis. Logic models for equipment failures and human error combinations that could lead to flammable gas explosions in various process tanks, or failure of critical support systems were developed for internal initiating events and for earthquakes. These fault trees provide frequency estimates for support systems failures and accidents that could lead to radioactive and hazardous chemical releases both on-site and off-site. Top event frequency results from these fault trees will be used in further APET analyses tomore » calculate accident risk associated with DWPF facility operations. This report lists and explains important underlying assumptions, provides references for failure data sources, and briefly describes the fault tree method used. Specific commitments from DWPF to provide new procedural/administrative controls or system design changes are listed in the ''Facility Commitments'' section. The purpose of the ''Assumptions'' section is to clarify the basis for fault tree modeling, and is not necessarily a list of items required to be protected by Technical Safety Requirements (TSRs).« less

Graphical fault tree analysis for fatal falls in the construction industry.

PubMed

Chi, Chia-Fen; Lin, Syuan-Zih; Dewi, Ratna Sari

2014-11-01

The current study applied a fault tree analysis to represent the causal relationships among events and causes that contributed to fatal falls in the construction industry. Four hundred and eleven work-related fatalities in the Taiwanese construction industry were analyzed in terms of age, gender, experience, falling site, falling height, company size, and the causes for each fatality. Given that most fatal accidents involve multiple events, the current study coded up to a maximum of three causes for each fall fatality. After the Boolean algebra and minimal cut set analyses, accident causes associated with each falling site can be presented as a fault tree to provide an overview of the basic causes, which could trigger fall fatalities in the construction industry. Graphical icons were designed for each falling site along with the associated accident causes to illustrate the fault tree in a graphical manner. A graphical fault tree can improve inter-disciplinary discussion of risk management and the communication of accident causation to first line supervisors. Copyright © 2014 Elsevier Ltd. All rights reserved.

A new model for cork weight estimation in Northern Portugal with methodology for construction of confidence intervals

Treesearch

Teresa J.F. Fonseca; Bernard R. Parresol

2001-01-01

Cork, a unique biological material, is a highly valued non-timber forest product. Portugal is the leading producer of cork with 52 percent of the world production. Tree cork weight models have been developed for Southern Portugal, but there are no representative published models for Northern Portugal. Because cork trees may have a different form between Northern and...

A new approach to quantify and map carbon stored, sequestered and emissions avoided by urban forests

Treesearch

E. Gregory McPherson; Qingfu Xiao; Elena Aguaron

2013-01-01

This paper describes the use of field surveys, biometric information for urban tree species and remote sensing to quantify and map carbon (C) storage, sequestration and avoided emissions from energy savings. Its primary contribution is methodological; the derivation and application of urban tree canopy (UTC) based transfer functions (t C ha-1 UTC). Findings for Los...

Using inventory data to determine the impact of drought on tree mortality

Treesearch

Greg C. Liknes; Christopher W. Woodall; Charles H. Perry

2012-01-01

Drought has been the subject of numerous recent studies that hint at an acceleration of tree mortality due to climate change. In particular, a recent global survey of tree mortality events implicates drought as the cause of quaking aspen mortality in Minnesota, USA in 2007. In this study, data from the Forest Inventory and Analysis program of the USDA Forest Service...

Correlation Between the System Capabilities Analytic Process (SCAP) and the Missions and Means Framework (MMF)

DTIC Science & Technology

2013-05-01

specifics of the correlation will be explored followed by discussion of new paradigms— the ordered event list (OEL) and the decision tree — that result from...4.2.1  Brief Overview of the Decision Tree Paradigm ................................................15  4.2.2  OEL Explained...6  Figure 3. A depiction of a notional fault/activation tree . ................................................................7

Predicting post-fire tree mortality for 14 conifers in the Pacific Northwest, USA: Model evaluation, development, and thresholds

Treesearch

Lindsay M. Grayson; Robert A. Progar; Sharon M. Hood

2017-01-01

Fire is a driving force in the North American landscape and predicting post-fire tree mortality is vital to land management. Post-fire tree mortality can have substantial economic and social impacts, and natural resource managers need reliable predictive methods to anticipate potential mortality following fire events. Current fire mortality models are limited to a few...

Continental-scale consequences of tree die-offs in North America: identifying where forest loss matters most

NASA Astrophysics Data System (ADS)

Swann, Abigail L. S.; Laguë, Marysa M.; Garcia, Elizabeth S.; Field, Jason P.; Breshears, David D.; Moore, David J. P.; Saleska, Scott R.; Stark, Scott C.; Villegas, Juan Camilo; Law, Darin J.; Minor, David M.

2018-05-01

Regional-scale tree die-off events driven by drought and warming and associated pests and pathogens have occurred recently on all forested continents and are projected to increase in frequency and extent with future warming. Within areas where tree mortality has occurred, ecological, hydrological and meteorological consequences are increasingly being documented. However, the potential for tree die-off to impact vegetation processes and related carbon dynamics in areas remote to where die-off occurs has rarely been systematically evaluated, particularly for multiple distinct regions within a given continent. Such remote impacts can occur when climate effects of local vegetation change are propagated by atmospheric circulation—the phenomena of ‘ecoclimate teleconnections’. We simulated tree die-off events in the 13 most densely forested US regions (selected from the 20 US National Ecological Observatory Network [NEON] domains) and found that tree die-off even for smaller regions has potential to affect climate and hence Gross Primary Productivity (GPP) in disparate regions (NEON domains), either positively or negatively. Some regions exhibited strong teleconnections to several others, and some regions were relatively sensitive to tree loss regardless of what other region the tree loss occurred in. For the US as a whole, loss of trees in the Pacific Southwest—an area undergoing rapid tree die-off—had the largest negative impact on remote US GPP whereas loss of trees in the Mid-Atlantic had the largest positive impact. This research lays a foundation for hypotheses that identify how the effects of tree die-off (or other types of tree loss such as deforestation) can ricochet across regions by revealing hot-spots of forcing and response. Such modes of connectivity have direct applicability for improving models of climate change impacts and for developing more informed and coordinated carbon accounting across regions.

[Decision modeling for economic evaluation of health technologies].

PubMed

de Soárez, Patrícia Coelho; Soares, Marta Oliveira; Novaes, Hillegonda Maria Dutilh

2014-10-01

Most economic evaluations that participate in decision-making processes for incorporation and financing of technologies of health systems use decision models to assess the costs and benefits of the compared strategies. Despite the large number of economic evaluations conducted in Brazil, there is a pressing need to conduct an in-depth methodological study of the types of decision models and their applicability in our setting. The objective of this literature review is to contribute to the knowledge and use of decision models in the national context of economic evaluations of health technologies. This article presents general definitions about models and concerns with their use; it describes the main models: decision trees, Markov chains, micro-simulation, simulation of discrete and dynamic events; it discusses the elements involved in the choice of model; and exemplifies the models addressed in national economic evaluation studies of diagnostic and therapeutic preventive technologies and health programs.

DTREEv2, a computer-based support system for the risk assessment of genetically modified plants.

PubMed

Pertry, Ine; Nothegger, Clemens; Sweet, Jeremy; Kuiper, Harry; Davies, Howard; Iserentant, Dirk; Hull, Roger; Mezzetti, Bruno; Messens, Kathy; De Loose, Marc; de Oliveira, Dulce; Burssens, Sylvia; Gheysen, Godelieve; Tzotzos, George

2014-03-25

Risk assessment of genetically modified organisms (GMOs) remains a contentious area and a major factor influencing the adoption of agricultural biotech. Methodologically, in many countries, risk assessment is conducted by expert committees with little or no recourse to databases and expert systems that can facilitate the risk assessment process. In this paper we describe DTREEv2, a computer-based decision support system for the identification of hazards related to the introduction of GM-crops into the environment. DTREEv2 structures hazard identification and evaluation by means of an Event-Tree type of analysis. The system produces an output flagging identified hazards and potential risks. It is intended to be used for the preparation and evaluation of biosafety dossiers and, as such, its usefulness extends to researchers, risk assessors and regulators in government and industry. Copyright © 2013 Elsevier B.V. All rights reserved.

CUTSETS - MINIMAL CUT SET CALCULATION FOR DIGRAPH AND FAULT TREE RELIABILITY MODELS

NASA Technical Reports Server (NTRS)

Iverson, D. L.

1994-01-01

Fault tree and digraph models are frequently used for system failure analysis. Both type of models represent a failure space view of the system using AND and OR nodes in a directed graph structure. Fault trees must have a tree structure and do not allow cycles or loops in the graph. Digraphs allow any pattern of interconnection between loops in the graphs. A common operation performed on digraph and fault tree models is the calculation of minimal cut sets. A cut set is a set of basic failures that could cause a given target failure event to occur. A minimal cut set for a target event node in a fault tree or digraph is any cut set for the node with the property that if any one of the failures in the set is removed, the occurrence of the other failures in the set will not cause the target failure event. CUTSETS will identify all the minimal cut sets for a given node. The CUTSETS package contains programs that solve for minimal cut sets of fault trees and digraphs using object-oriented programming techniques. These cut set codes can be used to solve graph models for reliability analysis and identify potential single point failures in a modeled system. The fault tree minimal cut set code reads in a fault tree model input file with each node listed in a text format. In the input file the user specifies a top node of the fault tree and a maximum cut set size to be calculated. CUTSETS will find minimal sets of basic events which would cause the failure at the output of a given fault tree gate. The program can find all the minimal cut sets of a node, or minimal cut sets up to a specified size. The algorithm performs a recursive top down parse of the fault tree, starting at the specified top node, and combines the cut sets of each child node into sets of basic event failures that would cause the failure event at the output of that gate. Minimal cut set solutions can be found for all nodes in the fault tree or just for the top node. The digraph cut set code uses the same techniques as the fault tree cut set code, except it includes all upstream digraph nodes in the cut sets for a given node and checks for cycles in the digraph during the solution process. CUTSETS solves for specified nodes and will not automatically solve for all upstream digraph nodes. The cut sets will be output as a text file. CUTSETS includes a utility program that will convert the popular COD format digraph model description files into text input files suitable for use with the CUTSETS programs. FEAT (MSC-21873) and FIRM (MSC-21860) available from COSMIC are examples of programs that produce COD format digraph model description files that may be converted for use with the CUTSETS programs. CUTSETS is written in C-language to be machine independent. It has been successfully implemented on a Sun running SunOS, a DECstation running ULTRIX, a Macintosh running System 7, and a DEC VAX running VMS. The RAM requirement varies with the size of the models. CUTSETS is available in UNIX tar format on a .25 inch streaming magnetic tape cartridge (standard distribution) or on a 3.5 inch diskette. It is also available on a 3.5 inch Macintosh format diskette or on a 9-track 1600 BPI magnetic tape in DEC VAX FILES-11 format. Sample input and sample output are provided on the distribution medium. An electronic copy of the documentation in Macintosh Microsoft Word format is included on the distribution medium. Sun and SunOS are trademarks of Sun Microsystems, Inc. DEC, DeCstation, ULTRIX, VAX, and VMS are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories. Macintosh is a registered trademark of Apple Computer, Inc.

Fault Tree in the Trenches, A Success Story

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Utilizing Lean Six Sigma Methodology to Improve the Authored Works Command Approval Process at Naval Medical Center San Diego.

PubMed

Valdez, Michelle M; Liwanag, Maureen; Mount, Charles; Rodriguez, Rechell; Avalos-Reyes, Elisea; Smith, Andrew; Collette, David; Starsiak, Michael; Green, Richard

2018-03-14

Inefficiencies in the command approval process for publications and/or presentations negatively impact DoD Graduate Medical Education (GME) residency programs' ability to meet ACGME scholarly activity requirements. A preliminary review of the authored works approval process at Naval Medical Center San Diego (NMCSD) disclosed significant inefficiency, variation in process, and a low level of customer satisfaction. In order to facilitate and encourage scholarly activity at NMCSD, and meet ACGME requirements, the Executive Steering Council (ESC) chartered an interprofessional team to lead a Lean Six Sigma (LSS) Rapid Improvement Event (RIE) project. Two major outcome metrics were identified: (1) the number of authored works submissions containing all required signatures and (2) customer satisfaction with the authored works process. Primary metric baseline data were gathered utilizing a Clinical Investigations database tracking publications and presentations. Secondary metric baseline data were collected via a customer satisfaction survey to GME faculty and residents. The project team analyzed pre-survey data and utilized LSS tools and methodology including a "gemba" (environment) walk, cause and effect diagram, critical to quality tree, voice of the customer, "muda" (waste) chart, and a pre- and post-event value stream map. The team selected an electronic submission system as the intervention most likely to positively impact the RIE project outcome measures. The number of authored works compliant with all required signatures improved from 52% to 100%. Customer satisfaction rated as "completely or mostly satisfied" improved from 24% to 97%. For both outcomes, signature compliance and customer satisfaction, statistical significance was achieved with a p < 0.0001. This RIE project utilized LSS methodology and tools to improve signature compliance and increase customer satisfaction with the authored works approval process, leading to 100% signature compliance, a comprehensive longitudinal repository of all authored work requests, and a 97% "completely or mostly satisfied" customer rating of the process.

Review: Evaluation of Foot-and-Mouth Disease Control Using Fault Tree Analysis.

PubMed

Isoda, N; Kadohira, M; Sekiguchi, S; Schuppers, M; Stärk, K D C

2015-06-01

An outbreak of foot-and-mouth disease (FMD) causes huge economic losses and animal welfare problems. Although much can be learnt from past FMD outbreaks, several countries are not satisfied with their degree of contingency planning and aiming at more assurance that their control measures will be effective. The purpose of the present article was to develop a generic fault tree framework for the control of an FMD outbreak as a basis for systematic improvement and refinement of control activities and general preparedness. Fault trees are typically used in engineering to document pathways that can lead to an undesired event, that is, ineffective FMD control. The fault tree method allows risk managers to identify immature parts of the control system and to analyse the events or steps that will most probably delay rapid and effective disease control during a real outbreak. The present developed fault tree is generic and can be tailored to fit the specific needs of countries. For instance, the specific fault tree for the 2001 FMD outbreak in the UK was refined based on control weaknesses discussed in peer-reviewed articles. Furthermore, the specific fault tree based on the 2001 outbreak was applied to the subsequent FMD outbreak in 2007 to assess the refinement of control measures following the earlier, major outbreak. The FMD fault tree can assist risk managers to develop more refined and adequate control activities against FMD outbreaks and to find optimum strategies for rapid control. Further application using the current tree will be one of the basic measures for FMD control worldwide. © 2013 Blackwell Verlag GmbH.

Seasonality and Disturbance Events in the Carbon Isotope Record of Pinus elliottii Tree Rings from Big Pine Key, Florida

NASA Astrophysics Data System (ADS)

Rebenack, C.; Anderson, W. T.; Cherubini, P.

2012-12-01

The South Florida coastal ecosystem is among the world's subtropical coastlines which are threatened by the potential effects of climate change. A well-developed localized paleohistory is essential in the understanding of the role climate variability/change has on both hydrological dynamics and disturbance event frequency and intensity; this understanding can then aid in the development of better predictive models. High resolution paleoclimate proxies, such as those developed from tree-ring archives, may be useful tools for extrapolating actual climate trends over time from the overlapping long-term and short-term climate cycles, such as the Atlantic Multidecadal Oscillation (AMO) and the El Niño-Southern Oscillation (ENSO). In South Florida, both the AMO and ENSO strongly influence seasonal precipitation, and a more complete grasp of how these cycles have affected the region in the past could be applied to future freshwater management practices. Dendrochronology records for the terrestrial subtropics, including South Florida, are sparse because seasonality for this region is precipitation-driven; this is in contrast to the drastic temperature changes experienced in the temperate latitudes. Subtropical seasonality may lead to the complete lack of visible rings or to the formation of ring structures that may or may not represent annual growth. Fortunately, it has recently been demonstrated that Pinus elliottii trees in South Florida produce distinct annual growth rings; however ring width was not found to significantly correlate with either the AMO or ENSO. Dendrochronology studies may be taken a step beyond the physical tree-ring proxies by using the carbon isotope ratios to infer information about physiological controls and environmental factors that affect the distribution of isotopes within the plant. It has been well established that the stable isotope composition of cellulose can be related to precipitation, drought, large-scale ocean/atmospheric oscillations, and disturbance events, such as tropical cyclone impacts. Because slash pine growth is dependent on water availability, a chronology developed using carbon isotopes may provide greater insight into plant stress over time and ultimately may lead to better correlations with climate oscillations. The work presented here is the result of a carbon-isotope study of four slash pine trees located across a freshwater gradient on Big Pine Key, Florida. A site chronology has been developed by cross-dating the δ13C records for each of the trees. The tree located on the distal edge of the freshwater gradient shows an overall enriched isotopic signature over time compared to the trees growing over a deeper part of the local freshwater lens, indicating that these trees are sensitive to water stress. In addition, the carbon isotope data show seasonal stomatal activity in the trees and indicate the timing of two disturbance events.

A Flexible Hierarchical Bayesian Modeling Technique for Risk Analysis of Major Accidents.

PubMed

Yu, Hongyang; Khan, Faisal; Veitch, Brian

2017-09-01

Safety analysis of rare events with potentially catastrophic consequences is challenged by data scarcity and uncertainty. Traditional causation-based approaches, such as fault tree and event tree (used to model rare event), suffer from a number of weaknesses. These include the static structure of the event causation, lack of event occurrence data, and need for reliable prior information. In this study, a new hierarchical Bayesian modeling based technique is proposed to overcome these drawbacks. The proposed technique can be used as a flexible technique for risk analysis of major accidents. It enables both forward and backward analysis in quantitative reasoning and the treatment of interdependence among the model parameters. Source-to-source variability in data sources is also taken into account through a robust probabilistic safety analysis. The applicability of the proposed technique has been demonstrated through a case study in marine and offshore industry. © 2017 Society for Risk Analysis.

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

Comparison of rainfall and stemflow peak intensities and infiltration patterns for a mature coastal forest in British Columbia, Canada

NASA Astrophysics Data System (ADS)

van Meerveld, Ilja; Spencer, Sheena

2017-04-01

Most studies on stemflow have focused on the amount of stemflow in different forests or for different rainfall events. So far, few studies have looked at how stemflow intensity varies during rainfall events and how peak stemflow intensities compare to peak rainfall intensities. High stemflow intensities at the base of the tree, where roots and other preferential flow pathways are prevalent, may lead to faster and deeper infiltration of stemflow than rainfall and thus affect soil moisture dynamics and potentially also subsurface stormflow generation. We measured stemflow intensities for three Western hemlock, two Western red cedar, two Douglas-fir and one Birch tree in a mature coniferous forest in coastal British Columbia to determine how stemflow intensities were related to rainfall intensity. We sprayed a blue dye tracer on two Western hemlock trees (29 and 52 cm diameter at breast height (DBH)) to determine how stemflow water flows through the soil and to what depth it infiltrates. We also applied the blue dye tracer to an area between the trees to compare infiltration of stemflow with rainfall. Stemflow increased linearly with event total precipitation for all trees. The larger trees almost exclusively had funneling ratios (i.e. the volume of stemflow per unit basal area divided by the rainfall) smaller than one, regardless of species and event size. The funneling ratios for the small trees were generally larger for larger events (up to a funneling ratio of 20) but there was considerable scatter in this relation. Trees with a DBH <35 cm, which represent 24% of the total basal area of the study site, contributed 72% of the estimated total stemflow amount. Stemflow intensities (volume of stemflow per unit basal area per hour) often increased in a stepwise manner. When there were two precipitation bursts, stemflow intensity was usually highest during the second precipitation burst. However, when there were several hours of very low rainfall intensity between consecutive precipitation bursts, stemflow intensity was lower during the first burst after the break in rainfall. Peak stemflow intensities were higher than the maximum precipitation intensity. The blue dye that was applied to the tree stems was found more frequently at depth than near the soil surface. Stemflow flowed primarily through the 10 cm organic rich upper layer of the soil around the tree before flowing between or along live and dead roots, inside dead roots, around rocks and boulders deeper into the soil. Lateral flow was observed above a dense clay layer but where roots were able to penetrate the clay layer, the infiltrating water flowed deeper into the soil and (almost) reached the soil-bedrock interface. Stemflow appeared to infiltrate deeper (122 cm) than rainfall (85 cm) but this difference was in part due to variations in maximum soil depth. These results suggest that even though stemflow is only a minor component of the water balance, the double funnelling of stemflow may significantly affect soil moisture, recharge and runoff generation.

Quantifying probabilities of eruptions at Mount Etna (Sicily, Italy).

NASA Astrophysics Data System (ADS)

Brancato, Alfonso

2010-05-01

One of the major goals of modern volcanology is to set up sound risk-based decision-making in land-use planning and emergency management. Volcanic hazard must be managed with reliable estimates of quantitative long- and short-term eruption forecasting, but the large number of observables involved in a volcanic process suggests that a probabilistic approach could be a suitable tool in forecasting. The aim of this work is to quantify probabilistic estimate of the vent location for a suitable lava flow hazard assessment at Mt. Etna volcano, through the application of the code named BET (Marzocchi et al., 2004, 2008). The BET_EF model is based on the event tree philosophy assessed by Newhall and Hoblitt (2002), further developing the concept of vent location, epistemic uncertainties, and a fuzzy approach for monitoring measurements. A Bayesian event tree is a specialized branching graphical representation of events in which individual branches are alternative steps from a general prior event, and evolving into increasingly specific subsequent states. Then, the event tree attempts to graphically display all relevant possible outcomes of volcanic unrest in progressively higher levels of detail. The procedure is set to estimate an a priori probability distribution based upon theoretical knowledge, to accommodate it by using past data, and to modify it further by using current monitoring data. For the long-term forecasting, an a priori model, dealing with the present tectonic and volcanic structure of the Mt. Etna, is considered. The model is mainly based on past vent locations and fracture location datasets (XX century of eruptive history of the volcano). Considering the variation of the information through time, and their relationship with the structural setting of the volcano, datasets we are also able to define an a posteriori probability map for next vent opening. For short-term forecasting vent opening hazard assessment, the monitoring has a leading role, primarily based on seismological and volcanological data, integrated with strain, geochemical, gravimetric and magnetic parameters. In the code, is necessary to fix an appropriate forecasting time window. On open-conduit volcanoes as Mt. Etna, a forecast time window of a month (as fixed in other applications worldwide) seems unduly long, because variations of the state of the volcano (significant variation of a specific monitoring parameter could occur in time scale shorter than the forecasting time window) are expected with shorter time scale (hour, day or week). This leads to set a week as forecasting time window, coherently with the number of weeks in which an unrest has been experienced. The short-term vent opening hazard assessment will be estimated during an unrest phase; the testing case (2001 July eruption) will include all the monitoring parameters collected at Mt. Etna during the six months preceding the eruption. The monitoring role has been assessed eliciting more than 50 parameters, including seismic activity, ground deformation, geochemistry, gravity, magnetism, and distributed inside the first three nodes of the procedure. Parameter values describe the Mt. Etna volcano activity, being more detailed through the code, particularly in time units. The methodology allows all assumptions and thresholds to be clearly identified and provides a rational means for their revision if new data or information are incoming. References Newhall C.G. and Hoblitt R.P.; 2002: Constructing event trees for volcanic crises, Bull. Volcanol., 64, 3-20, doi: 10.1007/s0044500100173. Marzocchi W., Sandri L., Gasparini P., Newhall C. and Boschi E.; 2004: Quantifying probabilities of volcanic events: The example of volcanic hazard at Mount Vesuvius, J. Geophys. Res., 109, B11201, doi:10.1029/2004JB00315U. Marzocchi W., Sandri, L. and Selva, J.; 2008: BET_EF: a probabilistic tool for long- and short-term eruption forecasting, Bull. Volcanol., 70, 623 - 632, doi: 10.1007/s00445-007-0157-y.

Phenology of Pacific Northwest tree species

Treesearch

Connie Harrington; Kevin Ford; Brad St. Clair

2016-01-01

Phenology is the study of the timing of recurring biological events. For foresters, the most commonly observed phenological events are budburst, flowering, and leaf fall, but other harder to observe events, such as diameter-growth initiation, are also important. Most events that occur in the spring are influenced by past exposure to cool (chilling) temperatures and...

Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological?

PubMed

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

2018-02-19

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

Extreme Drought Events Revealed in Amazon Tree Ring Records

NASA Astrophysics Data System (ADS)

Jenkins, H. S.; Baker, P. A.; Guilderson, T. P.

2010-12-01

The Amazon basin is a center of deep atmospheric convection and thus acts as a major engine for global hydrologic circulation. Yet despite its significance, a full understanding of Amazon rainfall variability remains elusive due to a poor historical record of climate. Temperate tree rings have been used extensively to reconstruct climate over the last thousand years, however less attention has been given to the application of dendrochronology in tropical regions, in large part due to a lower frequency of tree species known to produce annual rings. Here we present a tree ring record of drought extremes from the Madre de Dios region of southeastern Peru over the last 190 years. We confirm that tree ring growth in species Cedrela odorata is annual and show it to be well correlated with wet season precipitation. This correlation is used to identify extreme dry (and wet) events that have occurred in the past. We focus on drought events identified in the record as drought frequency is expected to increase over the Amazon in a warming climate. The Cedrela chronology records historic Amazon droughts of the 20th century previously identified in the literature and extends the record of drought for this region to the year 1816. Our analysis shows that there has been an increase in the frequency of extreme drought (mean recurrence interval = 5-6 years) since the turn of the 20th century and both Atlantic and Pacific sea surface temperature (SST) forcing mechanisms are implicated.

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

PubMed

Linden, Ariel; Yarnold, Paul R

2017-12-01

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

A survey of decision tree classifier methodology

NASA Technical Reports Server (NTRS)

Safavian, S. R.; Landgrebe, David

1991-01-01

Decision tree classifiers (DTCs) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps the most important feature of DTCs is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issues. After considering potential advantages of DTCs over single-state classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

A survey of decision tree classifier methodology

NASA Technical Reports Server (NTRS)

Safavian, S. Rasoul; Landgrebe, David

1990-01-01

Decision Tree Classifiers (DTC's) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps, the most important feature of DTC's is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issue. After considering potential advantages of DTC's over single stage classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

To live or to die? Evidence of variable drivers of wood d13C reveal different responses to disturbance in co-occurring oaks

NASA Astrophysics Data System (ADS)

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

2011-12-01

A major oak decline event in recent decades in Northwest Arkansas permits insight into disturbance impacts on forests, which is important for understanding global carbon, nutrient and climate cycles given projections of increasing disturbance event frequency in the future. The decline event, associated with an increase in population of a native, wood-boring insect, followed a cycle of droughts and resulted in a mosaic of apparently healthy red oaks (Quercus rubra) neighboring severely declining trees of the same species. Tree-ring evidence suggests decreased growth rates following increases in the insect's population decades prior to visible external decline symptoms (i.e. decreased crown coverage, mortality), but only in trees destined to die during the insect outbreak. Reasons why some trees experienced mortality and some remained healthy are unclear. Through analysis of stable isotopes of carbon (δ13C) and oxygen (δ18O) in wood and leaf δ13C and nitrogen among co-occurring trees, we can infer differential responses of red oaks to disturbance and associated resilience to mortality. Tree-ring a-cellulose δ13C varied from -27.3to -23.0%, and δ18O values varied from 27.5 to 31.8%. Neither δ13C nor δ18O exhibited signficant differences between healthy and declining trees. However, declining trees exhibited a significant, positive relationship between δ13C and δ18O (p <0.05, r2=0.15) prior to peak insect infestation. In contrast, apparently healthy individuals did not exhibit a significant relationship between these parameters, but exhibited significant, positive relationships between current year leaf δ13C and nitrogen content (p<0.05, r2=0.77). These results suggest that healthy and declining trees had different strategies for coping with insect infestation. Correlation between tree-ring δ13C and δ18O in dying trees suggests that trees destined to die during the infestation regulated their δ13C values primarily via stomatal conductance, a mechanism that influences both δ13C and δ18O. In contrast, δ13C values in apparently healthy trees did not vary with δ18O, indicating that stomatal conductance was not an important regulator of δ13C. The linkage between δ13C and nitrogen availability in these trees suggests that carbon sink strength, typically associated with plant nutrient status, may have played a more important role than carbon source strength (i.e. stomatal conductance) in governing tree-ring δ13C. These results suggest that 1) responses to disturbance of co-occurring trees of the same species can diverge in ways discernable decades later via stable isotopic analysis, and 2) the primary driver of wood δ13C values, whether carbon source (stomatal conductance) or sink (fixation capacity) strength, is linked to its fate.

Unified framework for triaxial accelerometer-based fall event detection and classification using cumulants and hierarchical decision tree classifier.

PubMed

Kambhampati, Satya Samyukta; Singh, Vishal; Manikandan, M Sabarimalai; Ramkumar, Barathram

2015-08-01

In this Letter, the authors present a unified framework for fall event detection and classification using the cumulants extracted from the acceleration (ACC) signals acquired using a single waist-mounted triaxial accelerometer. The main objective of this Letter is to find suitable representative cumulants and classifiers in effectively detecting and classifying different types of fall and non-fall events. It was discovered that the first level of the proposed hierarchical decision tree algorithm implements fall detection using fifth-order cumulants and support vector machine (SVM) classifier. In the second level, the fall event classification algorithm uses the fifth-order cumulants and SVM. Finally, human activity classification is performed using the second-order cumulants and SVM. The detection and classification results are compared with those of the decision tree, naive Bayes, multilayer perceptron and SVM classifiers with different types of time-domain features including the second-, third-, fourth- and fifth-order cumulants and the signal magnitude vector and signal magnitude area. The experimental results demonstrate that the second- and fifth-order cumulant features and SVM classifier can achieve optimal detection and classification rates of above 95%, as well as the lowest false alarm rate of 1.03%.

Application of fault tree approach for the causation mechanism of urban haze in Beijing--Considering the risk events related with exhausts of coal combustion.

PubMed

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

2016-02-15

Haze weather has become a serious environmental pollution problem which occurs in many Chinese cities. One of the most critical factors for the formation of haze weather is the exhausts of coal combustion, thus it is meaningful to figure out the causation mechanism between urban haze and the exhausts of coal combustion. Based on above considerations, the fault tree analysis (FAT) approach was employed for the causation mechanism of urban haze in Beijing by considering the risk events related with the exhausts of coal combustion for the first time. Using this approach, firstly the fault tree of the urban haze causation system connecting with coal combustion exhausts was established; consequently the risk events were discussed and identified; then, the minimal cut sets were successfully determined using Boolean algebra; finally, the structure, probability and critical importance degree analysis of the risk events were completed for the qualitative and quantitative assessment. The study results proved that the FTA was an effective and simple tool for the causation mechanism analysis and risk management of urban haze in China. Copyright © 2015 Elsevier B.V. All rights reserved.

Fire-mediated dieback and compositional cascade in an Amazonian forest.

PubMed

Barlow, Jos; Peres, Carlos A

2008-05-27

The only fully coupled land-atmosphere global climate model predicts a widespread dieback of Amazonian forest cover through reduced precipitation. Although these predictions are controversial, the structural and compositional resilience of Amazonian forests may also have been overestimated, as current vegetation models fail to consider the potential role of fire in the degradation of forest ecosystems. We examine forest structure and composition in the Arapiuns River basin in the central Brazilian Amazon, evaluating post-fire forest recovery and the consequences of recurrent fires for the patterns of dominance of tree species. We surveyed tree plots in unburned and once-burned forests examined 1, 3 and 9 years after an unprecedented fire event, in twice-burned forests examined 3 and 9 years after fire and in thrice-burned forests examined 5 years after the most recent fire event. The number of trees recorded in unburned primary forest control plots was stable over time. However, in both once- and twice-burned forest plots, there was a marked recruitment into the 10-20cm diameter at breast height tree size classes between 3 and 9 years post-fire. Considering tree assemblage composition 9 years after the first fire contact, we observed (i) a clear pattern of community turnover among small trees and the most abundant shrubs and saplings, and (ii) that species that were common in any of the four burn treatments (unburned, once-, twice- and thrice-burned) were often rare or entirely absent in other burn treatments. We conclude that episodic wildfires can lead to drastic changes in forest structure and composition, with cascading shifts in forest composition following each additional fire event. Finally, we use these results to evaluate the validity of the savannization paradigm.

Quantifying tree mortality in a mixed species woodland using multitemporal high spatial resolution satellite imagery

USGS Publications Warehouse

Garrity, Steven R.; Allen, Craig D.; Brumby, Steven P.; Gangodagamage, Chandana; McDowell, Nate G.; Cai, D. Michael

2013-01-01

Widespread tree mortality events have recently been observed in several biomes. To effectively quantify the severity and extent of these events, tools that allow for rapid assessment at the landscape scale are required. Past studies using high spatial resolution satellite imagery have primarily focused on detecting green, red, and gray tree canopies during and shortly after tree damage or mortality has occurred. However, detecting trees in various stages of death is not always possible due to limited availability of archived satellite imagery. Here we assess the capability of high spatial resolution satellite imagery for tree mortality detection in a southwestern U.S. mixed species woodland using archived satellite images acquired prior to mortality and well after dead trees had dropped their leaves. We developed a multistep classification approach that uses: supervised masking of non-tree image elements; bi-temporal (pre- and post-mortality) differencing of normalized difference vegetation index (NDVI) and red:green ratio (RGI); and unsupervised multivariate clustering of pixels into live and dead tree classes using a Gaussian mixture model. Classification accuracies were improved in a final step by tuning the rules of pixel classification using the posterior probabilities of class membership obtained from the Gaussian mixture model. Classifications were produced for two images acquired post-mortality with overall accuracies of 97.9% and 98.5%, respectively. Classified images were combined with land cover data to characterize the spatiotemporal characteristics of tree mortality across areas with differences in tree species composition. We found that 38% of tree crown area was lost during the drought period between 2002 and 2006. The majority of tree mortality during this period was concentrated in piñon-juniper (Pinus edulis-Juniperus monosperma) woodlands. An additional 20% of the tree canopy died or was removed between 2006 and 2011, primarily in areas experiencing wildfire and management activity. -Our results demonstrate that unsupervised clustering of bi-temporal NDVI and RGI differences can be used to detect tree mortality resulting from numerous causes and in several forest cover types.

A hybrid approach to select features and classify diseases based on medical data

NASA Astrophysics Data System (ADS)

AbdelLatif, Hisham; Luo, Jiawei

2018-03-01

Feature selection is popular problem in the classification of diseases in clinical medicine. Here, we developing a hybrid methodology to classify diseases, based on three medical datasets, Arrhythmia, Breast cancer, and Hepatitis datasets. This methodology called k-means ANOVA Support Vector Machine (K-ANOVA-SVM) uses K-means cluster with ANOVA statistical to preprocessing data and selection the significant features, and Support Vector Machines in the classification process. To compare and evaluate the performance, we choice three classification algorithms, decision tree Naïve Bayes, Support Vector Machines and applied the medical datasets direct to these algorithms. Our methodology was a much better classification accuracy is given of 98% in Arrhythmia datasets, 92% in Breast cancer datasets and 88% in Hepatitis datasets, Compare to use the medical data directly with decision tree Naïve Bayes, and Support Vector Machines. Also, the ROC curve and precision with (K-ANOVA-SVM) Achieved best results than other algorithms

Fault tree analysis of the causes of waterborne outbreaks.

PubMed

Risebro, Helen L; Doria, Miguel F; Andersson, Yvonne; Medema, Gertjan; Osborn, Keith; Schlosser, Olivier; Hunter, Paul R

2007-01-01

Prevention and containment of outbreaks requires examination of the contribution and interrelation of outbreak causative events. An outbreak fault tree was developed and applied to 61 enteric outbreaks related to public drinking water supplies in the EU. A mean of 3.25 causative events per outbreak were identified; each event was assigned a score based on percentage contribution per outbreak. Source and treatment system causative events often occurred concurrently (in 34 outbreaks). Distribution system causative events occurred less frequently (19 outbreaks) but were often solitary events contributing heavily towards the outbreak (a mean % score of 87.42). Livestock and rainfall in the catchment with no/inadequate filtration of water sources contributed concurrently to 11 of 31 Cryptosporidium outbreaks. Of the 23 protozoan outbreaks experiencing at least one treatment causative event, 90% of these events were filtration deficiencies; by contrast, for bacterial, viral, gastroenteritis and mixed pathogen outbreaks, 75% of treatment events were disinfection deficiencies. Roughly equal numbers of groundwater and surface water outbreaks experienced at least one treatment causative event (18 and 17 outbreaks, respectively). Retrospective analysis of multiple outbreaks of enteric disease can be used to inform outbreak investigations, facilitate corrective measures, and further develop multi-barrier approaches.

Fault and event tree analyses for process systems risk analysis: uncertainty handling formulations.

PubMed

Ferdous, Refaul; Khan, Faisal; Sadiq, Rehan; Amyotte, Paul; Veitch, Brian

2011-01-01

Quantitative risk analysis (QRA) is a systematic approach for evaluating likelihood, consequences, and risk of adverse events. QRA based on event (ETA) and fault tree analyses (FTA) employs two basic assumptions. The first assumption is related to likelihood values of input events, and the second assumption is regarding interdependence among the events (for ETA) or basic events (for FTA). Traditionally, FTA and ETA both use crisp probabilities; however, to deal with uncertainties, the probability distributions of input event likelihoods are assumed. These probability distributions are often hard to come by and even if available, they are subject to incompleteness (partial ignorance) and imprecision. Furthermore, both FTA and ETA assume that events (or basic events) are independent. In practice, these two assumptions are often unrealistic. This article focuses on handling uncertainty in a QRA framework of a process system. Fuzzy set theory and evidence theory are used to describe the uncertainties in the input event likelihoods. A method based on a dependency coefficient is used to express interdependencies of events (or basic events) in ETA and FTA. To demonstrate the approach, two case studies are discussed. © 2010 Society for Risk Analysis.

Growth-mortality relationships in piñon pine (Pinus edulis) during severe droughts of the past century: shifting processes in space and time.

PubMed

Macalady, Alison K; Bugmann, Harald

2014-01-01

The processes leading to drought-associated tree mortality are poorly understood, particularly long-term predisposing factors, memory effects, and variability in mortality processes and thresholds in space and time. We use tree rings from four sites to investigate Pinus edulis mortality during two drought periods in the southwestern USA. We draw on recent sampling and archived collections to (1) analyze P. edulis growth patterns and mortality during the 1950s and 2000s droughts; (2) determine the influence of climate and competition on growth in trees that died and survived; and (3) derive regression models of growth-mortality risk and evaluate their performance across space and time. Recent growth was 53% higher in surviving vs. dying trees, with some sites exhibiting decades-long growth divergences associated with previous drought. Differential growth response to climate partly explained growth differences between live and dead trees, with responses wet/cool conditions most influencing eventual tree status. Competition constrained tree growth, and reduced trees' ability to respond to favorable climate. The best predictors in growth-mortality models included long-term (15-30 year) average growth rate combined with a metric of growth variability and the number of abrupt growth increases over 15 and 10 years, respectively. The most parsimonious models had high discriminatory power (ROC>0.84) and correctly classified ∼ 70% of trees, suggesting that aspects of tree growth, especially over decades, can be powerful predictors of widespread drought-associated die-off. However, model discrimination varied across sites and drought events. Weaker growth-mortality relationships and higher growth at lower survival probabilities for some sites during the 2000s event suggest a shift in mortality processes from longer-term growth-related constraints to shorter-term processes, such as rapid metabolic decline even in vigorous trees due to acute drought stress, and/or increases in the attack rate of both chronically stressed and more vigorous trees by bark beetles.

Phytomonitoring of chlorinated ethenes in trees: a four-year study of seasonal chemodynamics in planta.

PubMed

Limmer, Matt A; Holmes, Amanda J; Burken, Joel G

2014-09-16

Long-term monitoring (LTM) of groundwater remedial projects is costly and time-consuming, particularly when using phytoremediation, a long-term remedial approach. The use of trees as sensors of groundwater contamination (i.e., phytoscreening) has been widely described, although the use of trees to provide long-term monitoring of such plumes (phytomonitoring) has been more limited due to unexplained variability of contaminant concentrations in trees. To assess this variability, we developed an in planta sampling method to obtain high-frequency measurements of chlorinated ethenes in oak (Quercus rubra) and baldcypress (Taxodium distichum) trees growing above a contaminated plume during a 4-year trial. The data set revealed that contaminant concentrations increased rapidly with transpiration in the spring and decreased in the fall, resulting in perchloroethene (PCE) and trichloroethene (TCE) sapwood concentrations an order of magnitude higher in late summer as compared to winter. Heartwood PCE and TCE concentrations were more buffered against seasonal effects. Rainfall events caused negligible dilution of contaminant concentrations in trees after precipitation events. Modeling evapotranspiration potential from meteorological data and comparing the modeled uptake and transport with the 4 years of high frequency data provides a foundation to advance the implementation of phytomonitoring and improved understanding of plant contaminant interactions.

Drivers and mechanisms of tree mortality in moist tropical forests.

PubMed

McDowell, Nate; Allen, Craig D; Anderson-Teixeira, Kristina; Brando, Paulo; Brienen, Roel; Chambers, Jeff; Christoffersen, Brad; Davies, Stuart; Doughty, Chris; Duque, Alvaro; Espirito-Santo, Fernando; Fisher, Rosie; Fontes, Clarissa G; Galbraith, David; Goodsman, Devin; Grossiord, Charlotte; Hartmann, Henrik; Holm, Jennifer; Johnson, Daniel J; Kassim, Abd Rahman; Keller, Michael; Koven, Charlie; Kueppers, Lara; Kumagai, Tomo'omi; Malhi, Yadvinder; McMahon, Sean M; Mencuccini, Maurizio; Meir, Patrick; Moorcroft, Paul; Muller-Landau, Helene C; Phillips, Oliver L; Powell, Thomas; Sierra, Carlos A; Sperry, John; Warren, Jeff; Xu, Chonggang; Xu, Xiangtao

2018-02-16

Tree mortality rates appear to be increasing in moist tropical forests (MTFs) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and identify the next steps for improved understanding and reduced prediction. Increasing mortality rates are associated with rising temperature and vapor pressure deficit, liana abundance, drought, wind events, fire and, possibly, CO 2 fertilization-induced increases in stand thinning or acceleration of trees reaching larger, more vulnerable heights. The majority of these mortality drivers may kill trees in part through carbon starvation and hydraulic failure. The relative importance of each driver is unknown. High species diversity may buffer MTFs against large-scale mortality events, but recent and expected trends in mortality drivers give reason for concern regarding increasing mortality within MTFs. Models of tropical tree mortality are advancing the representation of hydraulics, carbon and demography, but require more empirical knowledge regarding the most common drivers and their subsequent mechanisms. We outline critical datasets and model developments required to test hypotheses regarding the underlying causes of increasing MTF mortality rates, and improve prediction of future mortality under climate change. No claim to original US government works New Phytologist © 2018 New Phytologist Trust.

Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought

PubMed Central

Carnicer, Jofre; Coll, Marta; Ninyerola, Miquel; Pons, Xavier; Sánchez, Gerardo; Peñuelas, Josep

2011-01-01

Climate change is progressively increasing severe drought events in the Northern Hemisphere, causing regional tree die-off events and contributing to the global reduction of the carbon sink efficiency of forests. There is a critical lack of integrated community-wide assessments of drought-induced responses in forests at the macroecological scale, including defoliation, mortality, and food web responses. Here we report a generalized increase in crown defoliation in southern European forests occurring during 1987–2007. Forest tree species have consistently and significantly altered their crown leaf structures, with increased percentages of defoliation in the drier parts of their distributions in response to increased water deficit. We assessed the demographic responses of trees associated with increased defoliation in southern European forests, specifically in the Iberian Peninsula region. We found that defoliation trends are paralleled by significant increases in tree mortality rates in drier areas that are related to tree density and temperature effects. Furthermore, we show that severe drought impacts are associated with sudden changes in insect and fungal defoliation dynamics, creating long-term disruptive effects of drought on food webs. Our results reveal a complex geographical mosaic of species-specific responses to climate change–driven drought pressures on the Iberian Peninsula, with an overwhelmingly predominant trend toward increased drought damage. PMID:21220333

Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought.

PubMed

Carnicer, Jofre; Coll, Marta; Ninyerola, Miquel; Pons, Xavier; Sánchez, Gerardo; Peñuelas, Josep

2011-01-25

Climate change is progressively increasing severe drought events in the Northern Hemisphere, causing regional tree die-off events and contributing to the global reduction of the carbon sink efficiency of forests. There is a critical lack of integrated community-wide assessments of drought-induced responses in forests at the macroecological scale, including defoliation, mortality, and food web responses. Here we report a generalized increase in crown defoliation in southern European forests occurring during 1987-2007. Forest tree species have consistently and significantly altered their crown leaf structures, with increased percentages of defoliation in the drier parts of their distributions in response to increased water deficit. We assessed the demographic responses of trees associated with increased defoliation in southern European forests, specifically in the Iberian Peninsula region. We found that defoliation trends are paralleled by significant increases in tree mortality rates in drier areas that are related to tree density and temperature effects. Furthermore, we show that severe drought impacts are associated with sudden changes in insect and fungal defoliation dynamics, creating long-term disruptive effects of drought on food webs. Our results reveal a complex geographical mosaic of species-specific responses to climate change-driven drought pressures on the Iberian Peninsula, with an overwhelmingly predominant trend toward increased drought damage.

Environment and paleoecology of a 12 ka mid-North American Younger Dryas forest chronicled in tree rings

USGS Publications Warehouse

Panyushkina, Irina P.; Leavitt, Steven W.; Thompson, Todd A.; Schneider, Allan F.; Lange, Todd

2008-01-01

Until now, availability of wood from the Younger Dryas abrupt cooling event (YDE) in N. America ca. 12.9 to 11.6 ka has been insufficient to develop high-resolution chronologies for refining our understanding of YDE conditions. Here we present a multi-proxy tree-ring chronology (ring widths, “events” evidenced by microanatomy and macro features, stable isotopes) from a buried black spruce forest in the Great Lakes area (Liverpool East site), spanning 116 yr at ca. 12,000 cal yr BP. During this largely cold and wet period, the proxies convey a coherent and precise forest history including frost events, tilting, drowning and burial in estuarine sands as the Laurentide Ice Sheet deteriorated. In the middle of the period, a short mild interval appears to have launched the final and largest episode of tree recruitment. Ultimately the tops of the trees were sheared off after death, perhaps by wind-driven ice floes, culminating an interval of rising water and sediment deposition around the base of the trees. Although relative influences of the continental ice sheet and local effects from ancestral Lake Michigan are indeterminate, the tree-ring proxies provide important insight into environment and ecology of a N. American YDE boreal forest stand.

NLCD tree canopy cover (TCC) maps of the contiguous United States and coastal Alaska

Treesearch

Robert Benton; Bonnie Ruefenacht; Vicky Johnson; Tanushree Biswas; Craig Baker; Mark Finco; Kevin Megown; John Coulston; Ken Winterberger; Mark Riley

2015-01-01

A tree canopy cover (TCC) map is one of three elements in the National Land Cover Database (NLCD) 2011 suite of nationwide geospatial data layers. In 2010, the USDA Forest Service (USFS) committed to creating the TCC layer as a member of the Multi-Resolution Land Cover (MRLC) consortium. A general methodology for creating the TCC layer was reported at the 2012 FIA...

Forest service contributions to the national land cover database (NLCD): Tree Canopy Cover Production

Treesearch

Bonnie Ruefenacht; Robert Benton; Vicky Johnson; Tanushree Biswas; Craig Baker; Mark Finco; Kevin Megown; John Coulston; Ken Winterberger; Mark Riley

2015-01-01

A tree canopy cover (TCC) layer is one of three elements in the National Land Cover Database (NLCD) 2011 suite of nationwide geospatial data layers. In 2010, the USDA Forest Service (USFS) committed to creating the TCC layer as a member of the Multi-Resolution Land Cover (MRLC) consortium. A general methodology for creating the TCC layer was reported at the 2012 FIA...

Sampling small mammals in southeastern forests: the importance of trapping in trees

Treesearch

Susan C. Loeb; Gregg L. Chapman; Theodore R. Ridley

2001-01-01

Because estimates of small mammal species richness and diversity are strongly influenced by sampling methodology, 2 or more trap types are often used in studies of small mammal communities. However, in most cases, all traps are placed at ground level. In contrast, we used Sherman live traps placed at 1.5 m in trees in addition to Sherman live traps and Mosby box traps...

Applications of Photogrammetry for Analysis of Forest Plantations. Preliminary study: Analysis of individual trees

NASA Astrophysics Data System (ADS)

Mora, R.; Barahona, A.; Aguilar, H.

2015-04-01

This paper presents a method for using high detail volumetric information, captured with a land based photogrammetric survey, to obtain information from individual trees. Applying LIDAR analysis techniques it is possible to measure diameter at breast height, height at first branch (commercial height), basal area and volume of an individual tree. Given this information it is possible to calculate how much of that tree can be exploited as wood. The main objective is to develop a methodology for successfully surveying one individual tree, capturing every side of the stem a using high resolution digital camera and reference marks with GPS coordinates. The process is executed for several individuals of two species present in the metropolitan area in San Jose, Costa Rica, Delonix regia (Bojer) Raf. and Tabebuia rosea (Bertol.) DC., each one with different height, stem shape and crown area. Using a photogrammetry suite all the pictures are aligned, geo-referenced and a dense point cloud is generated with enough detail to perform the required measurements, as well as a solid tridimensional model for volume measurement. This research will open the way to develop a capture methodology with an airborne camera using close range UAVs. An airborne platform will make possible to capture every individual in a forest plantation, furthermore if the analysis techniques applied in this research are automated it will be possible to calculate with high precision the exploit potential of a forest plantation and improve its management.

Drought timing influences the legacy of tree growth recovery.

PubMed

Huang, Mengtian; Wang, Xuhui; Keenan, Trevor F; Piao, Shilong

2018-05-04

Whether and how the timing of extreme events affects the direction and magnitude of legacy effects on tree growth is poorly understood. In this study, we use a global database of Ring-Width Index (RWI) from 2,500 sites to examine the impact and legacy effects (the departure of observed RWI from expected RWI) of extreme drought events during 1948-2008, with a particular focus on the influence of drought timing. We assessed the recovery of stem radial growth in the years following severe drought events with separate groupings designed to characterize the timing of the drought. We found that legacies from extreme droughts during the dry season (DS droughts) lasted longer and had larger impacts in each of the 3 years post drought than those from extreme droughts during the wet season (WS droughts). At the global scale, the average integrated legacy from DS droughts (0.18) was about nine times that from WS droughts (0.02). Site-level comparisons also suggest stronger negative impacts or weaker positive impacts of DS droughts on tree growth than WS droughts. Our results, therefore, highlight that the timing of drought is a crucial factor determining drought impacts on tree recovery. Further increases in baseline aridity could therefore exacerbate the impact of punctuated droughts on terrestrial ecosystems. © 2018 John Wiley & Sons Ltd.

Reduced transpiration response to precipitation pulses precedes mortality in a piñon-juniper woodland subject to prolonged drought.

PubMed

Plaut, Jennifer A; Wadsworth, W Duncan; Pangle, Robert; Yepez, Enrico A; McDowell, Nate G; Pockman, William T

2013-10-01

Global climate change is predicted to alter the intensity and duration of droughts, but the effects of changing precipitation patterns on vegetation mortality are difficult to predict. Our objective was to determine whether prolonged drought or above-average precipitation altered the capacity to respond to the individual precipitation pulses that drive productivity and survival. We analyzed 5 yr of data from a rainfall manipulation experiment in piñon-juniper (Pinus edulis-Juniperus monosperma) woodland using mixed effects models of transpiration response to event size, antecedent soil moisture, and post-event vapor pressure deficit. Replicated treatments included irrigation, drought, ambient control and infrastructure control. Mortality was highest under drought, and the reduced post-pulse transpiration in the droughted trees that died was attributable to treatment effects beyond drier antecedent conditions and reduced event size. In particular, trees that died were nearly unresponsive to antecedent shallow soil moisture, suggesting reduced shallow absorbing root area. Irrigated trees showed an enhanced response to precipitation pulses. Prolonged drought initiates a downward spiral whereby trees are increasingly unable to utilize pulsed soil moisture. Thus, the additive effects of future, more frequent droughts may increase drought-related mortality. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

36 CFR 292.46 - Timber harvesting activities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... hazard trees; or to respond to natural events such as wildfire, flood, earthquake, volcanic eruption, high winds, and disease or insect infestation. (2) Where authorized, trees may be harvested by... landscape to the extent practicable. (b) Wild and Scenic Rivers. The following standards and guidelines...

36 CFR 292.46 - Timber harvesting activities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... hazard trees; or to respond to natural events such as wildfire, flood, earthquake, volcanic eruption, high winds, and disease or insect infestation. (2) Where authorized, trees may be harvested by... landscape to the extent practicable. (b) Wild and Scenic Rivers. The following standards and guidelines...

36 CFR 292.46 - Timber harvesting activities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... hazard trees; or to respond to natural events such as wildfire, flood, earthquake, volcanic eruption, high winds, and disease or insect infestation. (2) Where authorized, trees may be harvested by... landscape to the extent practicable. (b) Wild and Scenic Rivers. The following standards and guidelines...

36 CFR 292.46 - Timber harvesting activities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... hazard trees; or to respond to natural events such as wildfire, flood, earthquake, volcanic eruption, high winds, and disease or insect infestation. (2) Where authorized, trees may be harvested by... landscape to the extent practicable. (b) Wild and Scenic Rivers. The following standards and guidelines...

[Tree-ring growth responses of Mongolian oak (Quercus mongolica) to climate change in southern northeast: a case study in Qianshan Mountains].

PubMed

Teng, Li; Xing-Yuan, He; Zhen-Ju, Chen

2014-07-01

Mongolian oak is one of the most important broad-leaved tree species in forests, Northeast China. Based on the methodology of dendrochronology, the variations of tree ring radial growth of Mongolian oak in Qianshan Mountains, south of Northeast China, were analyzed. Combined with the temperature and precipitation data from meteorological stations since 1951, the relationships between standardized tree ring width chronology and main climatic factors were analyzed. In this region, the precipitation between April and July of the current year had an significant relationship with the tree ring width of Mongolian oak, and was the main factor limiting the radial growth. The extreme maximum temperature of May was also a key factor influencing the tree ring width, which had a significant on the tree ring width of Mongolian oak. The precipitation in April had a significant and stable relationship with the growth of Mongolian oak since the 1950s. The 'divergence problem' was found in the study area, which the sensitivity of tree growth to summer temperature reduced since the 1980s. The tree growth response to temperature showed a seasonal change from summer to spring.

Selection of organisms for the co-evolution-based study of protein interactions.

PubMed

Herman, Dorota; Ochoa, David; Juan, David; Lopez, Daniel; Valencia, Alfonso; Pazos, Florencio

2011-09-12

The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.

Selection of organisms for the co-evolution-based study of protein interactions

PubMed Central

2011-01-01

Background The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. Results We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. Conclusions In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest. PMID:21910884

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

The chordate proteome history database.

PubMed

Levasseur, Anthony; Paganini, Julien; Dainat, Jacques; Thompson, Julie D; Poch, Olivier; Pontarotti, Pierre; Gouret, Philippe

2012-01-01

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

Biogeochemical hotspots following a simulated tree mortality event of southern pine beetle

NASA Astrophysics Data System (ADS)

Siegert, C. M.; Renninger, H. J.; Karunarathna, S.; Hornslein, N.; Riggins, J. J.; Clay, N. A.; Tang, J. D.; Chaney, B.; Drotar, N.

2017-12-01

Disturbances in forest ecosystems can alter functions like productivity, respiration, and nutrient cycling through the creation of biogeochemical hotspots. These events occur sporadically across the landscape, leading to uncertainty in terrestrial biosphere carbon models, which have yet to capture the full complexity of biotic and abiotic factors driving ecological processes in the terrestrial environment. Given the widespread impact of southern pine beetle on forest ecosystems throughout the southeastern United States, it is critical to management and planning activities to understand the role of these disturbances. As such, we hypothesize that bark beetle killed trees create biogeochemical hotspots in the soils surrounding their trunk as they undergo mortality due to (1) increased soil moisture from reductions in plant water uptake and increased stemflow production, (2) enhanced canopy-derived inputs of carbon and nitrogen, and (3) increased microbial activity and root mortality. In 2015, a field experiment to mimic a southern pine beetle attack was established by girdling loblolly pine trees. Subsequent measurements of throughfall and stemflow for water quantity and quality, transpiration, stem respiration, soil respiration, and soil chemistry were used to quantify the extent of spatial and temporal impacts of tree mortality on carbon budgets. Compared to control trees, girdled trees exhibited reduced water uptake within the first 6 months of the study and succumbed to mortality within 18 months. Over two years, the girdled trees generated 33% more stemflow than control trees (7836 vs. 5882 L m-2). Preliminary analysis of carbon and nitrogen concentrations and dissolved organic matter quality are still pending. In the surrounding soils, C:N ratios were greater under control trees (12.8) than under girdled trees (12.1), which was driven by an increase in carbon around control trees (+0.13 mg C mg-1 soil) and not a decrease around girdled trees (-0.01 mg C mg-1 soil), with no observed differences in N concentrations. Although data from the remaining of the 2017 growing season are still pending, we have thus far demonstrated how tree mortality from southern pine beetle changes single tree hydrologic and biogeochemical cycles.

The Source of Adult Age Differences in Event-Based Prospective Memory: A Multinomial Modeling Approach

ERIC Educational Resources Information Center

Smith, Rebekah E.; Bayen, Ute J.

2006-01-01

Event-based prospective memory involves remembering to perform an action in response to a particular future event. Normal younger and older adults performed event-based prospective memory tasks in 2 experiments. The authors applied a formal multinomial processing tree model of prospective memory (Smith & Bayen, 2004) to disentangle age differences…

Modeling the Spatial Distribution and Fruiting Pattern of a Key Tree Species in a Neotropical Forest: Methodology and Potential Applications

PubMed Central

Scarpino, Samuel V.; Jansen, Patrick A.; Garzon-Lopez, Carol X.; Winkelhagen, Annemarie J. S.; Bohlman, Stephanie A.; Walsh, Peter D.

2010-01-01

Background The movement patterns of wild animals depend crucially on the spatial and temporal availability of resources in their habitat. To date, most attempts to model this relationship were forced to rely on simplified assumptions about the spatiotemporal distribution of food resources. Here we demonstrate how advances in statistics permit the combination of sparse ground sampling with remote sensing imagery to generate biological relevant, spatially and temporally explicit distributions of food resources. We illustrate our procedure by creating a detailed simulation model of fruit production patterns for Dipteryx oleifera, a keystone tree species, on Barro Colorado Island (BCI), Panama. Methodology and Principal Findings Aerial photographs providing GPS positions for large, canopy trees, the complete census of a 50-ha and 25-ha area, diameter at breast height data from haphazardly sampled trees and long-term phenology data from six trees were used to fit 1) a point process model of tree spatial distribution and 2) a generalized linear mixed-effect model of temporal variation of fruit production. The fitted parameters from these models are then used to create a stochastic simulation model which incorporates spatio-temporal variations of D. oleifera fruit availability on BCI. Conclusions and Significance We present a framework that can provide a statistical characterization of the habitat that can be included in agent-based models of animal movements. When environmental heterogeneity cannot be exhaustively mapped, this approach can be a powerful alternative. The results of our model on the spatio-temporal variation in D. oleifera fruit availability will be used to understand behavioral and movement patterns of several species on BCI. PMID:21124927

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

Water is a primary limiting factor for agricultural development in many arid and semi-arid regions in which a runoff generation is a rather frequent event. If conveyed to dyke surrounded plots and ponded, runoff water can thereafter be used for tree production. One of the most promising runoff collection configurations is that of micro-catchments in which water is collected close to the area in which runoff was generated and stored in adjacent shallow pits. The objective of this work was to assess the effect of the geometry of runoff water collection area (shallow pit or trench) on direct evaporative water losses and on the water use efficiency of olive trees grown in them. The study was conducted during the summer of 2013 and 2014. In this study regular micro-catchments with basins of 9 m2 (3 x 3 m) by 0.1 m deep were compared with trenches of one meter deep and one meter wide. Each configuration was replicated three times. One tree was planted in each shallow basin and the distance between trees in the 12 m long trench was four meters. Access tubes for neutron probes were installed in the micro-catchments and trenches (four and seven, respectively) to depths of 2.5 m. Soil water content in the soil profile was monitored periodically throughout drying periods in between simulated runoff events. Transpiration of the trees was estimated from half-hourly sap flow measurements using a Granier system. Total transpiration fluxes were computed for time intervals corresponding to consecutive soil water measurements. During the first year, a large runoff event was simulated by applying once four cubic meters to each plot; and in the second year the same volume of water was split into four applications, simulating a series of small runoff events. In both geometries, trees received the same amount of water per tree. Evaporation from trenches and micro-catchments was estimated as the difference between evapotranspiration obtained computing the differences in total soil water content between two consecutive measurements and transpiration for this interval estimated from sap flow measurements. In both years the evaporation from micro-catchments was significantly larger than that of trenches. The fractional loss due to evaporation from the total applied water for the second year for example, was 53% and 22% for micro-catchments and trenches, respectively. This indicates that a trench geometry reduces the amount of water lost to direct evaporation from the soil, and is thus more efficient in utilizing harvested runoff water.

Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

PubMed Central

MacLeod, Dave; Charlebois, Robert L; Doolittle, Ford; Bapteste, Eric

2005-01-01

Background When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies. Results We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients. Conclusion A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data. PMID:15819979

Temporal Dynamics in the Concentration, Flux, and Optical Properties of Tree-Derived Dissolved Organic Matter in an Epiphyte-Laden Oak-Cedar Forest

NASA Astrophysics Data System (ADS)

Van Stan, John T.; Wagner, Sasha; Guillemette, François; Whitetree, Ansley; Lewis, Julius; Silva, Leticia; Stubbins, Aron

2017-11-01

Studies on the fate and transport of dissolved organic matter (DOM) along the rainfall-to-discharge flow pathway typically begin in streams or soils, neglecting the initial enrichment of rainfall with DOM during contact with plant canopies. However, rain water can gather significant amounts of tree-derived DOM (tree-DOM) when it drains from the canopy, as throughfall, and down the stem, as stemflow. We examined the temporal variability of event-scale tree-DOM concentrations, yield, and optical (light absorbance and fluorescence) characteristics from an epiphyte-laden Quercus virginiana-Juniperus virginiana forest on Skidaway Island, Savannah, Georgia (USA). All tree-DOM fluxes were highly enriched in dissolved organic carbon (DOC) compared to rainfall, and epiphytes further increased concentrations. Stemflow DOC concentrations were greater than throughfall across study species, yet larger throughfall water yields produced greater DOC yields versus stemflow. Tree-DOM optical characteristics indicate it is aromatic-rich with fluorescent DOM dominated by humic-like fluorescence, containing 10-20% protein-like (tryptophan-like) fluorescence. Storm size was the only storm condition that strongly correlated with tree-DOM concentration and flux; however, throughfall and stemflow optical characteristics varied little across a wide range of storm conditions (from low magnitude events to intense tropical storms). Annual tree-DOM yields from the study forest (0.8-46 g C m-2 yr-1) were similar to other yields from discrete down-gradient fluxes (litter leachates, soil leachates, and stream discharge) along the rainfall-to-discharge flow path.

Particular geoscientific perspectives on stable isotope analysis in the arboreal system

NASA Astrophysics Data System (ADS)

Helle, Gerhard; Balting, Daniel; Pauly, Maren; Slotta, Franziska

2017-04-01

In geosciences stable isotopes of carbon, oxygen and hydrogen from the tree ring archive have been used for several decades to trace the course of past environmental and climatological fluctuations. In contrast to ice cores, the tree ring archive is of biological nature (like many other terrestrial archives), but provides the opportunity to establish site networks with very high resolution in space and time. Many of the basic physical mechanisms of isotope shifts are known, but biologically mediated processes may lead to isotope effects that are poorly understood. This implies that the many processes within the arboreal system leading to archived isotope ratios in wood material are governed by a multitude of environmental variables that are not only tied to the isotopic composition of atmospheric source values (precipitation, CO2), but also to seasonally changing metabolic flux rates and pool sizes of photosynthates within the trees. Consequently, the extraction of climate and environmental information is particularly challenging and reconstructions are still of rather qualitative nature. Over the last 10 years or so, monitoring studies have been implemented to investigate stable isotope, climate and environmental signal transfer within the arboreal system to develop transfer or response functions that can translate the relevant isotope values extracted from tree rings into climate or other environmental variables. To what extent have these efforts lead to a better understanding that helps improving the meaningfulness of tree ring isotope signals? For example, do monitoring studies help deciphering the causes for age-related trends in tree ring stable isotope sequences that are published in a growing number of papers. Are existing monitoring studies going into detail enough or is it already too much effort for the outcome? Based on what we know already particularly in mesic habitats, tree ring stable isotopes are much better climate proxies than other tree ring parameters. However, millennial or multi-millennial high quality reconstructions from tree ring isotopes are still rare. This is because of i) methodological constraints related to mass spectrometric analyses and ii) the nature of tree-ring chronologies that are put together by many trees of various individual ages. In view of this: What is the state-of-the-art in high throughput tree ring stable isotope analyses? Is it necessary to advance existing methodologies further to conserve the annual time resolution provided by the tree-ring archive? Other terrestrial archives, like lake sediments and speleothems rarely provide annually resolved stable isotope data. Furthermore, certain tree species from tropical or sub-tropical regions cannot be dated properly by dendrochronology and hence demand specific stable isotope measuring strategies, etc.. Although the points raised here do specifically apply for the tree ring archive, some of them are important for all proxy archives of organic origin.

The comparison of various approach to evaluation erosion risks and design control erosion measures

NASA Astrophysics Data System (ADS)

Kapicka, Jiri

2015-04-01

In the present is in the Czech Republic one methodology how to compute and compare erosion risks. This methodology contain also method to design erosion control measures. The base of this methodology is Universal Soil Loss Equation (USLE) and their result long-term average annual rate of erosion (G). This methodology is used for landscape planners. Data and statistics from database of erosion events in the Czech Republic shows that many troubles and damages are from local episodes of erosion events. An extent of these events and theirs impact are conditional to local precipitation events, current plant phase and soil conditions. These erosion events can do troubles and damages on agriculture land, municipally property and hydro components and even in a location is from point of view long-term average annual rate of erosion in good conditions. Other way how to compute and compare erosion risks is episodes approach. In this paper is presented the compare of various approach to compute erosion risks. The comparison was computed to locality from database of erosion events on agricultural land in the Czech Republic where have been records two erosion events. The study area is a simple agriculture land without any barriers that can have high influence to water flow and soil sediment transport. The computation of erosion risks (for all methodology) was based on laboratory analysis of soil samples which was sampled on study area. Results of the methodology USLE, MUSLE and results from mathematical model Erosion 3D have been compared. Variances of the results in space distribution of the places with highest soil erosion where compared and discussed. Other part presents variances of design control erosion measures where their design was done on based different methodology. The results shows variance of computed erosion risks which was done by different methodology. These variances can start discussion about different approach how compute and evaluate erosion risks in areas with different importance.

Analysis of biologically active oxyprenylated phenylpropanoids in Tea tree oil using selective solid-phase extraction with UHPLC-PDA detection.

PubMed

Scotti, Luca; Genovese, Salvatore; Bucciarelli, Tonino; Martini, Filippo; Epifano, Francesco; Fiorito, Serena; Preziuso, Francesca; Taddeo, Vito Alessandro

2018-05-30

An efficient analytical strategy based on different extraction methods of biologically active naturally occurring oxyprenylated umbelliferone and ferulic acid derivatives 7-isopentenyloxycoumarin, auraptene, umbelliprenin, boropinic acid, and 4'-geranyloxyferulic acid and quantification by UHPLC with spectrophotometric (UV/Vis) detection from Tea tree oil is reported. Absorption of the pure oil on Al 2 O 3 (Brockmann activity II) prior washing the resulting solid with MeOH and treatment of this latter with CH 2 Cl 2 resulted the best extraction methodology in terms of yields of oxyprenylated secondary metabolites. Among the five O-prenylphenylpropanoids herein under investigation auraptene and umbelliprenin were never detected while 4'-geranyloxyferulic acid was the most abundant compound resulting from all the three extraction methods employed. The UHPLC analytical methodology set up in the present study resulted to be an effective and versatile technique for the simultaneous characterization and quantification of prenyloxyphenylpropanoids in Tea tree oil and applicable to other complex matrices from the plant kingdom. Copyright © 2018 Elsevier B.V. All rights reserved.

Growth-Mortality Relationships in Piñon Pine (Pinus edulis) during Severe Droughts of the Past Century: Shifting Processes in Space and Time

PubMed Central

Macalady, Alison K.; Bugmann, Harald

2014-01-01

The processes leading to drought-associated tree mortality are poorly understood, particularly long-term predisposing factors, memory effects, and variability in mortality processes and thresholds in space and time. We use tree rings from four sites to investigate Pinus edulis mortality during two drought periods in the southwestern USA. We draw on recent sampling and archived collections to (1) analyze P. edulis growth patterns and mortality during the 1950s and 2000s droughts; (2) determine the influence of climate and competition on growth in trees that died and survived; and (3) derive regression models of growth-mortality risk and evaluate their performance across space and time. Recent growth was 53% higher in surviving vs. dying trees, with some sites exhibiting decades-long growth divergences associated with previous drought. Differential growth response to climate partly explained growth differences between live and dead trees, with responses wet/cool conditions most influencing eventual tree status. Competition constrained tree growth, and reduced trees’ ability to respond to favorable climate. The best predictors in growth-mortality models included long-term (15–30 year) average growth rate combined with a metric of growth variability and the number of abrupt growth increases over 15 and 10 years, respectively. The most parsimonious models had high discriminatory power (ROC>0.84) and correctly classified ∼70% of trees, suggesting that aspects of tree growth, especially over decades, can be powerful predictors of widespread drought-associated die-off. However, model discrimination varied across sites and drought events. Weaker growth-mortality relationships and higher growth at lower survival probabilities for some sites during the 2000s event suggest a shift in mortality processes from longer-term growth-related constraints to shorter-term processes, such as rapid metabolic decline even in vigorous trees due to acute drought stress, and/or increases in the attack rate of both chronically stressed and more vigorous trees by bark beetles. PMID:24786646

Examining the Relationship Between Edaphic Variables and the Rooting System of Abies concolor in the southern Sierra Nevada

NASA Astrophysics Data System (ADS)

Wilson, A.; Jackson, R. B.; Tumber-Davila, S. J.

2017-12-01

An increase in the frequency and severity of droughts has been associated with the changing climate. These events have the potential to alter the composition and biogeography of forests, as well as increase tree mortality related to climate-induced stress. Already, an increase in tree mortality has been observed throughout the US. The recent drought in California led to millions of tree mortalities in the southern Sierra Nevada alone. In order to assess the potential impacts of these events on forest systems, it is imperative to understand what factors contribute to tree mortality. As plants become water-stressed, they may invest carbon more heavily belowground to reach a bigger pool of water, but their ability to adapt may be limited by the characteristics of the soil. In the Southern Sierra Critical Zone Observatory, a high tree mortality zone, we have selected both dead and living trees to examine the factors that contribute to root zone variability and belowground biomass investment by individual plants. A series of 15 cores surrounding the tree were taken to collect root and soil samples. These were then used to compare belowground rooting distributions with soil characteristics (texture, water holding capacity, pH, electric conductivity). Abies concolor is heavily affected by drought-induced mortality, therefore the rooting systems of dead Abies concolor trees were examined to determine the relationship between their rooting systems and environmental conditions. Examining the relationship between soil characteristics and rooting systems of trees may shed light on the plasticity of rooting systems and how trees adapt based on the characteristics of its environment. A better understanding of the factors that contribute to tree mortality can improve our ability to predict how forest systems may be impacted by climate-induced stress. Key words: Root systems, soil characteristics, drought, adaptation, terrestrial carbon, forest ecology

Systematic review of the cost effectiveness of prophylactic treatments in the prevention of gastropathy in patients with rheumatoid arthritis or osteoarthritis taking non-steroidal anti-inflammatory drugs

PubMed Central

van Dieten, H. E M; Bos, I.; van Tulder, M. W; Lems, W.; Dijkmans, B.; Boers, M.

2000-01-01

A systematic review on the cost effectiveness of prophylactic treatments of non-steroidal anti-inflammatory drug (NSAID) induced gastropathy in patients with osteoarthritis or rheumatoid arthritis was conducted. Two reviewers conducted the literature search and the review. Both full and partial economic evaluations published in English, Dutch, or German were included. The criteria list published in the textbook of Drummond was used to determine the quality of the economic evaluations. The methodological quality of three randomised controlled trials (RCTs) in which the economic evaluations obtained probability estimates of NSAID induced gastropathy and adverse events was assessed by a list of internal validity criteria. The conclusions were based on a rating system consisting of four levels of evidence.
  Ten economic evaluations were included; three were based on RCTs. All evaluations studied misoprostol as prophylactic treatment: in one evaluation misoprostol was studied as a fixed component in a combination with diclofenac (Arthrotec). All economic evaluations comprised analytical studies containing a decision tree. The three trials were of high methodological quality. Nine economic evaluations were considered high quality and one economic evaluation was considered of low methodological quality. There is strong evidence (level "A") that the use of misoprostol for the prevention of NSAID induced gastropathy is cost effective, and limited evidence (level "C") that the use of Arthrotec is cost effective. Although the levels of evidence used in this review are arbitrary, it is believed that a qualitative analysis is useful: quantitative analyses in this field are hampered by the heterogeneity of economic evaluations. Existing criteria to evaluate the methodological quality of economic evaluations may need refinement for use in systematic reviews.

 PMID:11005773

Systematic review of the cost effectiveness of prophylactic treatments in the prevention of gastropathy in patients with rheumatoid arthritis or osteoarthritis taking non-steroidal anti-inflammatory drugs.

PubMed

van Dieten, H E; Korthals-de Bos, I B; van Tulder, M W; Lems, W F; Dijkmans, B A; Boers, M

2000-10-01

A systematic review on the cost effectiveness of prophylactic treatments of non-steroidal anti-inflammatory drug (NSAID) induced gastropathy in patients with osteoarthritis or rheumatoid arthritis was conducted. Two reviewers conducted the literature search and the review. Both full and partial economic evaluations published in English, Dutch, or German were included. The criteria list published in the textbook of Drummond was used to determine the quality of the economic evaluations. The methodological quality of three randomised controlled trials (RCTs) in which the economic evaluations obtained probability estimates of NSAID induced gastropathy and adverse events was assessed by a list of internal validity criteria. The conclusions were based on a rating system consisting of four levels of evidence. Ten economic evaluations were included; three were based on RCTs. All evaluations studied misoprostol as prophylactic treatment: in one evaluation misoprostol was studied as a fixed component in a combination with diclofenac (Arthrotec). All economic evaluations comprised analytical studies containing a decision tree. The three trials were of high methodological quality. Nine economic evaluations were considered high quality and one economic evaluation was considered of low methodological quality. There is strong evidence (level "A") that the use of misoprostol for the prevention of NSAID induced gastropathy is cost effective, and limited evidence (level "C") that the use of Arthrotec is cost effective. Although the levels of evidence used in this review are arbitrary, it is believed that a qualitative analysis is useful: quantitative analyses in this field are hampered by the heterogeneity of economic evaluations. Existing criteria to evaluate the methodological quality of economic evaluations may need refinement for use in systematic reviews.

Minority Elderly Adaptation to Life-Threatening Events: An Overview with Methodological Consideration.

ERIC Educational Resources Information Center

Trimble, Joseph E.; And Others

A review of pertinent research on the adaptation of ethnic minority elderly to life-threatening events (personal, man-made, or natural) exposes voids in the research, presents methodological considerations, and indicates that ethnic minority elderly are disproportionately victimized by life-threatening events. Unusually high numbers of…

Reconstruction of glacial lake outburst floods in northern Tien Shan: Implications for hazard assessment

NASA Astrophysics Data System (ADS)

Zaginaev, V.; Ballesteros-Cánovas, J. A.; Erokhin, S.; Matov, E.; Petrakov, D.; Stoffel, M.

2016-09-01

Glacier lake outburst floods (GLOFs) and related debris flows are among the most significant natural threats in the Tien Shan Mountains of Kyrgyzstan and have even caused the loss of life and damage to infrastructure in its capital Bishkek. An improved understanding of the occurrence of this process is essential so as to be able to design reliable disaster risk reduction strategies, even more so in view of ongoing climate change and scenarios of future evolutions. Here, we apply a dendrogeomorphic approach to reconstruct past debris-flow activity on the Aksay cone (Ala-Archa valley, Kyrgyz range), where outbursting glacier lakes and intense rainfalls have triggered huge debris flows over the past decades. A total of 96 Picea abies (L.) Karst. trees growing on the cone and along the main channel have been selected based on the evidence of past debris-flow damage in their trunks; these trees were then sampled using increment borers. The dating of past events was based on the assessment of growth disturbances (GD) in the tree-ring records and included the detection of injuries, tangential rows of traumatic resin ducts, reaction wood, and abrupt growth changes. In total, 320 GD were identified in the tree-ring samples. In combination with aerial imagery and geomorphic recognition in the field, reactions in trees and their position on the cone have allowed reconstruction of the main spatial patterns of past events on the Aksay cone. Our findings suggest that at least 27 debris flows have occurred on the site between 1877 and 2015 and point to the occurrence of at least 17 events that were not documented prior to this study. We also observe high process activity during the 1950s and 1960s, with major events on the cone in 1950, 1966, and 1968, coinciding with phases of slight glacier advance. The spatial analyses of events also point to two different spatial patterns, suggesting that quite dissimilar magnitudes probably occurred during glacier lake outburst floods and rainfall-induced debris-flow events. The results presented here represent the longest, annually resolved GLOF series in the region, which in turn has key implications on risk assessment, not just in the Ala-Archa valley, but also in the entire Kyrgyz range (northern Tien Shan).

Mortality in Subalpine Forests of the Sierra Nevada, California, USA: Differential Response of Pines (Pinus albicaulis and P. flexilis) to Climate Variability

NASA Astrophysics Data System (ADS)

Millar, C. I.; Westfall, R. D.; Delany, D. L.

2010-12-01

Widespread forest mortality in high-elevation forests has been increasing across western North American mountains in recent years, with climate, insects, and disease the primary causes. Subalpine forests in the eastern Sierra Nevada, by contrast, have experienced far less mortality than other ranges, and mortality events have been patchy and episodic. This situation, and lack of significant effect of non-native white-pine blister rust, enable investigation of fine-scale response of two subalpine Sierran species, whitebark pine (Pinus albicaulis, PiAl) and limber pine (P. flexilis, PiFl), to climate variability. We report similarities and differences between the two major mortality events in these pines in the last 150 years: 1988-1992 for PiFl and 2006-ongoing for PiAl. In both species, the events occurred within monotypic, closed-canopy, relatively young stands (< 200 yrs PiAl, < 300 yrs in PiFl); were localized to central-eastern Sierra Nevada; and occurred at 2740-2840 m along the eastern edge of the escarpment on north/northeast aspects with slopes > 40%. Mortality patches averaged 40-80 ha in both species, with mean stand mortality of trees > 10 cm diameter 91% in PiAl and 60% in PiFl. The ultimate cause of tree death was mountain pine beetle (Dendroctonus ponderosae) in both species, with increasing 20th/21st C minimum temperatures combined with drought the pre-conditioning factors. Overall growth in the past 150 years suggests that PiFl is more drought hardy than PiAl but responds sensitively to the combined effects of drought and increasing warmth. After the 1988-1992 drought, surviving PiFl recovered growth. PiAl trees grew very poorly during that drought, and continued poor growth in the years until 2006 when the mortality event occurred in PiAl. A significant species effect is the apparent difference in levels of within-stand genetic diversity for climate factors. Differential growth between 19th C (cool, wet) and 20th/21st C (warming, drying) of PiFl trees that died versus survivors indicates that considerable within-stand genetic diversity for climate existed in PiFl. For PiFl, the late 20th C mortality event acted as strong natural selection to improve within-stand fitness for warmer and drier conditions. PiFl trees that survived the 1988-1992 drought remained healthy through subsequent droughts, including the drought that is currently causing PiAl mortality. By contrast, the PiAl stands do not appear to have contained adaptive genetic diversity for drought and warmth, and PiAl trees growth behavior over the past 150 years was similar in pattern to the PiFl trees that died. As a result, the mortality event in PiAl is creating forest openings, with unknown future stand conditions, rather than rapid within-species adaptation that occurred in PiFl.

Bounding the Resource Availability of Partially Ordered Events with Constant Resource Impact

NASA Technical Reports Server (NTRS)

Frank, Jeremy

2004-01-01

We compare existing techniques to bound the resource availability of partially ordered events. We first show that, contrary to intuition, two existing techniques, one due to Laborie and one due to Muscettola, are not strictly comparable in terms of the size of the search trees generated under chronological search with a fixed heuristic. We describe a generalization of these techniques called the Flow Balance Constraint to tightly bound the amount of available resource for a set of partially ordered events with piecewise constant resource impact We prove that the new technique generates smaller proof trees under chronological search with a fixed heuristic, at little increase in computational expense. We then show how to construct tighter resource bounds but at increased computational cost.

Genetic diversity-seeing the forest through the trees

Treesearch

M. Thompson Conkle

1992-01-01

Forest trees, populations, races, species, and taxonomic groups above the species level display rich variation in biochemical markers. The variation stems from inherited modifications that trace back in time, through converging ancestries, towards common progenitors. Past movements of continents, mountain building events, and climate changes isolated forest populations...

30 CFR 250.618 - Tubing and wellhead equipment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... following requirements during well-workover operations with the tree removed: (a) No tubing string shall be... pressure integrity and is otherwise suitable for its intended use. (b) In the event of prolonged operations... Manager. (c) When reinstalling the tree, you must: (1) Equip wells to monitor for casing pressure...

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

PubMed Central

Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo

2017-01-01

Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking. PMID:28690608

Extensions and applications of ensemble-of-trees methods in machine learning

NASA Astrophysics Data System (ADS)

Bleich, Justin

Ensemble-of-trees algorithms have emerged to the forefront of machine learning due to their ability to generate high forecasting accuracy for a wide array of regression and classification problems. Classic ensemble methodologies such as random forests (RF) and stochastic gradient boosting (SGB) rely on algorithmic procedures to generate fits to data. In contrast, more recent ensemble techniques such as Bayesian Additive Regression Trees (BART) and Dynamic Trees (DT) focus on an underlying Bayesian probability model to generate the fits. These new probability model-based approaches show much promise versus their algorithmic counterparts, but also offer substantial room for improvement. The first part of this thesis focuses on methodological advances for ensemble-of-trees techniques with an emphasis on the more recent Bayesian approaches. In particular, we focus on extensions of BART in four distinct ways. First, we develop a more robust implementation of BART for both research and application. We then develop a principled approach to variable selection for BART as well as the ability to naturally incorporate prior information on important covariates into the algorithm. Next, we propose a method for handling missing data that relies on the recursive structure of decision trees and does not require imputation. Last, we relax the assumption of homoskedasticity in the BART model to allow for parametric modeling of heteroskedasticity. The second part of this thesis returns to the classic algorithmic approaches in the context of classification problems with asymmetric costs of forecasting errors. First we consider the performance of RF and SGB more broadly and demonstrate its superiority to logistic regression for applications in criminology with asymmetric costs. Next, we use RF to forecast unplanned hospital readmissions upon patient discharge with asymmetric costs taken into account. Finally, we explore the construction of stable decision trees for forecasts of violence during probation hearings in court systems.

Shape selection in Landsat time series: a tool for monitoring forest dynamics.

PubMed

Moisen, Gretchen G; Meyer, Mary C; Schroeder, Todd A; Liao, Xiyue; Schleeweis, Karen G; Freeman, Elizabeth A; Toney, Chris

2016-10-01

We present a new methodology for fitting nonparametric shape-restricted regression splines to time series of Landsat imagery for the purpose of modeling, mapping, and monitoring annual forest disturbance dynamics over nearly three decades. For each pixel and spectral band or index of choice in temporal Landsat data, our method delivers a smoothed rendition of the trajectory constrained to behave in an ecologically sensible manner, reflecting one of seven possible 'shapes'. It also provides parameters summarizing the patterns of each change including year of onset, duration, magnitude, and pre- and postchange rates of growth or recovery. Through a case study featuring fire, harvest, and bark beetle outbreak, we illustrate how resultant fitted values and parameters can be fed into empirical models to map disturbance causal agent and tree canopy cover changes coincident with disturbance events through time. We provide our code in the r package ShapeSelectForest on the Comprehensive R Archival Network and describe our computational approaches for running the method over large geographic areas. We also discuss how this methodology is currently being used for forest disturbance and attribute mapping across the conterminous United States. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Tree ring-based chronology of hydro-geomorphic processes as a fundament for identification of hydro-meteorological triggers in the Hrubý Jeseník Mountains (Central Europe).

PubMed

Tichavský, Radek; Šilhán, Karel; Tolasz, Radim

2017-02-01

Hydro-geomorphic processes have significantly influenced the recent development of valley floors, river banks and depositional forms in mountain environments, have caused considerable damage to manmade developments and have disrupted forest management. Trees growing along streams are affected by the transported debris mass and provide valuable records of debris flow/flood histories in their tree-ring series. Dendrogeomorphic approaches are currently the most accurate methods for creating a chronology of the debris flow/flood events in forested catchments without any field-monitoring or a stream-gauging station. Comprehensive studies focusing on the detailed chronology of hydro-geomorphic events and analysis of meteorological triggers and weather circulation patterns are still lacking for the studied area. We provide a spatio-temporal reconstruction of hydro-geomorphic events in four catchments of the Hrubý Jeseník Mountains, Czech Republic, with an analysis of their triggering factors using meteorological data from four nearby rain gauges. Increment cores from 794 coniferous trees (Picea abies [L.] Karst.) allowed the identification of 40 hydro-geomorphic events during the period of 1889-2013. Most of the events can be explained by extreme daily rainfalls (≥50mm) occurring in at least one rain gauge. However, in several cases, there was no record of extreme precipitation at rain gauges during the debris flow/flood event year, suggesting extremely localised rainstorms at the mountain summits. We concluded that the localisation, intensity and duration of rainstorms; antecedent moisture conditions; and amount of available sediments all influenced the initiation, spatial distribution and characteristics of hydro-geomorphic events. The most frequent synoptic situations responsible for the extreme rainfalls (1946-2015) were related to the meridional atmospheric circulation pattern. Our results enhance current knowledge of the occurrences and triggers of debris flows/floods in the Central European mountains in transition between temperate oceanic and continental climatic conditions and may prompt further research of these phenomena in the Eastern Sudetes in general. Copyright © 2016 Elsevier B.V. All rights reserved.

Modeling tree crown dynamics with 3D partial differential equations.

PubMed

Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

2014-01-01

We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications.

The ethnobotany of Christ's Thorn Jujube (Ziziphus spina-christi) in Israel.

PubMed

Dafni, Amots; Levy, Shay; Lev, Efraim

2005-09-28

This article surveys the ethnobotany of Ziziphus spina-christi (L.) Desf. in the Middle East from various aspects: historical, religious, philological, literary, linguistic, as well as pharmacological, among Muslims, Jews, and Christians. It is suggested that this is the only tree species considered "holy" by Muslims (all the individuals of the species are sanctified by religion) in addition to its status as "sacred tree " (particular trees which are venerated due to historical or magical events related to them, regardless of their botanical identity) in the Middle East. It has also a special status as "blessed tree" among the Druze.

Towards an Optimized Method of Olive Tree Crown Volume Measurement

PubMed Central

Miranda-Fuentes, Antonio; Llorens, Jordi; Gamarra-Diezma, Juan L.; Gil-Ribes, Jesús A.; Gil, Emilio

2015-01-01

Accurate crown characterization of large isolated olive trees is vital for adjusting spray doses in three-dimensional crop agriculture. Among the many methodologies available, laser sensors have proved to be the most reliable and accurate. However, their operation is time consuming and requires specialist knowledge and so a simpler crown characterization method is required. To this end, three methods were evaluated and compared with LiDAR measurements to determine their accuracy: Vertical Crown Projected Area method (VCPA), Ellipsoid Volume method (VE) and Tree Silhouette Volume method (VTS). Trials were performed in three different kinds of olive tree plantations: intensive, adapted one-trunked traditional and traditional. In total, 55 trees were characterized. Results show that all three methods are appropriate to estimate the crown volume, reaching high coefficients of determination: R2 = 0.783, 0.843 and 0.824 for VCPA, VE and VTS, respectively. However, discrepancies arise when evaluating tree plantations separately, especially for traditional trees. Here, correlations between LiDAR volume and other parameters showed that the Mean Vector calculated for VCPA method showed the highest correlation for traditional trees, thus its use in traditional plantations is highly recommended. PMID:25658396

Dendrogeomorphic reconstruction of lahar activity and triggers: Shiveluch volcano, Kamchatka Peninsula, Russia

NASA Astrophysics Data System (ADS)

Salaorni, E.; Stoffel, M.; Tutubalina, O.; Chernomorets, S.; Seynova, I.; Sorg, A.

2017-01-01

Lahars are highly concentrated, water-saturated volcanic hyperconcentrated flows or debris flows containing pyroclastic material and are a characteristic mass movement process on volcanic slopes. On Kamchatka Peninsula (Russian Federation), lahars are widespread and may affect remote settlements. Historical records of past lahar occurrences are generally sparse and mostly limited to events which damaged infrastructure on the slopes or at the foot of volcanoes. In this study, we present a tree-ring-based reconstruction of spatiotemporal patterns of past lahar activity at Shiveluch volcano. Using increment cores and cross sections from 126 Larix cajanderi trees, we document 34 events covering the period AD 1729-2012. Analyses of the seasonality of damage in trees reveal that 95% of all lahars occurred between October and May and thus point to the predominant role of the sudden melt of the snow cover by volcanic material. These observations suggest that most lahars were likely syn-eruptive and that lahar activity is largely restricted to periods of volcanic activity. By contrast, rainfall events do not seem to play a significant role in lahar triggering.

Rapid increase in cosmogenic 14C in AD 775 measured in New Zealand kauri trees indicates short-lived increase in 14C production spanning both hemispheres

NASA Astrophysics Data System (ADS)

Güttler, D.; Adolphi, F.; Beer, J.; Bleicher, N.; Boswijk, G.; Christl, M.; Hogg, A.; Palmer, J.; Vockenhuber, C.; Wacker, L.; Wunder, J.

2015-02-01

In 2012, Miyake et al. reported a sudden and strong increase of the atmospheric radiocarbon (14C) content in Japanese cedar trees of 1.2% between AD 774 and 775. While their findings were quickly confirmed by a German oak chronology for the Northern Hemisphere (NH), the question remained if the effect was seen in both hemispheres. Here we present the first annually resolved Southern Hemisphere (SH) 14C record spanning the interval AD 760-787, using New Zealand kauri (Agathis australis) chronology wood. An almost identical distinct increase compared to Northern Hemisphere data was observed, suggesting a cosmic event with globally uniform impact as a potential cause for the increase. Deploying a carbon cycle box model a worldwide averaged net 14C production of 2.2 ×108 14C atoms cm-2 was estimated, which is 3.7 times higher than the average annual 14C production. The immediate appearance of the event in tree rings on both hemispheres suggests a short duration event of significantly less than 1 yr.

Dendrogeomorphological analysis of a slope near Lago, Calabria (Italy)

NASA Astrophysics Data System (ADS)

Fantucci, Rosanna; Sorriso-Valvo, Marino

1999-10-01

The dendrogeomorphological analysis has been used to investigate the periods of disturbance on a slope affected by deep-seated gravitational movements. The method proved to be of great help in determining the temporal sequence of diffused slope movement in the study area, and, though to a lesser extent, to find out the possible causes of triggering the mass-movement. In general, leaning trees indicate that the movement is active. The visual growth analysis indicates that anomalies consisted of sudden decreases of the growth (suppression of tree-rings) induced by stress consequent on ground disturbance, followed in some cases by sudden increases of tree-ring width induced by the higher moisture content in the landslide body. By anomaly analysis, an increase of the anomaly index (It) occurred between 1840 and 1860; subsequently, a period of strongly oscillating values of It occurred that levelled off around 1950. It also appears that mass-movements began to affect this zone soon after 1850s, thus, we can tentatively assume that they have been the cause of the growth anomalies, with a maximum influence in the period between 1860 and 1895. As regards the causes for mass-movement, we inquired about timing of extreme meteorological events and earthquakes. The meteorological data obtained from raingauging stations are not so well related to mass-movement reactivation as the seismic data are. However, only a minority of extreme meteorological events may produce such a disturbance that can be recorded in the tree-ring record. Indeed, only 30% of anomalies can be explained in terms of extreme events. On the other hand, the continuous creeping of the sackung might irregularly trigger the movement of shallower landslides in non extreme-events years. We obtained, instead, a higher degree of coincidence between disturbing causes and anomalous tree growth using archive reports on extreme rainfall periods.

Application of Decision Tree to Obtain Optimal Operation Rules for Reservoir Flood Control Considering Sediment Desilting-Case Study of Tseng Wen Reservoir

NASA Astrophysics Data System (ADS)

ShiouWei, L.

2014-12-01

Reservoirs are the most important water resources facilities in Taiwan.However,due to the steep slope and fragile geological conditions in the mountain area,storm events usually cause serious debris flow and flood,and the flood then will flush large amount of sediment into reservoirs.The sedimentation caused by flood has great impact on the reservoirs life.Hence,how to operate a reservoir during flood events to increase the efficiency of sediment desilting without risk the reservoir safety and impact the water supply afterward is a crucial issue in Taiwan. 　Therefore,this study developed a novel optimization planning model for reservoir flood operation considering flood control and sediment desilting,and proposed easy to use operating rules represented by decision trees.The decision trees rules have considered flood mitigation,water supply and sediment desilting.The optimal planning model computes the optimal reservoir release for each flood event that minimum water supply impact and maximum sediment desilting without risk the reservoir safety.Beside the optimal flood operation planning model,this study also proposed decision tree based flood operating rules that were trained by the multiple optimal reservoir releases to synthesis flood scenarios.The synthesis flood scenarios consists of various synthesis storm events,reservoir's initial storage and target storages at the end of flood operating. 　Comparing the results operated by the decision tree operation rules(DTOR) with that by historical operation for Krosa Typhoon in 2007,the DTOR removed sediment 15.4% more than that of historical operation with reservoir storage only8.38×106m3 less than that of historical operation.For Jangmi Typhoon in 2008,the DTOR removed sediment 24.4% more than that of historical operation with reservoir storage only 7.58×106m3 less than that of historical operation.The results show that the proposed DTOR model can increase the sediment desilting efficiency and extend the reservoir life.

Simulation-Based Model Checking for Nondeterministic Systems and Rare Events

DTIC Science & Technology

2016-03-24

year, we have investigated AO* search and Monte Carlo Tree Search algorithms to complement and enhance CMU’s SMCMDP. 1 Final Report, March 14... tree , so we can use it to find the probability of reachability for a property in PRISM’s Probabilistic LTL. By finding the maximum probability of...savings, particularly when handling very large models. 2.3 Monte Carlo Tree Search The Monte Carlo sampling process in SMCMDP can take a long time to

Sequence evidence for the symbiotic origins of chloroplasts and mitochondria

NASA Technical Reports Server (NTRS)

George, D. G.; Hunt, L. T.; Dayhoff, M. O.

1983-01-01

The origin of mitochondria and chloroplasts is investigated on the basis of prokaryotic and early-eukaryotic evolutionary trees derived from protein and nucleic-acid sequences by the method of Dayhoff (1979). Trees for bacterial ferrodoxins, 5S ribosomal RNA, c-type cytochromes, the lipid-binding subunit of ATPase, and dihydrofolate reductase are presented and discussed. Good agreement among the trees is found, and it is argued that the mitochondria and chloroplasts evolved by multiple symbiotic events.

On the typology and the worship status of sacred trees with a special reference to the Middle East.

PubMed

Dafni, Amots

2006-05-15

This article contains the reasons for the establishment of sacred trees in Israel based on a field study. It includes 97 interviews with Muslim and Druze informants. While Muslims (Arabs and Bedouins) consider sacred trees especially as an abode of righteous figures' (Wellis') souls or as having a connection to their graves, the Druze relate sacred trees especially to the events or deeds in the lives of prophets and religious leaders. A literary review shows the existence of 24 known reasons for the establishment of sacred trees worldwide, 11 of which are known in Israel one of these is reported here for the first time. We found different trends in monotheistic and polytheistic religions concerning their current worship of sacred trees.

On the typology and the worship status of sacred trees with a special reference to the Middle East

PubMed Central

Dafni, Amots

2006-01-01

This article contains the reasons for the establishment of sacred trees in Israel based on a field study. It includes 97 interviews with Muslim and Druze informants. While Muslims (Arabs and Bedouins) consider sacred trees especially as an abode of righteous figures' (Wellis') souls or as having a connection to their graves, the Druze relate sacred trees especially to the events or deeds in the lives of prophets and religious leaders. A literary review shows the existence of 24 known reasons for the establishment of sacred trees worldwide, 11 of which are known in Israel one of these is reported here for the first time. We found different trends in monotheistic and polytheistic religions concerning their current worship of sacred trees. PMID:16700917

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

PubMed

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Risk-Informed Safety Assurance and Probabilistic Assessment of Mission-Critical Software-Intensive Systems

NASA Technical Reports Server (NTRS)

Guarro, Sergio B.

2010-01-01

This report validates and documents the detailed features and practical application of the framework for software intensive digital systems risk assessment and risk-informed safety assurance presented in the NASA PRA Procedures Guide for Managers and Practitioner. This framework, called herein the "Context-based Software Risk Model" (CSRM), enables the assessment of the contribution of software and software-intensive digital systems to overall system risk, in a manner which is entirely compatible and integrated with the format of a "standard" Probabilistic Risk Assessment (PRA), as currently documented and applied for NASA missions and applications. The CSRM also provides a risk-informed path and criteria for conducting organized and systematic digital system and software testing so that, within this risk-informed paradigm, the achievement of a quantitatively defined level of safety and mission success assurance may be targeted and demonstrated. The framework is based on the concept of context-dependent software risk scenarios and on the modeling of such scenarios via the use of traditional PRA techniques - i.e., event trees and fault trees - in combination with more advanced modeling devices such as the Dynamic Flowgraph Methodology (DFM) or other dynamic logic-modeling representations. The scenarios can be synthesized and quantified in a conditional logic and probabilistic formulation. The application of the CSRM method documented in this report refers to the MiniAERCam system designed and developed by the NASA Johnson Space Center.

Tree-ring based reconstruction of rockfalls at Cofre de Perote volcano, Mexico

NASA Astrophysics Data System (ADS)

Franco-Ramos, Osvaldo; Stoffel, Markus; Vázquez-Selem, Lorenzo

2017-08-01

In this study, dendrogeomorphic techniques are employed to analyse the temporal frequency and spatial distribution of rockfalls on a talus slope of La Teta valley, located on the NW slopes of Cofre de Perote volcano at 4000 m above sea level. Based on the interpretation of disturbance signals in growth rings of old-growth Pinus hartwegii Lindl. trees, we identify 100 growth disturbances related with rockfall events dated between 1780 and 2011, with slightly more than half of these events being dated to the last 50 years. The sectors most susceptible to rockfall correspond with the young rock lobes located at the foot of scarps. Roughly three in ten events has been triggered by regional, M > 6 earthquakes, whereas half of the events activity coincides with periods characterized by severe, prolonged summer rainfalls such as the ones occurred in 1995, 1998, 2005 and 2011.

Using multiple data sets to populate probabilistic volcanic event trees

USGS Publications Warehouse

Newhall, C.G.; Pallister, John S.

2014-01-01

The key parameters one needs to forecast outcomes of volcanic unrest are hidden kilometers beneath the Earth’s surface, and volcanic systems are so complex that there will invariably be stochastic elements in the evolution of any unrest. Fortunately, there is sufficient regularity in behaviour that some, perhaps many, eruptions can be forecast with enough certainty for populations to be evacuated and kept safe. Volcanologists charged with forecasting eruptions must try to understand each volcanic system well enough that unrest can be interpreted in terms of pre-eruptive process, but must simultaneously recognize and convey uncertainties in their assessment. We have found that use of event trees helps to focus discussion, integrate data from multiple sources, reach consensus among scientists about both pre-eruptive process and uncertainties and, in some cases, to explain all of this to officials. Figure 1 shows a generic volcanic event tree from Newhall and Hoblitt (2002) that can be modified as needed for each specific volcano. This paper reviews how we and our colleagues have used such trees during a number of volcanic crises worldwide, for rapid hazard assessments in situations in which more formal expert elicitations could not be conducted. We describe how Multiple Data Sets can be used to estimate probabilities at each node and branch. We also present case histories of probability estimation during crises, how the estimates were used by public officials, and some suggestions for future improvements.

Learning in data-limited multimodal scenarios: Scandent decision forests and tree-based features.

PubMed

Hor, Soheil; Moradi, Mehdi

2016-12-01

Incomplete and inconsistent datasets often pose difficulties in multimodal studies. We introduce the concept of scandent decision trees to tackle these difficulties. Scandent trees are decision trees that optimally mimic the partitioning of the data determined by another decision tree, and crucially, use only a subset of the feature set. We show how scandent trees can be used to enhance the performance of decision forests trained on a small number of multimodal samples when we have access to larger datasets with vastly incomplete feature sets. Additionally, we introduce the concept of tree-based feature transforms in the decision forest paradigm. When combined with scandent trees, the tree-based feature transforms enable us to train a classifier on a rich multimodal dataset, and use it to classify samples with only a subset of features of the training data. Using this methodology, we build a model trained on MRI and PET images of the ADNI dataset, and then test it on cases with only MRI data. We show that this is significantly more effective in staging of cognitive impairments compared to a similar decision forest model trained and tested on MRI only, or one that uses other kinds of feature transform applied to the MRI data. Copyright © 2016. Published by Elsevier B.V.

Forest understory trees can be segmented accurately within sufficiently dense airborne laser scanning point clouds.

PubMed

Hamraz, Hamid; Contreras, Marco A; Zhang, Jun

2017-07-28

Airborne laser scanning (LiDAR) point clouds over large forested areas can be processed to segment individual trees and subsequently extract tree-level information. Existing segmentation procedures typically detect more than 90% of overstory trees, yet they barely detect 60% of understory trees because of the occlusion effect of higher canopy layers. Although understory trees provide limited financial value, they are an essential component of ecosystem functioning by offering habitat for numerous wildlife species and influencing stand development. Here we model the occlusion effect in terms of point density. We estimate the fractions of points representing different canopy layers (one overstory and multiple understory) and also pinpoint the required density for reasonable tree segmentation (where accuracy plateaus). We show that at a density of ~170 pt/m² understory trees can likely be segmented as accurately as overstory trees. Given the advancements of LiDAR sensor technology, point clouds will affordably reach this required density. Using modern computational approaches for big data, the denser point clouds can efficiently be processed to ultimately allow accurate remote quantification of forest resources. The methodology can also be adopted for other similar remote sensing or advanced imaging applications such as geological subsurface modelling or biomedical tissue analysis.

The fault-tree compiler

NASA Technical Reports Server (NTRS)

Martensen, Anna L.; Butler, Ricky W.

1987-01-01

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 precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. 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 Corporation VAX with the VMS operation system.

Uranium mobility across annual growth rings in three deciduous tree species

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

McHugh, Kelly C.; Widom, Elisabeth; Spitz, Henry B.

Black walnut (Juglans nigra), slippery elm (Ulmus rubra), and white ash (Fraxinus americana) trees were evaluated as potential archives of past uranium (U) contamination. Like other metals, U mobility in annual growth rings of trees is potentially dependent on the tree species. Uranium concentrations and isotopic compositions (masses 234, 235, 236, and 238) were analyzed by thermal ionization mass spectrometry to test the efficacy of using tree rings to retroactively monitor U pollution from the FFMPC, a U purification facility operating from 1951 to 1989. This study found non-natural U (depleted U and detectable 236U) in growth rings of allmore » three tree species that pre-dated the start of operations at FFMPC and compositional trends that did not correspond with known contamination events. Therefore, the annual growth rings of these tree species cannot be used to reliably monitor the chronology of U contamination.« less

Uranium mobility across annual growth rings in three deciduous tree species.

PubMed

McHugh, Kelly C; Widom, Elisabeth; Spitz, Henry B; Wiles, Gregory C; Glover, Sam E

2018-02-01

Black walnut (Juglans nigra), slippery elm (Ulmus rubra), and white ash (Fraxinus americana) trees were evaluated as potential archives of past uranium (U) contamination. Like other metals, U mobility in annual growth rings of trees is dependent on the tree species. Uranium concentrations and isotopic compositions (masses 234, 235, 236, and 238) were analyzed by thermal ionization mass spectrometry to test the efficacy of using tree rings to retroactively monitor U pollution from the FFMPC, a U purification facility operating from 1951 to 1989. This study found non-natural U (depleted U and detectable 236 U) in growth rings of all three tree species that pre-dated the start of operations at FFMPC and compositional trends that did not correspond with known contamination events. Therefore, the annual growth rings of these tree species cannot be used to reliably monitor the chronology of U contamination. Copyright © 2017 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.

Quantifying Standing Dead Tree Volume and Structural Loss with Voxelized Terrestrial Lidar Data

NASA Astrophysics Data System (ADS)

Popescu, S. C.; Putman, E.

2017-12-01

Standing dead trees (SDTs) are an important forest component and impact a variety of ecosystem processes, yet the carbon pool dynamics of SDTs are poorly constrained in terrestrial carbon cycling models. The ability to model wood decay and carbon cycling in relation to detectable changes in tree structure and volume over time would greatly improve such models. The overall objective of this study was to provide automated aboveground volume estimates of SDTs and automated procedures to detect, quantify, and characterize structural losses over time with terrestrial lidar data. The specific objectives of this study were: 1) develop an automated SDT volume estimation algorithm providing accurate volume estimates for trees scanned in dense forests; 2) develop an automated change detection methodology to accurately detect and quantify SDT structural loss between subsequent terrestrial lidar observations; and 3) characterize the structural loss rates of pine and oak SDTs in southeastern Texas. A voxel-based volume estimation algorithm, "TreeVolX", was developed and incorporates several methods designed to robustly process point clouds of varying quality levels. The algorithm operates on horizontal voxel slices by segmenting the slice into distinct branch or stem sections then applying an adaptive contour interpolation and interior filling process to create solid reconstructed tree models (RTMs). TreeVolX estimated large and small branch volume with an RMSE of 7.3% and 13.8%, respectively. A voxel-based change detection methodology was developed to accurately detect and quantify structural losses and incorporated several methods to mitigate the challenges presented by shifting tree and branch positions as SDT decay progresses. The volume and structural loss of 29 SDTs, composed of Pinus taeda and Quercus stellata, were successfully estimated using multitemporal terrestrial lidar observations over elapsed times ranging from 71 - 753 days. Pine and oak structural loss rates were characterized by estimating the amount of volumetric loss occurring in 20 equal-interval height bins of each SDT. Results showed that large pine snags exhibited more rapid structural loss in comparison to medium-sized oak snags in this study.

Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple.

PubMed

Guitton, B; Kelner, J J; Celton, J M; Sabau, X; Renou, J P; Chagné, D; Costes, E

2016-02-29

The transition from vegetative to floral state in shoot apical meristems (SAM) is a key event in plant development and is of crucial importance for reproductive success. In perennial plants, this event is recurrent during tree life and subject to both within-tree and between-years heterogeneity. In the present study, our goal was to identify candidate processes involved in the repression or induction of flowering in apical buds of adult apple trees. Genes differentially expressed (GDE) were examined between trees artificially set in either 'ON' or 'OFF' situation, and in which floral induction (FI) was shown to be inhibited or induced in most buds, respectively, using qRT-PCR and microarray analysis. From the period of FI through to flower differentiation, GDE belonged to four main biological processes (i) response to stimuli, including response to oxidative stress; (ii) cellular processes, (iii) cell wall biogenesis, and (iv) metabolic processes including carbohydrate biosynthesis and lipid metabolic process. Several key regulator genes, especially TEMPRANILLO (TEM), FLORAL TRANSITION AT MERISTEM (FTM1) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) were found differentially expressed. Moreover, homologs of SPL and Leucine-Rich Repeat proteins were present under QTL zones previously detected for biennial bearing. This data set suggests that apical buds of 'ON' and 'OFF' trees were in different physiological states, resulting from different metabolic, hormonal and redox status which are likely to contribute to FI control in adult apple trees. Investigations on carbohydrate and hormonal fluxes from sources to SAM and on cell detoxification process are expected to further contribute to the identification of the underlying physiological mechanisms of FI in adult apple trees.

Factors impacting stemflow generation in a European beech forest: Individual tree versus neighborhood properties

NASA Astrophysics Data System (ADS)

Metzger, Johanna Clara; Germer, Sonja; Hildebrandt, Anke

2017-04-01

The redistribution of precipitation by canopies changes the water flow dynamics to the forest floor. The spatial pattern of throughfall has been researched in a number of studies in different ecosystems. Yet, also stemflow substantially influences water input patterns, constituting a mean of 12% of gross precipitation for European beech as one of the most abundant tree species in Central Europe. While the initiation of stemflow depends mostly on precipitation event properties, stemflow amounts are strongly shaped by canopy structure. Stemflow research has mainly addressed the impact of single tree morphological variables. In previous studies, the impact of forest structure on area-based stemflow was studied comparing plots with different properties using few exemplary stemflow measurements. In non-homogeneous stands, this approach might not be accurate, as the variation of stand properties like tree density could change tree individual stemflow fluxes. To investigate this, a total measurement of all trees per plot is required. We hypothesize, that in addition to individual tree metrics, tree neighborhood relations have a significant impact on stemflow generation in a heterogeneous beech forest. Our study site is located in the pristine forest of the National Park Hainich, central Germany. It is heterogeneous in respect to tree density, species composition and tree age. We measured stemflow in an areal approach, for all trees on 11 subplots (each 10 m x 10 m) spaced evenly throughout a 1 ha plot. This involved overall 65 trees, which is 11% of the plot's trees. 27 precipitation events were recorded in spring and early summer of 2015 and 2016. Stand properties were surveyed, including diameter at breast height, height, position and species of a tree. From this data, we calculated neighborhood properties for each tree, as number, basal area, and relative height of neighboring trees within a radius of the plot's mean tree distance. Using linear mixed effects models, we identified the different factors, individual and neighborhood, which significantly explain stemflow amount per tree. Preliminary results show, that the main impact on stemflow in our heterogeneous beech forest is due to individual tree diameter at breast height, while neighborhood factors have a smaller influence. This work defines the most important factors for stemflow fluxes, using easy-to-acquire tree and stand information, which allows the robust extrapolation of stemflow measurements and the generation of a spatially discrete pattern of stemflow input to the soil. Because of the high local and temporal concentration of precipitation, stemflow fluxes could be a key factor in forest soil water dynamics. On the long run, the results shall enable us to directly link soil water content measurements with estimated stemflow volumes for individual trees to trace stemflow fluxes into and through the soil.

Characterization of Extreme Deposition of Air Pollutants in MT. Mitchell State Park: Potential for Forest Decline and Opportunity for Cloud Deacidification

NASA Astrophysics Data System (ADS)

Defelice, Thomas Peter

The decline of forests has long been attributed to various natural (e.g. drought), man-made (e.g. logging), and perhaps, combinations of these (eg. fires caused by loggers) causes. A new type of forest decline (attributed to the deposition of air pollutants and other natural causes) has become apparent at high elevation sites in western Europe and North America; especially for above cloudbase forests like those in the Mt. Mitchell State Park. Investigations of air pollutant deposition are plentiful and laboratory studies have shown extreme deposition of these pollutants to be potentially harmful to forests. However, no field study has concentrated on these events. The primary objective of this study is to characterize (i.e., meterologically, microphysically, chemically) extreme episodes of air pollutant deposition. This study defines extreme aqueous events as having a pH < 3.1. pH's of this order are known to reduce laboratory tree growth depending on their age and species. On the average, one out of three aqueous events, sampled in the park during the 1986-1988 growing seasons (mid-May through mid-September), was extreme. Their occurrence over time may lead to the death of infant and 'old' trees, and to the reduced vigor of trees in their prime, as a result of triggering the decline mechanisms of these trees. These events usually last ~ 4.0 h, form during extended periods of high atmospheric pressure, have a liquid water content of ~ 0.10 gm^{-3}, and near typical cloud droplet sizes (~ 8.0 μm). Extreme aqueous events deposit most of their acid at their end. The deposition from the infrequent occurrences of very high ozone ( >=q100 ppb) and sulfur dioxide (>=q 5 ppb) concentrations in conjunction with these cloud events may be even more detrimental to the canopy, then that by extreme aqueous events alone. The physical characteristics of these combined events appear to include those of mature, precipitating clouds. Their occurrence may provide a clue as to how very low pH clouds might be deacidified. That is, base gases (eg. ammonia) locally introduced into such clouds at the proper time may render them harmless upon impact with the forest canopy, and beneficial to regional water supply users.

Best practices in incident investigation in the chemical process industries with examples from the industry sector and specifically from Nova Chemicals.

PubMed

Morrison, Lisa M

2004-07-26

This paper will summarize best practices in incident investigation in the chemical process industries and will provide examples from both the industry sector and specifically from NOVA Chemicals. As a sponsor of the Center for Chemical Process Safety (CCPS), an industry technology alliance of the American Institute of Chemical Engineers, NOVA Chemicals participates in a number of working groups to help develop best practices and tools for the chemical process and associated industries in order to advance chemical process safety. A recent project was to develop an update on guidelines for investigating chemical process incidents. A successful incident investigation management system must ensure that all incidents and near misses are reported, that root causes are identified, that recommendations from incident investigations identify appropriate preventive measures, and that these recommendations are resolved in a timely manner. The key elements of an effective management system for incident investigation will be described. Accepted definitions of such terms as near miss, incident, and root cause will be reviewed. An explanation of the types of incident classification systems in use, along with expected levels of follow-up, will be provided. There are several incident investigation methodologies in use today by members of the CCPS; most of these methodologies incorporate the use of several tools. These tools include: timelines, sequence diagrams, causal factor identification, brainstorming, checklists, pre-defined trees, and team-defined logic trees. Developing appropriate recommendations and then ensuring their resolution is the key to prevention of similar events from recurring, along with the sharing of lessons learned from incidents. There are several sources of information on previous incidents and lessons learned available to companies. In addition, many companies in the chemical process industries use their own internal databases to track recommendations from incidents and to share learnings internally.

Building National Capacity To Implement National Forest Monitoring System In Africa By GLAD

NASA Astrophysics Data System (ADS)

Lola Amani, P. K.

2017-12-01

Earth Observation data provide numerous information on the earth and its phenomena from space/satellite. They also offer the ability to compile and analyze information at global or local scales in a timely manner. However, to use them, it is important to develop methods that can enable the extraction of the desired information. Such methods should be robust and consistent enough to be considered for national monitoring systems. At the University of Maryland, the Global Land Analysis and Discovery (GLAD) Laboratory, led by Dr. Hansen, has developed automatic methods using Landsat data that have been applied for the Global Forest Change (GFC) in collaboration with the World Resources Institute (WRI), Google and others to providing information on tree cover loss throughout the global on a yearly basis, and on a daily basis a tree cover loss alert system to improve transparency and accessible at GFW Initiative (Global Forest Watch) website. Following the increasing interest in utilizing the GFC data, the GLAD Laboratory is working closely with national governments of different countries to reinforce their capacities in using the data in the best way and implementing the methodological framework for supporting their national forest monitoring, notification, and reporting (MNV) system. More precisely, the Lab supports step by step the countries in developing their reference emission levels and/or forest reference levels based on the country-specific needs, goals, and requirements, including the definition of the forest. Once in place, the methodology can easily be extended to different applications, such as monitoring the droughts events, etc. Here, we present the work accomplished with the national agencies of some countries in Africa, like Cameroon, Republic of Congo and Madagascar with the support of the Silva-Carbon and USAID-CARPE Programs and WRI. These countries are mainly engaged at different levels of the REDD+ process. Keywords: Earth Observation, Landsat data, Global Forest Change, National Monitoring System, Capacity Building, Africa

30 CFR 250.619 - Tubing and wellhead equipment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... during well-workover operations with the tree removed: (a) No tubing string shall be placed in service or... otherwise suitable for its intended use. (b) In the event of prolonged operations such as milling, fishing... the tree, you must: (1) Equip wells to monitor for casing pressure according to the following chart...

30 CFR 250.618 - Tubing and wellhead equipment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... during well-workover operations with the tree removed: (a) No tubing string shall be placed in service or... otherwise suitable for its intended use. (b) In the event of prolonged operations such as milling, fishing... the tree, you must: (1) Equip wells to monitor for casing pressure according to the following chart...

30 CFR 250.619 - Tubing and wellhead equipment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... during well-workover operations with the tree removed: (a) No tubing string shall be placed in service or... otherwise suitable for its intended use. (b) In the event of prolonged operations such as milling, fishing... the tree, you must: (1) Equip wells to monitor for casing pressure according to the following chart...

High-resolution climate signals in the Bølling Allerød Interstadial (Greenland Interstadial 1) as reflected in European tree-ring chronologies compared to marine varves and ice-core records

NASA Astrophysics Data System (ADS)

Friedrich, Michael; Kromer, Bernd; Kaiser, Klaus F.; Spurk, Marco; Hughen, Konrad A.; Johnsen, Sigfus J.

2001-05-01

Lateglacial and Holocene tree-ring chronologies are unique archives, which provide various information on past environments on a true annual time scale. Changes in ring-width can be related to past climate anomalies and dendrodated wood provides an ideal source for radiocarbon calibration. We present a 1051 year tree-ring chronology from the Late Glacial, built from subfossil Scots pines (Pinus sylvestris) that grew in different regions of Central and Southern Europe. Through a series of high-precision radiocarbon measurements we obtained a floating radiocarbon chronology, which allowed accurate wiggle-matching to the INTCAL98 calibration curve. The trees show a coherent pattern in ring-width variations throughout Central Europe, and extending into the Mediterranean, which indicates a strong external climatic factor, most probably temperature during the growing season. We identified major growth events, which appear synchronous with events seen in isotopic and tracer signals in the Greenland ice cores and with changes in the strength of upwelling in the Cariaco Basin.

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees.

PubMed

van Iersel, Leo; Kelk, Steven; Lekić, Nela; Scornavacca, Celine

2014-05-05

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

The atmospheric CO2 concentration is increasing rapidly due to anthropogenic emissions but the effect on the Earth's biosphere is poorly understood. The ability of the biosphere to fix CO2 through photosynthesis will determine future atmospheric CO2 concentrations as well as future productivity of crops and forests. Manipulative CO2 enrichment experiments (e.g. FACE) are limited to (i) short time spans, (ii) few locations and (iii) large step increases in [CO2]. Here, we apply new stable isotope methodology to tree-ring archives, to study the effect of increasing CO2 concentrations retrospectively during the past centuries. We cover the whole [CO2] increase since industrialization, and sample trees with global distribution. Instead of isotope ratios of whole molecules, we use intramolecular isotope distributions, a new tool for tree-ring analysis with decisive advantages. In experiments on annual plants, we have found that the intramolecular distribution of deuterium (equivalent to ratios of isotopomer abundances) in photosynthetic glucose depends on growth [CO2] and reflects the metabolic flux ratio of photosynthesis to photorespiration. By applying this isotopomer methodology to trees from Oak Ridge FACE experiment, we show that this CO2 response is present in trees on the leaf level. This CO2 dependence constitutes a physiological signal, which is transferred to the wood of the tree rings. In trees from 13 locations on all continents the isotopomer ratio of tree-ring cellulose is correlated to atmospheric [CO2] during the past 200 years. The shift of the isotopomer ratio is universal for all 12 species analyzed, including both broad-leafed trees and conifers. Because the trees originate from sites with widely differing D/H ratios of precipitation, the generality of the response demonstrates that the signal is independent of the source isotope ratio, because it is encoded in an isotopomer abundance ratio. This decoupling of climate signals and physiological signals is a fundamental advantage of isotopomer ratios (Augusti et al., Chem. Geol 2008). These results demonstrate that increasing [CO2] has reduced the ratio of photorespiration to photosynthesis on a global scale. Photorespiration is a side reaction that decreases the C gain of plants; the suppression of photorespiration in all analyzed trees indicates that increasing atmospheric [CO2] is enhancing the photosynthetic efficiency of trees world-wide. The consensus response of the trees agrees with the response of annual plants in greenhouse experiments, with three important conclusions. First, the generality of the isotopomer shift confirms that the CO2 response reflects the ratio of photosynthesis to photorespiration, and that it creates a robust signal in tree rings. Second, the agreement between greenhouse-grown plants and trees indicates that there has not been an acclimation response of the trees during the past centuries. Third, the results show that the regulation of tree gas exchange has during past centuries been governed by the same rules as observed in manipulative experiments, in contradiction to recent reports (Keenan et al., Nature 2013).

Seasonally Resolved Oxygen Isotope Paleoclimate Proxy in Tree-Ring Cellulose from the Southeastern U.S.

NASA Astrophysics Data System (ADS)

Miller, D. L.; Mora, C. I.; Grissino-Mayer, H. D.; Mock, C. J.

2004-12-01

Stable isotopes in precipitation reflect changes in climate, moisture source, and extreme events such as tropical cyclones, and an oxygen isotope proxy record of these changes through time and space is preserved in tree-ring cellulose. Extreme climate events such as droughts and hurricanes are formidable natural disasters in the southeastern United States, and considerable efforts have been made to understand factors controlling their frequency, whether natural or anthropogenic. Tree rings offer an unusually well-resolved, dateable record of climate events extending beyond modern or historical (documentary) records. Oxygen isotopes in alpha-cellulose of shallowly-rooted conifers predominately reflect the composition of precipitation. Tropical storm convection results in marked 18O depletion in storm precipitation, to -15‰ relative to source seawater (~0‰ ). The depletion increases towards the eyewall of the cyclone, however, isotopically depleted precipitation may extend outward many 100's of km. Storm water 18O depletion translates to soil water 18O depletion that may persist for many weeks until ameliorated by soil water evaporation. Tree growth during that time will take up the anomalous isotopic compositions. Distinctive earlywood (EW ~March-June) versus latewood (LW ~July-October) growth allows the rings to be resolved at an intra-annual (seasonal) scale. By comparison to average soil water, droughts result in 18O-enriched soil water compositions. Seasonal drought or years of continued drought will be similarly captured in the isotope compositions of tree-ring cellulose. A 227-year (1770-1997) seasonally-resolved record of tropical cyclone and drought activity was obtained from cross-sections of felled slash pines (Pinus elliottii Engelm.) and remnant longleaf pines (Pinus palustris Mill.) from southern Georgia. Interpretations of drought or hurricane events were tested by comparison with recent, detailed meteorological records. The 227-year record reveals most previously established hurricane events, including Florence (1953) and the Great Hurricane of 1780. Newly recognized tropical storms such as 1857 are also evident. Significant seasonal droughts such as 1955, 1927, 1904 and 1896, are observed for southeastern Georgia. Larger-scale climate oscillations appear to overprint the EW and LW isotope series, displaying periods of relatively large or small differences in EW and LW δ 18O values. The oscillations are interpreted to reflect dominant climate modes that influence moisture source or seasonal temperature variation. The tree-ring record potentially extends many centuries. A preliminary record through a portion of the North American "Little Ice Age" (1580-1650) indicates a significant reduction in tropical cyclone activity.

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.

Water uptake of trees in a montane forest catchment and the geomorphological potential of root growth in Boulder Creek Critical Zone Observatory, Rocky Mountains, Colorado

NASA Astrophysics Data System (ADS)

Skeets, B.; Barnard, H. R.; Byers, A.

2011-12-01

The influence of vegetation on the hydrological cycle and the possible effect of roots in geomorphological processes are poorly understood. Gordon Gulch watershed in the Front Range of the Rocky Mountains, Colorado, is a montane climate ecosystem of the Boulder Creek Critical Zone Observatory whose study adds to the database of ecohydrological work in different climates. This work sought to identify the sources of water used by different tree species and to determine how trees growing in rock outcrops may contribute to the fracturing and weathering of rock. Stable isotopes (18O and 2H) were analyzed from water extracted from soil and xylem samples. Pinus ponderosa on the south-facing slope consumes water from deeper depths during dry periods and uses newly rain-saturated soils, after rainfall events. Pinus contorta on the north -facing slope shows a similar, expected response in water consumption, before and after rain. Two trees (Pinus ponderosa) growing within rock outcrops demonstrate water use from cracks replenished by new rains. An underexplored question in geomorphology is whether tree roots growing in rock outcrops contribute to long-term geomorphological processes by physically deteriorating the bedrock. The dominant roots of measured trees contributed approximately 30 - 80% of total water use, seen especially after rainfall events. Preliminary analysis of root growth rings indicates that root growth is capable of expanding rock outcrop fractures at an approximate rate of 0.6 - 1.0 mm per year. These results demonstrate the significant role roots play in tree physiological processes and in bedrock deterioration.

Dendrogeomorphic analysis of flash floods in a small ungauged mountain catchment (Central Spain)

NASA Astrophysics Data System (ADS)

Ruiz-Villanueva, Virginia; Díez-Herrero, Andrés; Stoffel, Markus; Bollschweiler, Michelle; Bodoque, José M.; Ballesteros, Juan A.

2010-06-01

Flash floods represent one of the most significant natural hazards with serious death tolls and economic damage at a worldwide level in general and in Mediterranean mountain catchments in particular. In these environments, systematic data is often lacking and analyses have to be based on alternative approaches such as dendrogeomorphology. In this study, we focus on the identification of flash floods based on growth disturbances (GD) observed in 98 heavily affected Mediterranean pine trees ( Pinus pinaster Ait.) located in or next to the torrential channel of the Pelayo River in the Spanish Central System. Flash floods are quite common in this catchment and are triggered by heavy storms, with high discharge and debris transport rates favoured by high stream gradients. Comparison of the anomalies in tree morphology and the position of the trees in the channel showed that the intensity of the disturbance clearly depends on geomorphology. The dating of past flash flood events was based on the number and intensity of GD observed in the tree-ring series and on the spatial distribution of affected trees along the torrent, thus allowing seven flash flood events during the last 50 years to be dated, namely in 1963, 1966, 1973, 1976, 1996, 2000, and 2005.

Dendrogeomorphic analysis of Flash Floods in a small ungauged mountain catchment (Central Spain)

NASA Astrophysics Data System (ADS)

Ruiz-Villanueva, Virginia; Díez-Herrero, Andrés.; Stoffel, Markus; Bollschweiler, Michelle; María Bodoque, José; Ballesteros, Juan Antonio

2010-05-01

Flash floods represent one of the most significant natural hazards with serious death tolls and economic damage at a worldwide level in general and in Mediterranean mountain catchments in particular. In these environments, systematic data is often lacking and analyses have to be based on alternative approaches such as dendrogeomorphology. In this study, we focus on the identification of flash floods based on growth disturbances (GD) observed in 98 heavily affected Mediterranean pine trees (Pinus pinaster Ait.) located in or next to the torrential channel of the Pelayo River in the Spanish Central System. Flash floods are quite common in this catchment and are triggered by heavy storms, with high discharge and debris transport rates favoured by high stream gradients. Comparison of the anomalies in tree morphology and the position of the trees in the channel showed that the intensity of the disturbance clearly depends on geomorphology. The dating of past flash-flood events was based on the number and intensity of GD observed in the tree-ring series, and on the spatial distribution of affected trees along the torrent, thus allowing seven flash-flood events during the last ~50 years to be dated, namely in 1963, 1966, 1973, 1976, 1996, 2000, and 2005.

Estimation on rubber tree disturbance caused by typhoon Damery (200518) with Landsat and MODIS data in Hainan Island of China

NASA Astrophysics Data System (ADS)

Tan, Chenyan; Fang, Weihua; Li, Jian

2016-04-01

In 2005, Typhoon Damery (200518) caused severe damage to the rubber trees in Hainan Island with its destructive winds and rainfall. Selection of proper vegetation indices using multi-source remote sensing data is critical to the assessment of forest disturbance and damage loss for this event. In this study, we will compare the performance of seven vegetation indices derived from MODIS and Landsat TM imageries prior to and after typhoon Damery, in order to select an optimal index for identifying rubber tree disturbance. The indices to be compared are normalized difference vegetation index (NDVI), Normalized Difference Water Index (NDWI), Normalized Difference Infrared Index (NDII), Enhanced vegetation index (EVI), Leaf area index (LAI), forest z-score (IFZ), and Disturbance Index (DI). The ground truth data of rubber tree damage collected through field investigation was used to verify and compare the results. Our preliminary result for the area with ground-truth data shows that DI has the most significant performance for disturbance detection for this typhoon event. This index DI is then applied to all the areas in Hainan Island hit by Darmey to evaluate the overall forest damage severity. At last, rubber tree damage severity is analyzed with other typhoon hazard factors such as wind, topography, soil and precipitation.

Tree diversity does not always improve resistance of forest ecosystems to drought.

PubMed

Grossiord, Charlotte; Granier, André; Ratcliffe, Sophia; Bouriaud, Olivier; Bruelheide, Helge; Chećko, Ewa; Forrester, David Ian; Dawud, Seid Muhie; Finér, Leena; Pollastrini, Martina; Scherer-Lorenzen, Michael; Valladares, Fernando; Bonal, Damien; Gessler, Arthur

2014-10-14

Climate models predict an increase in the intensity and frequency of drought episodes in the Northern Hemisphere. Among terrestrial ecosystems, forests will be profoundly impacted by drier climatic conditions, with drastic consequences for the functions and services they supply. Simultaneously, biodiversity is known to support a wide range of forest ecosystem functions and services. However, whether biodiversity also improves the resistance of these ecosystems to drought remains unclear. We compared soil drought exposure levels in a total of 160 forest stands within five major forest types across Europe along a gradient of tree species diversity. We assessed soil drought exposure in each forest stand by calculating the stand-level increase in carbon isotope composition of late wood from a wet to a dry year (Δδ(13)CS). Δδ(13)CS exhibited a negative linear relationship with tree species diversity in two forest types, suggesting that species interactions in these forests diminished the drought exposure of the ecosystem. However, the other three forest types were unaffected by tree species diversity. We conclude that higher diversity enhances resistance to drought events only in drought-prone environments. Managing forest ecosystems for high tree species diversity does not necessarily assure improved adaptability to the more severe and frequent drought events predicted for the future.

Computing all hybridization networks for multiple binary phylogenetic input trees.

PubMed

Albrecht, Benjamin

2015-07-30

The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2018-02-28

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest.

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

PubMed Central

Sayyari, Erfan

2018-01-01

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. PMID:29495636

Temperature response surfaces for mortality risk of tree species with future drought

DOE PAGES

Adams, Henry D.; Barron-Gafford, Greg A.; Minor, Rebecca L.; ...

2017-11-17

Widespread, high levels of tree mortality, termed forest die-off, associated with drought and rising temperatures, are disrupting forests worldwide. Drought will likely become more frequent with climate change, but even without more frequent drought, higher temperatures can exacerbate tree water stress. The temperature sensitivity of drought-induced mortality of tree species has been evaluated experimentally for only single-step changes in temperature (ambient compared to ambient + increase) rather than as a response surface (multiple levels of temperature increase), which constrains our ability to relate changes in the driver with the biological response. Here we show that time-to-mortality during drought for seedlingsmore » of two western United States tree species, Pinus edulis (Engelm.) and Pinus ponderosa (Douglas ex C. Lawson), declined in continuous proportion with increasing temperature spanning a 7.7 °C increase. Although P. edulis outlived P. ponderosa at all temperatures, both species had similar relative declines in time-to-mortality as temperature increased (5.2% per °C for P. edulis; 5.8% per °C for P. ponderosa). When combined with the non-linear frequency distribution of drought duration—many more short droughts than long droughts—these findings point to a progressive increase in mortality events with global change due to warming alone and independent of additional changes in future drought frequency distributions. As such, dire future forest recruitment patterns are projected assuming the calculated 7–9 seedling mortality events per species by 2100 under business-as-usual warming occur, congruent with additional vulnerability predicted for adult trees from stressors like pathogens and pests. Our progressive projection for increased mortality events was driven primarily by the non-linear shape of the drought duration frequency distribution, a common climate feature of drought-affected regions. These results illustrate profound benefits for reducing emissions of carbon to the atmosphere from anthropogenic sources and slowing warming as rapidly as possible to maximize forest persistence.« less

Temperature response surfaces for mortality risk of tree species with future drought

NASA Astrophysics Data System (ADS)

Adams, Henry D.; Barron-Gafford, Greg A.; Minor, Rebecca L.; Gardea, Alfonso A.; Bentley, Lisa Patrick; Law, Darin J.; Breshears, David D.; McDowell, Nate G.; Huxman, Travis E.

2017-11-01

Widespread, high levels of tree mortality, termed forest die-off, associated with drought and rising temperatures, are disrupting forests worldwide. Drought will likely become more frequent with climate change, but even without more frequent drought, higher temperatures can exacerbate tree water stress. The temperature sensitivity of drought-induced mortality of tree species has been evaluated experimentally for only single-step changes in temperature (ambient compared to ambient + increase) rather than as a response surface (multiple levels of temperature increase), which constrains our ability to relate changes in the driver with the biological response. Here we show that time-to-mortality during drought for seedlings of two western United States tree species, Pinus edulis (Engelm.) and Pinus ponderosa (Douglas ex C. Lawson), declined in continuous proportion with increasing temperature spanning a 7.7 °C increase. Although P. edulis outlived P. ponderosa at all temperatures, both species had similar relative declines in time-to-mortality as temperature increased (5.2% per °C for P. edulis; 5.8% per °C for P. ponderosa). When combined with the non-linear frequency distribution of drought duration—many more short droughts than long droughts—these findings point to a progressive increase in mortality events with global change due to warming alone and independent of additional changes in future drought frequency distributions. As such, dire future forest recruitment patterns are projected assuming the calculated 7-9 seedling mortality events per species by 2100 under business-as-usual warming occur, congruent with additional vulnerability predicted for adult trees from stressors like pathogens and pests. Our progressive projection for increased mortality events was driven primarily by the non-linear shape of the drought duration frequency distribution, a common climate feature of drought-affected regions. These results illustrate profound benefits for reducing emissions of carbon to the atmosphere from anthropogenic sources and slowing warming as rapidly as possible to maximize forest persistence.

Temperature response surfaces for mortality risk of tree species with future drought

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

Adams, Henry D.; Barron-Gafford, Greg A.; Minor, Rebecca L.

Widespread, high levels of tree mortality, termed forest die-off, associated with drought and rising temperatures, are disrupting forests worldwide. Drought will likely become more frequent with climate change, but even without more frequent drought, higher temperatures can exacerbate tree water stress. The temperature sensitivity of drought-induced mortality of tree species has been evaluated experimentally for only single-step changes in temperature (ambient compared to ambient + increase) rather than as a response surface (multiple levels of temperature increase), which constrains our ability to relate changes in the driver with the biological response. Here we show that time-to-mortality during drought for seedlingsmore » of two western United States tree species, Pinus edulis (Engelm.) and Pinus ponderosa (Douglas ex C. Lawson), declined in continuous proportion with increasing temperature spanning a 7.7 °C increase. Although P. edulis outlived P . ponderosa at all temperatures, both species had similar relative declines in time-to-mortality as temperature increased (5.2% per °C for P. edulis; 5.8% per °C for P. ponderosa). When combined with the non-linear frequency distribution of drought duration—many more short droughts than long droughts—these findings point to a progressive increase in mortality events with global change due to warming alone and independent of additional changes in future drought frequency distributions. As such, dire future forest recruitment patterns are projected assuming the calculated 7-9 seedling mortality events per species by 2100 under business-as-usual warming occurs, congruent with additional vulnerability predicted for adult trees from stressors like pathogens and pests. Our progressive projection for increased mortality events was driven primarily by the non-linear shape of the drought duration frequency distribution, a common climate feature of drought-affected regions. These results illustrate profound benefits for reducing emissions of carbon to the atmosphere from anthropogenic sources and slowing warming as rapidly as possible to maximize forest persistence.« less

Temperature response surfaces for mortality risk of tree species with future drought

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

Adams, Henry D.; Barron-Gafford, Greg A.; Minor, Rebecca L.

Widespread, high levels of tree mortality, termed forest die-off, associated with drought and rising temperatures, are disrupting forests worldwide. Drought will likely become more frequent with climate change, but even without more frequent drought, higher temperatures can exacerbate tree water stress. The temperature sensitivity of drought-induced mortality of tree species has been evaluated experimentally for only single-step changes in temperature (ambient compared to ambient + increase) rather than as a response surface (multiple levels of temperature increase), which constrains our ability to relate changes in the driver with the biological response. Here we show that time-to-mortality during drought for seedlingsmore » of two western United States tree species, Pinus edulis (Engelm.) and Pinus ponderosa (Douglas ex C. Lawson), declined in continuous proportion with increasing temperature spanning a 7.7 °C increase. Although P. edulis outlived P. ponderosa at all temperatures, both species had similar relative declines in time-to-mortality as temperature increased (5.2% per °C for P. edulis; 5.8% per °C for P. ponderosa). When combined with the non-linear frequency distribution of drought duration—many more short droughts than long droughts—these findings point to a progressive increase in mortality events with global change due to warming alone and independent of additional changes in future drought frequency distributions. As such, dire future forest recruitment patterns are projected assuming the calculated 7–9 seedling mortality events per species by 2100 under business-as-usual warming occur, congruent with additional vulnerability predicted for adult trees from stressors like pathogens and pests. Our progressive projection for increased mortality events was driven primarily by the non-linear shape of the drought duration frequency distribution, a common climate feature of drought-affected regions. These results illustrate profound benefits for reducing emissions of carbon to the atmosphere from anthropogenic sources and slowing warming as rapidly as possible to maximize forest persistence.« less

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

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

PubMed Central

Giaro, Krzysztof

2017-01-01

Abstract Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson–Foulds distance. In this article, we define a new metric for rooted trees—the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events. PMID:28177699

Description of an establishment event by the invasive Asian longhorned beetle (Anoplophora glabripennis) in a suburban landscape in the northeastern United States

PubMed Central

Pepper, Eugene; Davis, Kevin; Trotter, Robert Talbot

2017-01-01

The establishment of non-native species is commonly described as occurring in three phases: arrival, establishment, and dispersal. Both arrival and dispersal by the Asian longhorned beetle (Anoplophora glabripennis Motschulsky), a xylophagous Cerambycid native to China and the Korean peninsula, has been documented for multiple locations in both North America and Europe, however the transitional phase, establishment, is not well understood for this species due to the need to rapidly remove populations to prevent dispersal and assist eradication, and the evident variation in the behavior of populations. Here we describe the dynamics of an establishment event for the Asian longhorned beetle in a small, isolated population within the regulated quarantine zone near Worcester, Massachusetts, USA. These data were collected during an opportunity afforded by logistical limits on the Cooperative Asian Longhorned Beetle Eradication Program administered by state, federal, and local government partners. Seventy-one infested red maple (Acer rubrum) trees and 456 interspersed un-infested trees were surveyed in an isolated, recently established population within a ~0.29 ha stand in a suburban wetland conservation area in which nearly 90% of the trees were host species, and nearly 80% were Acer rubrum. Tree-ring analyses show that within this establishing population, Asian longhorned beetles initially infested one or two A. rubrum, before moving through the stand to infest additional A. rubrum based not on distance or direction, but on tree size, with infestation biased towards trees with larger trunk diameters. Survey data from the larger landscape suggest this population may have generated long-distance dispersers (~1400 m), and that these dispersal events occurred before the originally infested host trees were fully exploited by the beetle. The distribution and intensity of damage documented in this population suggest dispersal here may have been spatially more rapid and diffuse than in other documented infestations. Dispersal at these larger spatial scales also implies that when beetles move beyond the closed canopy of the stand, the direction of dispersal may be linked to prevailing winds. PMID:28727772

Abrupt Increases in Amazonian Tree Mortality Due to Drought-Fire Interactions

NASA Technical Reports Server (NTRS)

Brando, Paulo Monteiro; Balch, Jennifer K.; Nepstad, Daniel C.; Morton, Douglas C.; Putz, Francis E.; Coe, Michael T.; Silverio, Divino; Macedo, Marcia N.; Davidson, Eric A.; Nobrega, Caroline C.;

Abrupt increases in Amazonian tree mortality due to drought-fire interactions.

PubMed

Brando, Paulo Monteiro; Balch, Jennifer K; Nepstad, Daniel C; Morton, Douglas C; Putz, Francis E; Coe, Michael T; Silvério, Divino; Macedo, Marcia N; Davidson, Eric A; Nóbrega, Caroline C; Alencar, Ane; Soares-Filho, Britaldo S

2014-04-29

Interactions between climate and land-use change may drive widespread degradation of Amazonian forests. High-intensity fires associated with extreme weather events could accelerate this degradation by abruptly increasing tree mortality, but this process remains poorly understood. Here we present, to our knowledge, the first field-based evidence of a tipping point in Amazon forests due to altered fire regimes. Based on results of a large-scale, long-term experiment with annual and triennial burn regimes (B1yr and B3yr, respectively) in the Amazon, we found abrupt increases in fire-induced tree mortality (226 and 462%) during a severe drought event, when fuel loads and air temperatures were substantially higher and relative humidity was lower than long-term averages. This threshold mortality response had a cascading effect, causing sharp declines in canopy cover (23 and 31%) and aboveground live biomass (12 and 30%) and favoring widespread invasion by flammable grasses across the forest edge area (80 and 63%), where fires were most intense (e.g., 220 and 820 kW ⋅ m(-1)). During the droughts of 2007 and 2010, regional forest fires burned 12 and 5% of southeastern Amazon forests, respectively, compared with <1% in nondrought years. These results show that a few extreme drought events, coupled with forest fragmentation and anthropogenic ignition sources, are already causing widespread fire-induced tree mortality and forest degradation across southeastern Amazon forests. Future projections of vegetation responses to climate change across drier portions of the Amazon require more than simulation of global climate forcing alone and must also include interactions of extreme weather events, fire, and land-use change.

Estimating drought induced tree mortality in the Amazon rainforest: A simulation study with a focus on plant hydraulic processes

NASA Astrophysics Data System (ADS)

Papastefanou, P.; Fleischer, K.; Hickler, T.; Grams, T.; Lapola, D.; Quesada, C. A.; Zang, C.; Rammig, A.

2017-12-01

The Amazon basin was recently hit by severe drought events that were unprecedented in their severity and spatial extent, e.g. during 2005, 2010 and 2015/2016. Significant amounts of biomass were lost, turning large parts of the rainforest from a carbon sink into a carbon source. It is assumed that drought-induced tree mortality from hydraulic failure played an important role during these events and may become more frequent in the Amazon region in the future. Many state-of-the-art dynamic vegetation models do not include plant hydraulic processes and fail to reproduce observed rainforest responses to drought events, such as e.g. increased tree mortality. We address this research gap by developing a simple plant-hydraulic module for the dynamic vegetation model LPJ-GUESS. This plant-hydraulic module uses leaf water potential and cavitation as baseline processes to simulate tree mortality under drought stress. Furthermore, we introduce different plant strategies in the model, which describe e.g. differences in the stomatal regulation under drought stress. To parameterize and evaluate our hydraulic module, we use a set of available observational data from the Amazon region. We apply our model to the Amazon Basin and highlight similarities and differences across other measured and predicted drought responses, e.g. extrapolated observations and data derived from satellite measurements. Our results highlight the importance of including plant hydraulic processes in dynamic vegetation models to correctly predict vegetation dynamics under drought stress and show major differences on the vegetation dynamics depending on the selected plant strategies. We also identify gaps in process understanding of the triggering factors, the extent and the consequences of drought responses that hampers our ability to predict potential impact of future drought events on the Amazon rainforest.

Abrupt increases in Amazonian tree mortality due to drought–fire interactions

PubMed Central

Brando, Paulo Monteiro; Balch, Jennifer K.; Nepstad, Daniel C.; Morton, Douglas C.; Putz, Francis E.; Coe, Michael T.; Silvério, Divino; Macedo, Marcia N.; Davidson, Eric A.; Nóbrega, Caroline C.; Alencar, Ane; Soares-Filho, Britaldo S.

2014-01-01

Interactions between climate and land-use change may drive widespread degradation of Amazonian forests. High-intensity fires associated with extreme weather events could accelerate this degradation by abruptly increasing tree mortality, but this process remains poorly understood. Here we present, to our knowledge, the first field-based evidence of a tipping point in Amazon forests due to altered fire regimes. Based on results of a large-scale, long-term experiment with annual and triennial burn regimes (B1yr and B3yr, respectively) in the Amazon, we found abrupt increases in fire-induced tree mortality (226 and 462%) during a severe drought event, when fuel loads and air temperatures were substantially higher and relative humidity was lower than long-term averages. This threshold mortality response had a cascading effect, causing sharp declines in canopy cover (23 and 31%) and aboveground live biomass (12 and 30%) and favoring widespread invasion by flammable grasses across the forest edge area (80 and 63%), where fires were most intense (e.g., 220 and 820 kW⋅m−1). During the droughts of 2007 and 2010, regional forest fires burned 12 and 5% of southeastern Amazon forests, respectively, compared with <1% in nondrought years. These results show that a few extreme drought events, coupled with forest fragmentation and anthropogenic ignition sources, are already causing widespread fire-induced tree mortality and forest degradation across southeastern Amazon forests. Future projections of vegetation responses to climate change across drier portions of the Amazon require more than simulation of global climate forcing alone and must also include interactions of extreme weather events, fire, and land-use change. PMID:24733937

The ethnobotany of Christ's Thorn Jujube (Ziziphus spina-christi) in Israel

PubMed Central

Dafni, Amots; Levy, Shay; Lev, Efraim

2005-01-01

This article surveys the ethnobotany of Ziziphus spina-christi (L.) Desf. in the Middle East from various aspects: historical, religious, philological, literary, linguistic, as well as pharmacological, among Muslims, Jews, and Christians. It is suggested that this is the only tree species considered "holy" by Muslims (all the individuals of the species are sanctified by religion) in addition to its status as "sacred tree " (particular trees which are venerated due to historical or magical events related to them, regardless of their botanical identity) in the Middle East. It has also a special status as "blessed tree" among the Druze. PMID:16270941

The importance of drought-pathogen interactions in driving oak mortality events in the Ozark Border Region

NASA Astrophysics Data System (ADS)

Wood, Jeffrey D.; Knapp, Benjamin O.; Muzika, Rose-Marie; Stambaugh, Michael C.; Gu, Lianhong

2018-01-01

Forests are expected to become more vulnerable to drought-induced tree mortality owing to rising temperatures and changing precipitation patterns that amplify drought lethality. There is a crucial knowledge gap regarding drought-pathogen interactions and their effects on tree mortality. The objectives of this research were to examine whether stand dynamics and ‘background’ mortality rates were affected by a severe drought in 2012; and to evaluate the importance of drought-pathogen interactions within the context of a mortality event that killed 10.0% and 26.5% of white (Quercus alba L.) and black (Q. velutina Lam.) oak stems, respectively, in a single year. We synthesized (i) forest inventory data (24 years), (ii) 11 years of ecosystem flux data with supporting biological data including predawn leaf water potential and annual forest inventories, (iii) tree-ring analyses of individual white oaks that were alive and ones that died in 2013, and (iv) documentation of a pathogen infection. This forest displayed stand dynamics consistent with expected patterns of decreasing tree density and increasing basal area. Continued basal area growth outpaced mortality implying a net accumulation of live biomass, which was supported by eddy covariance ecosystem carbon flux observations. Individual white and black oaks that died in 2013 displayed historically lower growth with the majority of dead trees exhibiting Biscogniauxia cankers. Our observations point to the importance of event-based oak mortality and that drought-Biscogniauxia interactions are important in shaping oak stand dynamics in this region. Although forest function has not been significantly impaired, these drought-pathogen interactions could amplify mortality under future climate conditions and thus warrant further investigation.

Dendrogeomorphic Assessment of the Rattlesnake Gulf Landslide in the Tully Valley, Onondaga County, New York

USGS Publications Warehouse

Tamulonis, Kathryn L.; Kappel, William M.

2009-01-01

Dendrogeomorphic techniques were used to assess soil movement within the Rattlesnake Gulf landslide in the Tully Valley of central New York during the last century. This landslide is a postglacial, slow-moving earth slide that covers 23 acres and consists primarily of rotated, laminated, glaciolacustrine silt and clay. Sixty-two increment cores were obtained from 30 hemlock (Tsuga canadensis) trees across the active part of the landslide and from 3 control sites to interpret the soil-displacement history. Annual growth rings were measured and reaction wood was identified to indicate years in which ring growth changed from concentric to eccentric, on the premise that soil movement triggered compensatory growth in displaced trees. These data provided a basis for an 'event index' to identify years of landslide activity over the 108 years of record represented by the oldest trees. Event-index values and total annual precipitation increased during this time, but years with sudden event-index increases did not necessarily correspond to years with above-average precipitation. Multiple-regression and residual-values analyses indicated a possible correlation between precipitation and movement within the landslide and a possible cyclic (decades-long) tree-ring response to displacement within the landslide area from the toe upward to, and possibly beyond, previously formed landslide features. The soil movement is triggered by a sequence of factors that include (1) periods of several months with below-average precipitation followed by persistent above-average precipitation, (2) the attendant increase in streamflow, which erodes the landslide toe and results in an upslope propagation of slumping, and (3) the harvesting of mature trees within this landslide during the last century and continuing to the present.

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

PubMed Central

2017-01-01

Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four processes, or are tailored to specific datasets with matching model assumptions and code. To obtain a method with wider applicability, we have developed a novel approach to reconstruct transmission trees with sequence data. Our approach combines elementary models for transmission, case observation, within-host pathogen dynamics, and mutation, under the assumption that the outbreak is over and all cases have been observed. We use Bayesian inference with MCMC for which we have designed novel proposal steps to efficiently traverse the posterior distribution, taking account of all unobserved processes at once. This allows for efficient sampling of transmission trees from the posterior distribution, and robust estimation of consensus transmission trees. We implemented the proposed method in a new R package phybreak. The method performs well in tests of both new and published simulated data. We apply the model to five datasets on densely sampled infectious disease outbreaks, covering a wide range of epidemiological settings. Using only sampling times and sequences as data, our analyses confirmed the original results or improved on them: the more realistic infection times place more confidence in the inferred transmission trees. PMID:28545083

Effects of a natural dam-break flood on geomorphology and vegetation on the Elwha River, Washington, U.S.A.

USGS Publications Warehouse

Acker, S.A.; Beechie, T.J.; Shafroth, P.B.

2008-01-01

Ephemeral dams caused by landslides have been observed around the world, yet little is known about the effects of their failure on landforms and vegetation. In 1967, a landslide-dam-break flood in a pristine reach of the Elwha River valley filled the former channel and diverted the river. The reach is a reference site for restoration following the planned removal of dams on the river. We identified five surfaces on the 25 ha debris fan deposited by the flood. Based on tree ages and historic air photos, three of the surfaces formed in 1967, while two formed later. The surfaces varied in substrate (silt and sand, to boulders), and height above the river channel. Tree mortality resulted from tree removal and burial by sediment, the latter leaving snags and some surviving trees. Tree species composition was generally consistent within each surface. Dominant species included red alder (Alnus rubra) and Sitka willow (Salix sitchensis), alone or in combination, a combination of Douglas-fir (Pseudotsuga menziesii) and black cottonwood (Populus balsamifera ssp. trichocarpa), or a combination of alder and Cottonwood. There were significant differences between surfaces in stem density, basal area, and rate of basal area growth. The large degree of heterogeneity in forest structure, composition, and productivity within a relatively small floodplain feature is in part due to spatial variability in the intensity of a single disturbance event, and in part due to the occurrence of subsequent, smaller events. To recreate natural diversity of riparian forests may require mimicking the variety of physical and biotic habitats that a single, complex disturbance event may create.

The importance of drought–pathogen interactions in driving oak mortality events in the Ozark Border Region

DOE PAGES

Wood, Jeffrey D.; Knapp, Benjamin O.; Muzika, Rose-Marie; ...

2017-10-20

Forests are expected to become more vulnerable to drought-induced tree mortality owing to rising temperatures and changing precipitation patterns that amplify drought lethality. There is a crucial knowledge gap regarding drought–pathogen interactions and their effects on tree mortality. The objectives of this research were to examine whether stand dynamics and 'background' mortality rates were affected by a severe drought in 2012; and to evaluate the importance of drought–pathogen interactions within the context of a mortality event that killed 10.0% and 26.5% of white (Quercus alba L.) and black (Q. velutina Lam.) oak stems, respectively, in a single year. We synthesizedmore » (i) forest inventory data (24 years), (ii) 11 years of ecosystem flux data with supporting biological data including predawn leaf water potential and annual forest inventories, (iii) tree-ring analyses of individual white oaks that were alive and ones that died in 2013, and (iv) documentation of a pathogen infection. This forest displayed stand dynamics consistent with expected patterns of decreasing tree density and increasing basal area. Continued basal area growth outpaced mortality implying a net accumulation of live biomass, which was supported by eddy covariance ecosystem carbon flux observations. Individual white and black oaks that died in 2013 displayed historically lower growth with the majority of dead trees exhibiting Biscogniauxia cankers. Our observations point to the importance of event-based oak mortality and that drought–Biscogniauxia interactions are important in shaping oak stand dynamics in this region. Although forest function has not been significantly impaired, these drought–pathogen interactions could amplify mortality under future climate conditions and thus warrant further investigation.« less

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.

PubMed

Klinkenberg, Don; Backer, Jantien A; Didelot, Xavier; Colijn, Caroline; Wallinga, Jacco

2017-05-01

Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four processes, or are tailored to specific datasets with matching model assumptions and code. To obtain a method with wider applicability, we have developed a novel approach to reconstruct transmission trees with sequence data. Our approach combines elementary models for transmission, case observation, within-host pathogen dynamics, and mutation, under the assumption that the outbreak is over and all cases have been observed. We use Bayesian inference with MCMC for which we have designed novel proposal steps to efficiently traverse the posterior distribution, taking account of all unobserved processes at once. This allows for efficient sampling of transmission trees from the posterior distribution, and robust estimation of consensus transmission trees. We implemented the proposed method in a new R package phybreak. The method performs well in tests of both new and published simulated data. We apply the model to five datasets on densely sampled infectious disease outbreaks, covering a wide range of epidemiological settings. Using only sampling times and sequences as data, our analyses confirmed the original results or improved on them: the more realistic infection times place more confidence in the inferred transmission trees.

The importance of drought–pathogen interactions in driving oak mortality events in the Ozark Border Region

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

Wood, Jeffrey D.; Knapp, Benjamin O.; Muzika, Rose-Marie

Forests are expected to become more vulnerable to drought-induced tree mortality owing to rising temperatures and changing precipitation patterns that amplify drought lethality. There is a crucial knowledge gap regarding drought–pathogen interactions and their effects on tree mortality. The objectives of this research were to examine whether stand dynamics and 'background' mortality rates were affected by a severe drought in 2012; and to evaluate the importance of drought–pathogen interactions within the context of a mortality event that killed 10.0% and 26.5% of white (Quercus alba L.) and black (Q. velutina Lam.) oak stems, respectively, in a single year. We synthesizedmore » (i) forest inventory data (24 years), (ii) 11 years of ecosystem flux data with supporting biological data including predawn leaf water potential and annual forest inventories, (iii) tree-ring analyses of individual white oaks that were alive and ones that died in 2013, and (iv) documentation of a pathogen infection. This forest displayed stand dynamics consistent with expected patterns of decreasing tree density and increasing basal area. Continued basal area growth outpaced mortality implying a net accumulation of live biomass, which was supported by eddy covariance ecosystem carbon flux observations. Individual white and black oaks that died in 2013 displayed historically lower growth with the majority of dead trees exhibiting Biscogniauxia cankers. Our observations point to the importance of event-based oak mortality and that drought–Biscogniauxia interactions are important in shaping oak stand dynamics in this region. Although forest function has not been significantly impaired, these drought–pathogen interactions could amplify mortality under future climate conditions and thus warrant further investigation.« less

Individual tree detection in intact forest and degraded forest areas in the north region of Mato Grosso State, Brazilian Amazon

NASA Astrophysics Data System (ADS)

Santos, E. G.; Jorge, A.; Shimabukuro, Y. E.; Gasparini, K.

2017-12-01

The State of Mato Grosso - MT has the second largest area with degraded forest among the states of the Brazilian Legal Amazon. Land use and land cover change processes that occur in this region cause the loss of forest biomass, releasing greenhouse gases that contribute to the increase of temperature on earth. These degraded forest areas lose biomass according to the intensity and magnitude of the degradation type. The estimate of forest biomass, commonly performed by forest inventory through sample plots, shows high variance in degraded forest areas. Due to this variance and complexity of tropical forests, the aim of this work was to estimate forest biomass using LiDAR point clouds in three distinct forest areas: one degraded by fire, another by selective logging and one area of intact forest. The approach applied in these areas was the Individual Tree Detection (ITD). To isolate the trees, we generated Canopy Height Models (CHM) images, which are obtained by subtracting the Digital Elevation Model (MDE) and the Digital Terrain Model (MDT), created by the cloud of LiDAR points. The trees in the CHM images are isolated by an algorithm provided by the Quantitative Ecology research group at the School of Forestry at Northern Arizona University (SILVA, 2015). With these points, metrics were calculated for some areas, which were used in the model of biomass estimation. The methodology used in this work was expected to reduce the error in biomass estimate in the study area. The cloud points of the most representative trees were analyzed, and thus field data was correlated with the individual trees found by the proposed algorithm. In a pilot study, the proposed methodology was applied generating the individual tree metrics: total height and area of the crown. When correlating 339 isolated trees, an unsatisfactory R² was obtained, as heights found by the algorithm were lower than those obtained in the field, with an average difference of 2.43 m. This shows that the algorithm used to isolate trees in temperate areas did not obtained satisfactory results in the tropical forest of Mato Grosso State. Due to this, in future works two algorithms, one developed by Dalponte et al. (2015) and another by Li et al. (2012) will be used.

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2014-01-01

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

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

PubMed Central

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-01-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

PubMed

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-02-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

The Minnesota Wetland Evaluation Methodology for the North Central United States

DTIC Science & Technology

1988-09-01

ground water recharge, and other public benefits ." The realization of the enormity of the job led us in the Spring of 1983 to focus these efforts on...looking for drift lines or subwatersheds, routing flows through upstream de- pollen nngsaround trees along the wetland’s banks. tention basins, and...field observa- tion 2, above) to assess the significance of volume tions such as debris lines or pollen rings on trees changes. adjacent to the site

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles

PubMed Central

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models. PMID:26393926

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

PubMed

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

2012-02-01

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

3D Tree Dimensionality Assessment Using Photogrammetry and Small Unmanned Aerial Vehicles.

PubMed

Gatziolis, Demetrios; Lienard, Jean F; Vogs, Andre; Strigul, Nikolay S

2015-01-01

Detailed, precise, three-dimensional (3D) representations of individual trees are a prerequisite for an accurate assessment of tree competition, growth, and morphological plasticity. Until recently, our ability to measure the dimensionality, spatial arrangement, shape of trees, and shape of tree components with precision has been constrained by technological and logistical limitations and cost. Traditional methods of forest biometrics provide only partial measurements and are labor intensive. Active remote technologies such as LiDAR operated from airborne platforms provide only partial crown reconstructions. The use of terrestrial LiDAR is laborious, has portability limitations and high cost. In this work we capitalized on recent improvements in the capabilities and availability of small unmanned aerial vehicles (UAVs), light and inexpensive cameras, and developed an affordable method for obtaining precise and comprehensive 3D models of trees and small groups of trees. The method employs slow-moving UAVs that acquire images along predefined trajectories near and around targeted trees, and computer vision-based approaches that process the images to obtain detailed tree reconstructions. After we confirmed the potential of the methodology via simulation we evaluated several UAV platforms, strategies for image acquisition, and image processing algorithms. We present an original, step-by-step workflow which utilizes open source programs and original software. We anticipate that future development and applications of our method will improve our understanding of forest self-organization emerging from the competition among trees, and will lead to a refined generation of individual-tree-based forest models.

Derailment-based Fault Tree Analysis on Risk Management of Railway Turnout Systems

NASA Astrophysics Data System (ADS)

Dindar, Serdar; Kaewunruen, Sakdirat; An, Min; Gigante-Barrera, Ángel

2017-10-01

Railway turnouts are fundamental mechanical infrastructures, which allow a rolling stock to divert one direction to another. As those are of a large number of engineering subsystems, e.g. track, signalling, earthworks, these particular sub-systems are expected to induce high potential through various kind of failure mechanisms. This could be a cause of any catastrophic event. A derailment, one of undesirable events in railway operation, often results, albeit rare occurs, in damaging to rolling stock, railway infrastructure and disrupt service, and has the potential to cause casualties and even loss of lives. As a result, it is quite significant that a well-designed risk analysis is performed to create awareness of hazards and to identify what parts of the systems may be at risk. This study will focus on all types of environment based failures as a result of numerous contributing factors noted officially as accident reports. This risk analysis is designed to help industry to minimise the occurrence of accidents at railway turnouts. The methodology of the study relies on accurate assessment of derailment likelihood, and is based on statistical multiple factors-integrated accident rate analysis. The study is prepared in the way of establishing product risks and faults, and showing the impact of potential process by Boolean algebra.

Landscape-scale consequences of differential tree mortality from catastrophic wind disturbance in the Amazon.

PubMed

Rifai, Sami W; Urquiza Muñoz, José D; Negrón-Juárez, Robinson I; Ramírez Arévalo, Fredy R; Tello-Espinoza, Rodil; Vanderwel, Mark C; Lichstein, Jeremy W; Chambers, Jeffrey Q; Bohlman, Stephanie A

2016-10-01

Wind disturbance can create large forest blowdowns, which greatly reduces live biomass and adds uncertainty to the strength of the Amazon carbon sink. Observational studies from within the central Amazon have quantified blowdown size and estimated total mortality but have not determined which trees are most likely to die from a catastrophic wind disturbance. Also, the impact of spatial dependence upon tree mortality from wind disturbance has seldom been quantified, which is important because wind disturbance often kills clusters of trees due to large treefalls killing surrounding neighbors. We examine (1) the causes of differential mortality between adult trees from a 300-ha blowdown event in the Peruvian region of the northwestern Amazon, (2) how accounting for spatial dependence affects mortality predictions, and (3) how incorporating both differential mortality and spatial dependence affect the landscape level estimation of necromass produced from the blowdown. Standard regression and spatial regression models were used to estimate how stem diameter, wood density, elevation, and a satellite-derived disturbance metric influenced the probability of tree death from the blowdown event. The model parameters regarding tree characteristics, topography, and spatial autocorrelation of the field data were then used to determine the consequences of non-random mortality for landscape production of necromass through a simulation model. Tree mortality was highly non-random within the blowdown, where tree mortality rates were highest for trees that were large, had low wood density, and were located at high elevation. Of the differential mortality models, the non-spatial models overpredicted necromass, whereas the spatial model slightly underpredicted necromass. When parameterized from the same field data, the spatial regression model with differential mortality estimated only 7.5% more dead trees across the entire blowdown than the random mortality model, yet it estimated 51% greater necromass. We suggest that predictions of forest carbon loss from wind disturbance are sensitive to not only the underlying spatial dependence of observations, but also the biological differences between individuals that promote differential levels of mortality. © 2016 by the Ecological Society of America.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

Phylogenetic classification and the universal tree.

PubMed

Doolittle, W F

1999-06-25

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Oncogenetic tree model of somatic mutations and DNA methylation in colon tumors.

PubMed

Sweeney, Carol; Boucher, Kenneth M; Samowitz, Wade S; Wolff, Roger K; Albertsen, Hans; Curtin, Karen; Caan, Bette J; Slattery, Martha L

2009-01-01

Our understanding of somatic alterations in colon cancer has evolved from a concept of a series of events taking place in a single sequence to a recognition of multiple pathways. An oncogenetic tree is a model intended to describe the pathways and sequence of somatic alterations in carcinogenesis without assuming that tumors will fall in mutually exclusive categories. We applied this model to data on colon tumor somatic alterations. An oncogenetic tree model was built using data on mutations of TP53, KRAS2, APC, and BRAF genes, methylation at CpG sites of MLH1 and TP16 genes, methylation in tumor (MINT) markers, and microsatellite instability (MSI) for 971 colon tumors from a population-based series. Oncogenetic tree analysis resulted in a reproducible tree with three branches. The model represents methylation of MINT markers as initiating a branch and predisposing to MSI, methylation of MHL1 and TP16, and BRAF mutation. APC mutation is the first alteration in an independent branch and is followed by TP53 mutation. KRAS2 mutation was placed a third independent branch, implying that it neither depends on, nor predisposes to, the other alterations. Individual tumors were observed to have alteration patterns representing every combination of one, two, or all three branches. The oncogenetic tree model assumptions are appropriate for the observed heterogeneity of colon tumors, and the model produces a useful visual schematic of the sequence of events in pathways of colon carcinogenesis.

Earthquake signals in tree-ring data from the New Madrid seismic zone and implications for paleoseismicity

NASA Astrophysics Data System (ADS)

van Arsdale, Roy B.; Stahle, David W.; Cleaveland, Malcolm K.; Guccione, Margaret J.

1998-06-01

Severe ground shaking and the formation of Reelfoot Lake during the great New Madrid earthquakes of a.d. 1811 1812 had a profound effect on baldcypress trees that still survive in Reelfoot Lake of northwestern Tennessee. Inundation greatly increased baldcypress radial growth from 1812 to 1819 and permanently decreased wood density after 1811. Ground shaking fractured the baldcypress stems that were present during the 1811 1812 event, but fractures are absent in the post-1811 growth. In contrast, the growth of old baldcypress trees in the St. Francis sunkland of northeastern Arkansas was severely suppressed for almost 50 yr following the 1811 1812 New Madrid earthquakes. Thus, there are two opposite but profound growth responses to the same earthquake events preserved in baldcypress trees of the New Madrid seismic zone. The tree-ring chronology at Reelfoot Lake extends from a.d. 1682 to 1990, but the 1812 1819 growth surge was the only extreme growth anomaly in this 309 yr period. The St. Francis sunkland chronology extends from a.d. 1321 to 1990, and the 1812 1857 growth suppression is the most severe and prolonged growth anomaly of this entire 670 year period. Thus, the tree-ring record indicates that there was not a great earthquake during the 129 yr prior to 1811 in the Reelfoot Lake basin, nor during the 490 yr prior to 1811 in the St. Francis sunkland.

The critical amplifying role of increasing atmospheric moisture demand on tree mortality and associated regional die-off

DOE PAGES

Breshears, David D.; Adams, Henry D.; Eamus, Derek; ...

2013-08-02

Drought-induced tree mortality, including large-scale die-off events and increases in background rates of mortality, is a global phenomenon (Allen et al., 2010) that can directly impact numerous earth system properties and ecosystem goods and services (Adams et al., 2010; Breshears et al., 2011; Anderegg et al., 2013). Tree mortality is particularly of concern because of the likelihood that it will increase in frequency and extent with climate change (McDowell et al., 2008, 2011; Adams et al., 2009; McDowell, 2011; Williams et al., 2013). Recent plant science advances related to drought have focused on understanding the physiological mechanisms that not onlymore » affect plant growth and associated carbon metabolism, but also the more challenging issue of predicting plant mortality thresholds (McDowell et al., 2013). Although some advances related to mechanisms of mortality have been made and have increased emphasis on interrelationships between carbon metabolism and plant hydraulics (McDowell et al., 2011), notably few studies have specifically evaluated effects of increasing atmospheric demand for moisture (i.e., vapour pressure deficit; VPD) on rates of tree death. In this opinion article we highlight the importance of considering the key risks of future large-scale tree die-off and other mortality events arising from increased VPD. Here we focus on mortality of trees, but our point about the importance of VPD is also relevant to other vascular plants.« less

Spatial contagiousness of canopy disturbance in tropical rain forest: an individual-tree-based test.

PubMed

Jansen, Patrick A; van der Meer, Peter J; Bongers, Frans

2008-12-01

Spatial contagiousness of canopy dynamics-the tendency of canopy disturbances to occur nearby existing canopy openings due to an elevated risk of tree fall around gaps-has been demonstrated in many temperate-zone forests, but only inferentially for tropical forests. Hypothesized mechanisms increasing the risk of tree fall around tropical forest gaps are (1) increased tree exposure to wind around gaps, (2) reduced stability of trees alongside gaps due to crown asymmetry, or (3) reduced tree health around gaps due to damage from prior disturbances. One hypothesized consequence of elevated disturbance levels around gaps would be that gap-edge zones offer relatively favorable prospects for seedling recruitment, growth, and survival. We tested whether disturbance levels are indeed elevated around natural canopy gaps in a neotropical rain forest in French Guiana, and more so as gaps are larger. We followed the fate of 5660 trees >10 cm stem diameter over five years across 12 ha of old-growth forest and analyzed the risk and magnitude of canopy disturbance events in relation to tree diameter and the proximity and size of natural canopy gaps. We found that the cumulative incidence of disturbance over the five-year survey was not significantly elevated around preexisting gaps, and only weakly related to gap size. Also, neither the risk nor the magnitude of canopy disturbances increased significantly with the proximity of gaps. Moreover, canopy disturbance risk around gaps was independent of gap size, while the magnitude of disturbance events around gaps was weakly related to gap size. Tree size was the major driver of disturbance risk as well as magnitude. We did find an elevated incidence of disturbance inside preexisting gaps, but this "repeat disturbance" was due to an elevated disturbance risk inside gaps, not around gaps. Overall, we found no strong evidence for canopy dynamics in this rain forest being spatially contagious. Our findings are consistent with the traditional view of tropical rain forests as mosaics of patches with predictable regeneration cycles.

A Fault Tree Approach to Analysis of Behavioral Systems: An Overview.

ERIC Educational Resources Information Center

Stephens, Kent G.

Developed at Brigham Young University, Fault Tree Analysis (FTA) is a technique for enhancing the probability of success in any system by analyzing the most likely modes of failure that could occur. It provides a logical, step-by-step description of possible failure events within a system and their interaction--the combinations of potential…

Rene Saldana's "The Jumping Tree": Exploring Childhood Universals through a Hispanic Novel

ERIC Educational Resources Information Center

Newman, Beatrice Mendez

2006-01-01

In "The Jumping Tree", set in Nuevo Penitas, an actual South Texas town, 12-year-old Rey Castaneda recounts landmark events in his journey toward becoming a man. Rey's stories of his childhood escapades, adventures, and everyday experiences could be anyone's childhood stories. When readers have finished the last page, they have relived the…

Basic tree-ring sample preparation techniques for aging aspen

Treesearch

Lance A. Asherin; Stephen A. Mata

2001-01-01

Aspen is notoriously difficult to age because of its light-colored wood and faint annual growth rings. Careful preparation and processing of aspen ring samples can overcome these problems, yield accurate age and growth estimates, and concisely date disturbance events present in the tree-ring record. Proper collection of aspen wood is essential in obtaining usable ring...

Seasonality and Disturbance Events in the Carbon Isotope Record of Slash Pine (Pinus elliottii) Tree Rings from Big Pine Key, Florida

NASA Astrophysics Data System (ADS)

Rebenack, C.; Anderson, W. T.; Cherubini, P.

2011-12-01

The South Florida coastal ecosystem is among the world's subtropical coastlines which are threatened by the potential effects of climate change. A well-developed localized paleohistory is essential in the understanding of the role climate variability/change has on both hydrological dynamics and disturbance event frequency and intensity; this understanding can then aid in the development of better predictive models. High resolution paleoclimate proxies, such as those developed from tree-ring archives, may be useful tools for extrapolating actual climate trends over time from the overlapping long-term and short-term climate cycles, such as the Atlantic Multidecadal Oscillation (AMO) and the El Niño-Southern Oscillation (ENSO). In South Florida, both the AMO and ENSO strongly influence seasonal precipitation, and a more complete grasp of how these cycles have affected the region in the past could be applied to future freshwater management practices. Dendrochronology records for the terrestrial subtropics, including South Florida, are sparse because seasonality for this region is precipitation driven; this is in contrast to the drastic temperature changes experienced in the temperate latitudes. Subtropical seasonality may lead to the complete lack of visible rings or to the formation of ring structures that may or may not represent annual growth. Fortunately, it has recently been demonstrated that Pinus elliottii trees in South Florida produce distinct annual growth rings; however ring width was not found to significantly correlate with either the AMO or ENSO. Dendrochronology studies may be taken a step beyond the physical tree-ring proxies by using the carbon isotope ratios to infer information about physiological controls and environmental factors that affect the distribution of isotopes within the plant. It has been well established that the stable isotope composition of cellulose can be related to precipitation, drought, large-scale ocean/atmospheric oscillations, and disturbance events. Because slash pine growth is dependent on water availability, a chronology developed using carbon isotopes may provide greater insight into plant stress over time and ultimately may lead to better correlations with climate oscillations. The work presented here is the preliminary result of a carbon-isotope study of four slash pine trees from Big Pine Key, Florida. Initial δ13C data show seasonal stomatal activity in the trees and indicate the timing of possible disturbance events.

Quantifying construction and demolition waste: An analytical review

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

Wu, Zezhou; Yu, Ann T.W., E-mail: bsannyu@polyu.edu.hk; Shen, Liyin

2014-09-15

Highlights: • Prevailing C and D waste quantification methodologies are identified and compared. • One specific methodology cannot fulfill all waste quantification scenarios. • A relevance tree for appropriate quantification methodology selection is proposed. • More attentions should be paid to civil and infrastructural works. • Classified information is suggested for making an effective waste management plan. - Abstract: Quantifying construction and demolition (C and D) waste generation is regarded as a prerequisite for the implementation of successful waste management. In literature, various methods have been employed to quantify the C and D waste generation at both regional and projectmore » levels. However, an integrated review that systemically describes and analyses all the existing methods has yet to be conducted. To bridge this research gap, an analytical review is conducted. Fifty-seven papers are retrieved based on a set of rigorous procedures. The characteristics of the selected papers are classified according to the following criteria - waste generation activity, estimation level and quantification methodology. Six categories of existing C and D waste quantification methodologies are identified, including site visit method, waste generation rate method, lifetime analysis method, classification system accumulation method, variables modelling method and other particular methods. A critical comparison of the identified methods is given according to their characteristics and implementation constraints. Moreover, a decision tree is proposed for aiding the selection of the most appropriate quantification method in different scenarios. Based on the analytical review, limitations of previous studies and recommendations of potential future research directions are further suggested.« less

Facility Targeting, Protection and Mission Decision Making Using the VISAC Code

NASA Technical Reports Server (NTRS)

Morris, Robert H.; Sulfredge, C. David

2011-01-01

The Visual Interactive Site Analysis Code (VISAC) has been used by DTRA and several other agencies to aid in targeting facilities and to predict the associated collateral effects for the go, no go mission decision making process. VISAC integrates the three concepts of target geometric modeling, damage assessment capabilities, and an event/fault tree methodology for evaluating accident/incident consequences. It can analyze a variety of accidents/incidents at nuclear or industrial facilities, ranging from simple component sabotage to an attack with military or terrorist weapons. For nuclear facilities, VISAC predicts the facility damage, estimated downtime, amount and timing of any radionuclides released. Used in conjunction with DTRA's HPAC code, VISAC also can analyze transport and dispersion of the radionuclides, levels of contamination of the surrounding area, and the population at risk. VISAC has also been used by the NRC to aid in the development of protective measures for nuclear facilities that may be subjected to attacks by car/truck bombs.

Monte Carlo sensitivity analysis of unknown parameters in hazardous materials transportation risk assessment.

PubMed

Pet-Armacost, J J; Sepulveda, J; Sakude, M

1999-12-01

The US Department of Transportation was interested in the risks associated with transporting Hydrazine in tanks with and without relief devices. Hydrazine is both highly toxic and flammable, as well as corrosive. Consequently, there was a conflict as to whether a relief device should be used or not. Data were not available on the impact of relief devices on release probabilities or the impact of Hydrazine on the likelihood of fires and explosions. In this paper, a Monte Carlo sensitivity analysis of the unknown parameters was used to assess the risks associated with highway transport of Hydrazine. To help determine whether or not relief devices should be used, fault trees and event trees were used to model the sequences of events that could lead to adverse consequences during transport of Hydrazine. The event probabilities in the event trees were derived as functions of the parameters whose effects were not known. The impacts of these parameters on the risk of toxic exposures, fires, and explosions were analyzed through a Monte Carlo sensitivity analysis and analyzed statistically through an analysis of variance. The analysis allowed the determination of which of the unknown parameters had a significant impact on the risks. It also provided the necessary support to a critical transportation decision even though the values of several key parameters were not known.

Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis

PubMed Central

Wang, Yanqun; Liu, Di; Shi, Weifeng; Lu, Roujian; Wang, Wenling; Zhao, Yanjie; Deng, Yao; Zhou, Weimin; Ren, Hongguang; Wu, Jun; Wang, Yu; Wu, Guizhen

2015-01-01

ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. PMID:26350969

Sexually mature transgenic American chestnut trees via embryogenic suspension-based transformation.

PubMed

Andrade, Gisele M; Nairn, Campbell J; Le, Huong T; Merkle, Scott A

2009-09-01

The availability of a system for direct transfer of anti-fungal candidate genes into American chestnut (Castanea dentata), devastated by a fungal blight in the last century, would offer an alternative or supplemental approach to conventional breeding for production of chestnut trees resistant to the blight fungus and other pathogens. By taking advantage of the strong ability of embryogenic American chestnut cultures to proliferate in suspension, a high-throughput Agrobacterium tumefaciens-mediated transformation protocol for stable integration of foreign genes into the tree was established. Proembryogenic masses (PEMs) were co-cultivated with A. tumefaciens strain AGL1 harboring the plasmid pCAMBIA 2301, followed by stringent selection with 50 or 100 mg/l Geneticin. A protocol employing size-fractionation to enrich for small PEMs to use as target material and selection in suspension culture was applied to rapidly produce transgenic events with an average efficiency of four independent transformation events per 50 mg of target tissue and minimal escapes. Mature somatic embryos, representing 18 transgenic events and derived from multiple American chestnut target genotypes, were germinated and over 100 transgenic somatic seedlings were produced and acclimatized to greenhouse conditions. Multiple vigorous transgenic somatic seedlings produced functional staminate flowers within 3 years following regeneration.

Adaptable Constrained Genetic Programming: Extensions and Applications

NASA Technical Reports Server (NTRS)

Janikow, Cezary Z.

2005-01-01

An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.

Omics studies of citrus, grape and rosaceae fruit trees

PubMed Central

Shiratake, Katsuhiro; Suzuki, Mami

2016-01-01

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted. PMID:27069397

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

Omics studies of citrus, grape and rosaceae fruit trees.

PubMed

Shiratake, Katsuhiro; Suzuki, Mami

2016-01-01

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

Higher-Order Corrections to Timelike Jets

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

Giele, W.T.; /Fermilab; Kosower, D.A.

2011-02-01

We present a simple formalism for the evolution of timelike jets in which tree-level matrix element corrections can be systematically incorporated, up to arbitrary parton multiplicities and over all of phase space, in a way that exponentiates the matching corrections. The scheme is cast as a shower Markov chain which generates one single unweighted event sample, that can be passed to standard hadronization models. Remaining perturbative uncertainties are estimated by providing several alternative weight sets for the same events, at a relatively modest additional overhead. As an explicit example, we consider Z {yields} q{bar q} evolution with unpolarized, massless quarksmore » and include several formally subleading improvements as well as matching to tree-level matrix elements through {alpha}{sub s}{sup 4}. The resulting algorithm is implemented in the publicly available VINCIA plugin to the PYTHIA8 event generator.« less

Seismic Hazard and Ground Motion Characterization at the Itoiz Dam (Northern Spain)

NASA Astrophysics Data System (ADS)

Rivas-Medina, A.; Santoyo, M. A.; Luzón, F.; Benito, B.; Gaspar-Escribano, J. M.; García-Jerez, A.

2012-08-01

This paper presents a new hazard-consistent ground motion characterization of the Itoiz dam site, located in Northern Spain. Firstly, we propose a methodology with different approximation levels to the expected ground motion at the dam site. Secondly, we apply this methodology taking into account the particular characteristics of the site and of the dam. Hazard calculations were performed following the Probabilistic Seismic Hazard Assessment method using a logic tree, which accounts for different seismic source zonings and different ground-motion attenuation relationships. The study was done in terms of peak ground acceleration and several spectral accelerations of periods coinciding with the fundamental vibration periods of the dam. In order to estimate these ground motions we consider two different dam conditions: when the dam is empty ( T = 0.1 s) and when it is filled with water to its maximum capacity ( T = 0.22 s). Additionally, seismic hazard analysis is done for two return periods: 975 years, related to the project earthquake, and 4,975 years, identified with an extreme event. Soil conditions were also taken into account at the site of the dam. Through the proposed methodology we deal with different forms of characterizing ground motion at the study site. In a first step, we obtain the uniform hazard response spectra for the two return periods. In a second step, a disaggregation analysis is done in order to obtain the controlling earthquakes that can affect the dam. Subsequently, we characterize the ground motion at the dam site in terms of specific response spectra for target motions defined by the expected values SA ( T) of T = 0.1 and 0.22 s for the return periods of 975 and 4,975 years, respectively. Finally, synthetic acceleration time histories for earthquake events matching the controlling parameters are generated using the discrete wave-number method and subsequently analyzed. Because of the short relative distances between the controlling earthquakes and the dam site we considered finite sources in these computations. We conclude that directivity effects should be taken into account as an important variable in this kind of studies for ground motion characteristics.

Hurricane impacts on forest resources in the Eastern United States: a post-sandy assessment

Treesearch

Greg C. Liknes; Susan J. Crocker; Randall S. Morin; Brian F. Walters

2015-01-01

Extreme weather events play a role in shaping the composition and structure of forests. Responding to and mitigating a storm event in a forested environment requires information about the location and severity of tree damage. However, this information can be difficult to obtain immediately following an event. Post-storm assessments using regularly collected forest...

Pareto-optimal phylogenetic tree reconciliation

PubMed Central

Libeskind-Hadas, Ran; Wu, Yi-Chieh; Bansal, Mukul S.; Kellis, Manolis

2014-01-01

Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Availability and implementation: Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. Contact: mukul@engr.uconn.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24932009

Establishing Decision Trees for Predicting Successful Postpyloric Nasoenteric Tube Placement in Critically Ill Patients.

PubMed

Chen, Weisheng; Sun, Cheng; Wei, Ru; Zhang, Yanlin; Ye, Heng; Chi, Ruibin; Zhang, Yichen; Hu, Bei; Lv, Bo; Chen, Lifang; Zhang, Xiunong; Lan, Huilan; Chen, Chunbo

2016-08-31

Despite the use of prokinetic agents, the overall success rate for postpyloric placement via a self-propelled spiral nasoenteric tube is quite low. This retrospective study was conducted in the intensive care units of 11 university hospitals from 2006 to 2016 among adult patients who underwent self-propelled spiral nasoenteric tube insertion. Success was defined as postpyloric nasoenteric tube placement confirmed by abdominal x-ray scan 24 hours after tube insertion. Chi-square automatic interaction detection (CHAID), simple classification and regression trees (SimpleCart), and J48 methodologies were used to develop decision tree models, and multiple logistic regression (LR) methodology was used to develop an LR model for predicting successful postpyloric nasoenteric tube placement. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of these models. Successful postpyloric nasoenteric tube placement was confirmed in 427 of 939 patients enrolled. For predicting successful postpyloric nasoenteric tube placement, the performance of the 3 decision trees was similar in terms of the AUCs: 0.715 for the CHAID model, 0.682 for the SimpleCart model, and 0.671 for the J48 model. The AUC of the LR model was 0.729, which outperformed the J48 model. Both the CHAID and LR models achieved an acceptable discrimination for predicting successful postpyloric nasoenteric tube placement and were useful for intensivists in the setting of self-propelled spiral nasoenteric tube insertion. © 2016 American Society for Parenteral and Enteral Nutrition.

Establishing Decision Trees for Predicting Successful Postpyloric Nasoenteric Tube Placement in Critically Ill Patients.

PubMed

Chen, Weisheng; Sun, Cheng; Wei, Ru; Zhang, Yanlin; Ye, Heng; Chi, Ruibin; Zhang, Yichen; Hu, Bei; Lv, Bo; Chen, Lifang; Zhang, Xiunong; Lan, Huilan; Chen, Chunbo

2018-01-01

Despite the use of prokinetic agents, the overall success rate for postpyloric placement via a self-propelled spiral nasoenteric tube is quite low. This retrospective study was conducted in the intensive care units of 11 university hospitals from 2006 to 2016 among adult patients who underwent self-propelled spiral nasoenteric tube insertion. Success was defined as postpyloric nasoenteric tube placement confirmed by abdominal x-ray scan 24 hours after tube insertion. Chi-square automatic interaction detection (CHAID), simple classification and regression trees (SimpleCart), and J48 methodologies were used to develop decision tree models, and multiple logistic regression (LR) methodology was used to develop an LR model for predicting successful postpyloric nasoenteric tube placement. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of these models. Successful postpyloric nasoenteric tube placement was confirmed in 427 of 939 patients enrolled. For predicting successful postpyloric nasoenteric tube placement, the performance of the 3 decision trees was similar in terms of the AUCs: 0.715 for the CHAID model, 0.682 for the SimpleCart model, and 0.671 for the J48 model. The AUC of the LR model was 0.729, which outperformed the J48 model. Both the CHAID and LR models achieved an acceptable discrimination for predicting successful postpyloric nasoenteric tube placement and were useful for intensivists in the setting of self-propelled spiral nasoenteric tube insertion. © 2016 American Society for Parenteral and Enteral Nutrition.

Tree Circumference Dynamics in Four Forests Characterized Using Automated Dendrometer Bands

PubMed Central

McMahon, Sean M.; Detto, Matteo; Lutz, James A.; Davies, Stuart J.; Chang-Yang, Chia-Hao; Anderson-Teixeira, Kristina J.

2016-01-01

Stem diameter is one of the most commonly measured attributes of trees, forming the foundation of forest censuses and monitoring. Changes in tree stem circumference include both irreversible woody stem growth and reversible circumference changes related to water status, yet these fine-scale dynamics are rarely leveraged to understand forest ecophysiology and typically ignored in plot- or stand-scale estimates of tree growth and forest productivity. Here, we deployed automated dendrometer bands on 12–40 trees at four different forested sites—two temperate broadleaf deciduous, one temperate conifer, and one tropical broadleaf semi-deciduous—to understand how tree circumference varies on time scales of hours to months, how these dynamics relate to environmental conditions, and whether the structure of these variations might introduce substantive error into estimates of woody growth. Diurnal stem circumference dynamics measured over the bark commonly—but not consistently—exhibited daytime shrinkage attributable to transpiration-driven changes in stem water storage. The amplitude of this shrinkage was significantly correlated with climatic variables (daily temperature range, vapor pressure deficit, and radiation), sap flow and evapotranspiration. Diurnal variations were typically <0.5 mm circumference in amplitude and unlikely to be of concern to most studies of tree growth. Over time scales of multiple days, the bands captured circumference increases in response to rain events, likely driven by combinations of increased stem water storage and bark hydration. Particularly at the tropical site, these rain responses could be quite substantial, ranging up to 1.5 mm circumference expansion within 48 hours following a rain event. We conclude that over-bark measurements of stem circumference change sometimes correlate with but have limited potential for directly estimating daily transpiration, but that they can be valuable on time scales of days to weeks for characterizing changes in stem growth and hydration. PMID:28030646

Predicting the disease of Alzheimer with SNP biomarkers and clinical data using data mining classification approach: decision tree.

PubMed

Erdoğan, Onur; Aydin Son, Yeşim

2014-01-01

Single Nucleotide Polymorphisms (SNPs) are the most common genomic variations where only a single nucleotide differs between individuals. Individual SNPs and SNP profiles associated with diseases can be utilized as biological markers. But there is a need to determine the SNP subsets and patients' clinical data which is informative for the diagnosis. Data mining approaches have the highest potential for extracting the knowledge from genomic datasets and selecting the representative SNPs as well as most effective and informative clinical features for the clinical diagnosis of the diseases. In this study, we have applied one of the widely used data mining classification methodology: "decision tree" for associating the SNP biomarkers and significant clinical data with the Alzheimer's disease (AD), which is the most common form of "dementia". Different tree construction parameters have been compared for the optimization, and the most accurate tree for predicting the AD is presented.

Characterisation of Feature Points in Eye Fundus Images

NASA Astrophysics Data System (ADS)

Calvo, D.; Ortega, M.; Penedo, M. G.; Rouco, J.

The retinal vessel tree adds decisive knowledge in the diagnosis of numerous opthalmologic pathologies such as hypertension or diabetes. One of the problems in the analysis of the retinal vessel tree is the lack of information in terms of vessels depth as the image acquisition usually leads to a 2D image. This situation provokes a scenario where two different vessels coinciding in a point could be interpreted as a vessel forking into a bifurcation. That is why, for traking and labelling the retinal vascular tree, bifurcations and crossovers of vessels are considered feature points. In this work a novel method for these retinal vessel tree feature points detection and classification is introduced. The method applies image techniques such as filters or thinning to obtain the adequate structure to detect the points and sets a classification of these points studying its environment. The methodology is tested using a standard database and the results show high classification capabilities.

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

PubMed Central

Farreras, Montse

2014-01-01

Abstract The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes. PMID:24597675

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Chicago Sanitary and Ship Canal (CSSC) Marine Safety Risk Assessment

DTIC Science & Technology

2013-12-01

calculation of the rate of loss events and the associated consequences. Further, the selected tool supports a clear understanding of the drivers of failures...spreadsheet software. The event tree has a series of events stated in a success mode, or simply as the occurrence of a phenomenological condition. The...Public | December 2013 of a “transit” (when applicable). As subsequent events occur, there is a branch point, one branch representing success and the

Urban Tree Species Show the Same Hydraulic Response to Vapor Pressure Deficit across Varying Tree Size and Environmental Conditions

PubMed Central

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

2012-01-01

Background The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations. Methodology/Principal Findings We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP). The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1) the influence of tree species and size on transpiration, and 2) the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH) and tree canopy transpiration amount (E c) was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between G c at VPD = 1 kPa (G cref) and the G c sensitivity to VPD (−dG c/dlnVPD) across studied species as well as under contrasting soil water and R s conditions in the urban area. Conclusions/Significance We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of G cref. PMID:23118904

Accuracy and Calibration of Computational Approaches for Inpatient Mortality Predictive Modeling.

PubMed

Nakas, Christos T; Schütz, Narayan; Werners, Marcus; Leichtle, Alexander B

2016-01-01

Electronic Health Record (EHR) data can be a key resource for decision-making support in clinical practice in the "big data" era. The complete database from early 2012 to late 2015 involving hospital admissions to Inselspital Bern, the largest Swiss University Hospital, was used in this study, involving over 100,000 admissions. Age, sex, and initial laboratory test results were the features/variables of interest for each admission, the outcome being inpatient mortality. Computational decision support systems were utilized for the calculation of the risk of inpatient mortality. We assessed the recently proposed Acute Laboratory Risk of Mortality Score (ALaRMS) model, and further built generalized linear models, generalized estimating equations, artificial neural networks, and decision tree systems for the predictive modeling of the risk of inpatient mortality. The Area Under the ROC Curve (AUC) for ALaRMS marginally corresponded to the anticipated accuracy (AUC = 0.858). Penalized logistic regression methodology provided a better result (AUC = 0.872). Decision tree and neural network-based methodology provided even higher predictive performance (up to AUC = 0.912 and 0.906, respectively). Additionally, decision tree-based methods can efficiently handle Electronic Health Record (EHR) data that have a significant amount of missing records (in up to >50% of the studied features) eliminating the need for imputation in order to have complete data. In conclusion, we show that statistical learning methodology can provide superior predictive performance in comparison to existing methods and can also be production ready. Statistical modeling procedures provided unbiased, well-calibrated models that can be efficient decision support tools for predicting inpatient mortality and assigning preventive measures.

Which sociodemographic factors are important on smoking behaviour of high school students? The contribution of classification and regression tree methodology in a broad epidemiological survey.

PubMed

Ozge, C; Toros, F; Bayramkaya, E; Camdeviren, H; Sasmaz, T

2006-08-01

The purpose of this study is to evaluate the most important sociodemographic factors on smoking status of high school students using a broad randomised epidemiological survey. Using in-class, self administered questionnaire about their sociodemographic variables and smoking behaviour, a representative sample of total 3304 students of preparatory, 9th, 10th, and 11th grades, from 22 randomly selected schools of Mersin, were evaluated and discriminative factors have been determined using appropriate statistics. In addition to binary logistic regression analysis, the study evaluated combined effects of these factors using classification and regression tree methodology, as a new statistical method. The data showed that 38% of the students reported lifetime smoking and 16.9% of them reported current smoking with a male predominancy and increasing prevalence by age. Second hand smoking was reported at a 74.3% frequency with father predominance (56.6%). The significantly important factors that affect current smoking in these age groups were increased by household size, late birth rank, certain school types, low academic performance, increased second hand smoking, and stress (especially reported as separation from a close friend or because of violence at home). Classification and regression tree methodology showed the importance of some neglected sociodemographic factors with a good classification capacity. It was concluded that, as closely related with sociocultural factors, smoking was a common problem in this young population, generating important academic and social burden in youth life and with increasing data about this behaviour and using new statistical methods, effective coping strategies could be composed.

Ecosystem transformation by emerging infectious disease: loss of large tanoak from California forests

Treesearch

Richard C. Cobb; Joao A.N. Filipe; Ross K. Meentemeyer; Christopher A. Gilligan; David M. Rizzo

2012-01-01

1. Few pathogens are the sole or primary cause of species extinctions, but forest disease has caused spectacular declines in North American overstorey trees and restructured forest ecosystems at large spatial scales over the past 100 years. These events threaten biodiversity associated with impacted host trees and other resources valued by human societies even when...

Quantifying the legacy of foliar winter injury on woody aboveground carbon sequestration of red spruce trees

Treesearch

Alexandra M. Kosiba; Paul G. Schaberg; Gary J. Hawley; Christopher F. Hansen

2013-01-01

Red spruce (Picea rubens Sarg.) decline has been quantitatively attributed to foliar winter injury caused by freezing damage. The results of this injury include foliar mortality, crown deterioration, and negative carbon (C) balances that can lead to tree health declines and eventual mortality. In 2003, a severe region-wide event damaged over 90% of...

Seedling establishment in a masting desert shrub parallels the pattern for forest trees

Treesearch

Susan E. Meyer; Burton K. Pendleton

2015-01-01

The masting phenomenon along with its accompanying suite of seedling adaptive traits has been well studied in forest trees but has rarely been examined in desert shrubs. Blackbrush (Coleogyne ramosissima) is a regionally dominant North American desert shrub whose seeds are produced in mast events and scatter-hoarded by rodents. We followed the fate of seedlings in...

Kernel Smoothing Methods for Non-Poissonian Seismic Hazard Analysis

NASA Astrophysics Data System (ADS)

Woo, Gordon

2017-04-01

For almost fifty years, the mainstay of probabilistic seismic hazard analysis has been the methodology developed by Cornell, which assumes that earthquake occurrence is a Poisson process, and that the spatial distribution of epicentres can be represented by a set of polygonal source zones, within which seismicity is uniform. Based on Vere-Jones' use of kernel smoothing methods for earthquake forecasting, these methods were adapted in 1994 by the author for application to probabilistic seismic hazard analysis. There is no need for ambiguous boundaries of polygonal source zones, nor for the hypothesis of time independence of earthquake sequences. In Europe, there are many regions where seismotectonic zones are not well delineated, and where there is a dynamic stress interaction between events, so that they cannot be described as independent. From the Amatrice earthquake of 24 August, 2016, the subsequent damaging earthquakes in Central Italy over months were not independent events. Removing foreshocks and aftershocks is not only an ill-defined task, it has a material effect on seismic hazard computation. Because of the spatial dispersion of epicentres, and the clustering of magnitudes for the largest events in a sequence, which might all be around magnitude 6, the specific event causing the highest ground motion can vary from one site location to another. Where significant active faults have been clearly identified geologically, they should be modelled as individual seismic sources. The remaining background seismicity should be modelled as non-Poissonian using statistical kernel smoothing methods. This approach was first applied for seismic hazard analysis at a UK nuclear power plant two decades ago, and should be included within logic-trees for future probabilistic seismic hazard at critical installations within Europe. In this paper, various salient European applications are given.

Dendrogeochronologic and Anatomic Analysis of Excavated Plains Cottonwoods Determine Overbank Sedimentation Rates and Historical Channel Positions Along the Interior of a Migrating Meander Bend, Powder River, Montana

NASA Astrophysics Data System (ADS)

Metzger, T. L.; Pizzuto, J. E.; Schook, D. M.; Hasse, T. R.; Affinito, R. A.

2017-12-01

Dendrochronological dating of buried trees precisely determines the germination year and identifies the stratigraphic context of germination for the trees. This recently developed application of dendrochronology provides accurate time-averaged sedimentation rates of overbank deposition along floodplains and can be used to identify burial events. Previous studies have demonstrated that tamarisk (Tamarix ramosissima) and sandbar willow (Salix exigua) develop anatomical changes within the tree rings (increased vessel size and decreased ring widths) on burial, but observations of plains cottonwood (Populus deltoides ssp. monilifera) are lacking. In September 2016 and June 2017, five buried plains cottonwoods were excavated along a single transect of the interior of a meander bend of the Powder River, Montana. Sediment samples were obtained near each tree for 210Pb and 137Cs dating, which will allow for comparison between dendrochronological and isotopic dating methods. The plains cottonwood samples collected exhibit anatomical changes associated with burial events that are observed in other species. All trees germinated at the boundary between thinly bedded fine sand and mud and coarse sand underlain by sand and gravel, indicating plains cottonwoods germinate on top of point bars prior to overbank deposition. The precise germination age and depth provide elevations and minimum age constraints for the point bar deposits and maximum ages for the overlying sediment, helping constrain past channel positions and overbank deposition rates. Germination years of the excavated trees, estimated from cores taken 1.5 m above ground level, range from 2014 to 1862. Accurate establishment years determined by cross-dating the buried section of the tree can add an additional 10 years to the cored age. The sedimentation rate and accumulation thickness varied with tree age. The germination year, total sediment accumulation, and average sedimentation rate at the five sampled trees is: 2011, 35 cm, 7.0 cm/year; 1973, 77 cm, 1.8 cm/year; 1962, 140 cm, 2.6 cm/year; 1960, 123 cm, 2.2 cm/year; and 1862, 112 cm, 0.7 cm/year. These sedimentation rates indicate that the cumulative sedimentation decreases as a power law with increasing tree age.

Declining Radial Growth Response of Coastal Forests to Hurricanes and Nor'easters

NASA Astrophysics Data System (ADS)

Fernandes, Arnold; Rollinson, Christine R.; Kearney, William S.; Dietze, Michael C.; Fagherazzi, Sergio

2018-03-01

The Mid-Atlantic coastal forests in Virginia are stressed by episodic disturbance from hurricanes and nor'easters. Using annual tree ring data, we adopt a dendroclimatic and statistical modeling approach to understand the response and resilience of a coastal pine forest to extreme storm events, over the past few decades. Results indicate that radial growth of trees in the study area is influenced by age, regional climate trends, and individual tree effects but dominated periodically by growth disturbance due to storms. We evaluated seven local extreme storm events to understand the effect of nor'easters and hurricanes on radial growth. A general decline in radial growth was observed in the year of the extreme storm and 3 years following it, after which the radial growth started recovering. The decline in radial growth showed a statistically significant correlation with the magnitude of the extreme storm (storm surge height and wind speed). This study contributes to understanding declining tree growth response and resilience of coastal forests to past disturbances. Given the potential increase in hurricanes and storm surge severity in the region, this can help predict vegetation response patterns to similar disturbances in the future.

Calculation of Individual Tree Water Use in a Bornean Tropical Rain Forest Using Individual-Based Dynamic Vegetation Model SEIB-DGVM

NASA Astrophysics Data System (ADS)

Nakai, T.; Kumagai, T.; Saito, T.; Matsumoto, K.; Kume, T.; Nakagawa, M.; Sato, H.

2015-12-01

Bornean tropical rain forests are among the moistest biomes of the world with abundant rainfall throughout the year, and considered to be vulnerable to a change in the rainfall regime; e.g., high tree mortality was reported in such forests induced by a severe drought associated with the ENSO event in 1997-1998. In order to assess the effect (risk) of future climate change on eco-hydrology in such tropical rain forests, it is important to understand the water use of trees individually, because the vulnerability or mortality of trees against climate change can depend on the size of trees. Therefore, we refined the Spatially Explicit Individual-Based Dynamic Global Vegetation Model (SEIB-DGVM) so that the transpiration and its control by stomata are calculated for each individual tree. By using this model, we simulated the transpiration of each tree and its DBH-size dependency, and successfully reproduced the measured data of sap flow of trees and eddy covariance flux data obtained in a Bornean lowland tropical rain forest in Lambir Hills National Park, Sarawak, Malaysia.

Reliability and Probabilistic Risk Assessment - How They Play Together

NASA Technical Reports Server (NTRS)

Safie, Fayssal M.; Stutts, Richard G.; Zhaofeng, Huang

2015-01-01

PRA methodology is one of the probabilistic analysis methods that NASA brought from the nuclear industry to assess the risk of LOM, LOV and LOC for launch vehicles. PRA is a system scenario based risk assessment that uses a combination of fault trees, event trees, event sequence diagrams, and probability and statistical data to analyze the risk of a system, a process, or an activity. It is a process designed to answer three basic questions: What can go wrong? How likely is it? What is the severity of the degradation? Since 1986, NASA, along with industry partners, has conducted a number of PRA studies to predict the overall launch vehicles risks. Planning Research Corporation conducted the first of these studies in 1988. In 1995, Science Applications International Corporation (SAIC) conducted a comprehensive PRA study. In July 1996, NASA conducted a two-year study (October 1996 - September 1998) to develop a model that provided the overall Space Shuttle risk and estimates of risk changes due to proposed Space Shuttle upgrades. After the Columbia accident, NASA conducted a PRA on the Shuttle External Tank (ET) foam. This study was the most focused and extensive risk assessment that NASA has conducted in recent years. It used a dynamic, physics-based, integrated system analysis approach to understand the integrated system risk due to ET foam loss in flight. Most recently, a PRA for Ares I launch vehicle has been performed in support of the Constellation program. Reliability, on the other hand, addresses the loss of functions. In a broader sense, reliability engineering is a discipline that involves the application of engineering principles to the design and processing of products, both hardware and software, for meeting product reliability requirements or goals. It is a very broad design-support discipline. It has important interfaces with many other engineering disciplines. Reliability as a figure of merit (i.e. the metric) is the probability that an item will perform its intended function(s) for a specified mission profile. In general, the reliability metric can be calculated through the analyses using reliability demonstration and reliability prediction methodologies. Reliability analysis is very critical for understanding component failure mechanisms and in identifying reliability critical design and process drivers. The following sections discuss the PRA process and reliability engineering in detail and provide an application where reliability analysis and PRA were jointly used in a complementary manner to support a Space Shuttle flight risk assessment.

Event- and interval-based measurement of stuttering: a review.

PubMed

Valente, Ana Rita S; Jesus, Luis M T; Hall, Andreia; Leahy, Margaret

2015-01-01

Event- and interval-based measurements are two different ways of computing frequency of stuttering. Interval-based methodology emerged as an alternative measure to overcome problems associated with reproducibility in the event-based methodology. No review has been made to study the effect of methodological factors in interval-based absolute reliability data or to compute the agreement between the two methodologies in terms of inter-judge, intra-judge and accuracy (i.e., correspondence between raters' scores and an established criterion). To provide a review related to reproducibility of event-based and time-interval measurement, and to verify the effect of methodological factors (training, experience, interval duration, sample presentation order and judgment conditions) on agreement of time-interval measurement; in addition, to determine if it is possible to quantify the agreement between the two methodologies The first two authors searched for articles on ERIC, MEDLINE, PubMed, B-on, CENTRAL and Dissertation Abstracts during January-February 2013 and retrieved 495 articles. Forty-eight articles were selected for review. Content tables were constructed with the main findings. Articles related to event-based measurements revealed values of inter- and intra-judge greater than 0.70 and agreement percentages beyond 80%. The articles related to time-interval measures revealed that, in general, judges with more experience with stuttering presented significantly higher levels of intra- and inter-judge agreement. Inter- and intra-judge values were beyond the references for high reproducibility values for both methodologies. Accuracy (regarding the closeness of raters' judgements with an established criterion), intra- and inter-judge agreement were higher for trained groups when compared with non-trained groups. Sample presentation order and audio/video conditions did not result in differences in inter- or intra-judge results. A duration of 5 s for an interval appears to be an acceptable agreement. Explanation for high reproducibility values as well as parameter choice to report those data are discussed. Both interval- and event-based methodologies used trained or experienced judges for inter- and intra-judge determination and data were beyond the references for good reproducibility values. Inter- and intra-judge values were reported in different metric scales among event- and interval-based methods studies, making it unfeasible to quantify the agreement between the two methods. © 2014 Royal College of Speech and Language Therapists.

A new methodology to integrate planetary quarantine requirements into mission planning, with application to a Jupiter orbiter

NASA Technical Reports Server (NTRS)

Howard, R. A.; North, D. W.; Pezier, J. P.

1975-01-01

A new methodology is proposed for integrating planetary quarantine objectives into space exploration planning. This methodology is designed to remedy the major weaknesses inherent in the current formulation of planetary quarantine requirements. Application of the methodology is illustrated by a tutorial analysis of a proposed Jupiter Orbiter mission. The proposed methodology reformulates planetary quarantine planning as a sequential decision problem. Rather than concentrating on a nominal plan, all decision alternatives and possible consequences are laid out in a decision tree. Probabilities and values are associated with the outcomes, including the outcome of contamination. The process of allocating probabilities, which could not be made perfectly unambiguous and systematic, is replaced by decomposition and optimization techniques based on principles of dynamic programming. Thus, the new methodology provides logical integration of all available information and allows selection of the best strategy consistent with quarantine and other space exploration goals.

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

PubMed Central

Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay

2016-01-01

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

High resolution tree-ring based spatial reconstructions of snow avalanche activity in Glacier National Park, Montana, USA

USGS Publications Warehouse

Pederson, Gregory T.; Reardon, Blase; Caruso, C.J.; Fagre, Daniel B.

2006-01-01

Effective design of avalanche hazard mitigation measures requires long-term records of natural avalanche frequency and extent. Such records are also vital for determining whether natural avalanche frequency and extent vary over time due to climatic or biophysical changes. Where historic records are lacking, an accepted substitute is a chronology developed from tree-ring responses to avalanche-induced damage. This study evaluates a method for using tree-ring chronologies to provide spatially explicit differentiations of avalanche frequency and temporally explicit records of avalanche extent that are often lacking. The study area - part of John F. Stevens Canyon on the southern border of Glacier National Park – is within a heavily used railroad and highway corridor with two dozen active avalanche paths. Using a spatially geo-referenced network of avalanche-damaged trees (n=109) from a single path, we reconstructed a 96-year tree-ring based chronology of avalanche extent and frequency. Comparison of the chronology with historic records revealed that trees recorded all known events as well as the same number of previously unidentified events. Kriging methods provided spatially explicit estimates of avalanche return periods. Estimated return periods for the entire avalanche path averaged 3.2 years. Within this path, return intervals ranged from ~2.3 yrs in the lower track, to ~9-11 yrs and ~12 to >25 yrs in the runout zone, where the railroad and highway are located. For avalanche professionals, engineers, and transportation managers this technique proves a powerful tool in landscape risk assessment and decision making.

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

Attribution of Disturbances Causing Tree Mortality for the Continental U.S.

NASA Astrophysics Data System (ADS)

Wang, M.; Xu, C.; Allen, C. D.; McDowell, N. G.

2016-12-01

Broad-scale tree mortality has been frequently reported and documented to increase with warming climate and human activities. However, there is so far no general method to quantify the relative contributions of different disturbances on observed broad-scale tree mortality. In this study, we presented a framework to investigate the contribution of various disturbances causing tree mortality for 2000-2014 in the continental US. Our work is based on the high-resolution forest-loss data developed by Hansen et al. (2013). Firstly, fire-driven mortality was determined using the data from Monitoring Trends in Burn Severity (MTBS) project. Secondly, a landscape-pattern-recognition approach focusing on the differences of boundary complexity caused by natural and anthropogenic disturbances was developed to attribute harvest-driven mortality patches. Then, a drought threshold was determined through conducting an intensive literature survey for attribution of drought-driven mortality. Our results showed that we can correctly attribute 85% harvest-driven mortality as compared to Forest Inventory and Analysis (FIA) data. Based on Evaporative Stress Index (ESI), our literature survey suggests that most mortality events happened at extreme drought (37.7%), then severe (31.4%) and moderate (23.4%) drought. In total, 92.6% of drought-induced mortality events observed during 2000-2014 occurred at drought conditions of moderate or worse with corresponding ESI values ranging from -0.9 -2.49. Therefore, -0.9 will be used as the threshold to attribute drought-driven tree mortality. Overall, these results imply a great potential for using these methods to identify and attribute disturbances driving tree death at broad spatial scales.

Spatial Structure of Evolutionary Models of Dialects in Contact

PubMed Central

Murawaki, Yugo

2015-01-01

Phylogenetic models, originally developed to demonstrate evolutionary biology, have been applied to a wide range of cultural data including natural language lexicons, manuscripts, folktales, material cultures, and religions. A fundamental question regarding the application of phylogenetic inference is whether trees are an appropriate approximation of cultural evolutionary history. Their validity in cultural applications has been scrutinized, particularly with respect to the lexicons of dialects in contact. Phylogenetic models organize evolutionary data into a series of branching events through time. However, branching events are typically not included in dialectological studies to interpret the distributions of lexical terms. Instead, dialectologists have offered spatial interpretations to represent lexical data. For example, new lexical items that emerge in a politico-cultural center are likely to spread to peripheries, but not vice versa. To explore the question of the tree model’s validity, we present a simple simulation model in which dialects form a spatial network and share lexical items through contact rather than through common ancestors. We input several network topologies to the model to generate synthetic data. We then analyze the synthesized data using conventional phylogenetic techniques. We found that a group of dialects can be considered tree-like even if it has not evolved in a temporally tree-like manner but has a temporally invariant, spatially tree-like structure. In addition, the simulation experiments appear to reproduce unnatural results observed in reconstructed trees for real data. These results motivate further investigation into the spatial structure of the evolutionary history of dialect lexicons as well as other cultural characteristics. PMID:26221958

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.

Using dendrochonology to crossdate year of death in trees: limitations with stressed trees in a diffuse mortality context. (Invited)

NASA Astrophysics Data System (ADS)

Angers, V. A.; Bergeron, Y.; Drapeau, P.

2013-12-01

Dendrochronological crossdating of dead trees is commonly used to reconstruct mortality patterns over time. This method assumes that the year of formation of the last growth ring corresponds to the year of the death of the tree. Trees experiencing important stress, such as defoliation, drought or senescence, may rely on very few resources to allocate to growth and may favour other vital physiological functions over growth. Even if the tree is still living, growth may thus be reduced or even supressed during a stressful event. When a tree dies following this event and that there is a lag between year of last ring production and year of actual death, crossdating underestimates the actual year of death. As ring formation is not uniform across the bole, growth may occur only in some parts of the tree and may be detectable only if multiple bole samples are analysed. In this study, we wanted to investigate how the growth patterns of dying trees influence estimation of year of death when crossdating. Our research questions were the following 1) Is there a difference (hereafter referred as 'lag') between the last year of growth ring formation in disc samples collected at different heights in dead trees? 2) If so, what is the range of magnitude of these lags? and 3) Is this magnitude range influenced by the causes of death? Sampled sites were located in northwestern Quebec (Canada), over an area overlapping the eastern mixedwood and coniferous boreal forests. Four tree species were examined: Trembling aspen (Populus tremuloides Michx.), balsam fir (Abies balsamea (L.) Mill.), jack pine (Pinus banksiana Lamb.) and black spruce (Picea mariana (Mill.) BSP). Trees that died following fire, self-thinning, defoliation and senescence were sampled. Two to three discs were collected on each dead tree (snags and logs) at different heights. Dendrochronological analyses were conducted to determine year of last growth ring production by crossdating. The more severe the disturbance, the narrower the lag between years of last ring production among samples collected in a given tree. In fire-induced death, lag was whether absent or very narrow, usually no more than one year. In defoliation-induced death, most lags were under two years. In competition-induced death, the vast majority of lags were shorter than 5 years. In old, senescent black spruce trees, lags were considerably longer as compared to other causes of death, exceeding 10 years in numerous cases. Based on these results, we suggest that investigators should consider collecting samples at different heights along the stem when reconstructing fine patterns of senescence-induced mortality using crossdating in order to avoid as much as possible bias due to variable growth in dying trees.

Deep Phylogeny—How a Tree Can Help Characterize Early Life on Earth

PubMed Central

Gaucher, Eric A.; Kratzer, James T.; Randall, Ryan N.

2010-01-01

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history. “You know, a tree is a tree.  How many more do you need to look at?” –Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966 PMID:20182607

Do hummocks provide a physiological advantage to even the most flood tolerant of tidal freshwater trees?

USGS Publications Warehouse

Duberstein, Jamie A.; Krauss, Ken W.; Conner, William H.; Bridges, William C.; Shelburne, Victor B.

2013-01-01

Hummock and hollow microtopography is pervasive in tidal freshwater swamps. Many tree species grow atop hummocks significantly more than in hollows, leading to the hypothesis that hummocks provide preferred locations for maximizing physiological proficiency of inhabiting trees that experience repeated flooding. We used thermal dissipation probes to measure the ecophysiological proficiency of a very flood-tolerant tree, Taxodium distichum, as manifested through in-situ changes in sapflow (a proxy for transpiration) in 11 trees on hummocks and 11 trees in hollows. Overall, sapflow increased significantly by 3.3 g H2O m−2 s−1 (11 %) in trees on both hummocks and hollows during flooding, contrary to our expectations. We found no significant differences in sapflow rates between T. distichum trees positioned on hummocks versus hollows in relation to discrete flood events. Coincidentally, hummock elevations were equivalent to the flood depths that promoted greatest physiological proficiency in T. distichum, suggesting a physiological role for the maintenance of hummock height in tidal swamps. While we reject our original hypotheses that flooding and positioning in hollows will reduce sapflow in T. distichum, this research reveals a potentially important feedback between hummock height, flood depth, and maximum tree physiological response.

Deep phylogeny--how a tree can help characterize early life on Earth.

PubMed

Gaucher, Eric A; Kratzer, James T; Randall, Ryan N

2010-01-01

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history."You know, a tree is a tree. How many more do you need to look at?"--Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966.

Larger trees suffer most during drought in forests worldwide

USGS Publications Warehouse

Bennett, Amy C.; McDowell, Nathan G.; Allen, Craig D.; Anderson-Teixeira, Kristina J.

2015-01-01

The frequency of severe droughts is increasing in many regions around the world as a result of climate change. Droughts alter the structure and function of forests. Site- and region-specific studies suggest that large trees, which play keystone roles in forests and can be disproportionately important to ecosystem carbon storage and hydrology, exhibit greater sensitivity to drought than small trees. Here, we synthesize data on tree growth and mortality collected during 40 drought events in forests worldwide to see whether this size-dependent sensitivity to drought holds more widely. We find that droughts consistently had a more detrimental impact on the growth and mortality rates of larger trees. Moreover, drought-related mortality increased with tree size in 65% of the droughts examined, especially when community-wide mortality was high or when bark beetles were present. The more pronounced drought sensitivity of larger trees could be underpinned by greater inherent vulnerability to hydraulic stress, the higher radiation and evaporative demand experienced by exposed crowns, and the tendency for bark beetles to preferentially attack larger trees. We suggest that future droughts will have a more detrimental impact on the growth and mortality of larger trees, potentially exacerbating feedbacks to climate change.