Observing of tree trunks and other cylindrical objects using GPR

NASA Astrophysics Data System (ADS)

Jezova, Jana; Lambot, Sebastien

2016-04-01

Trees are a part of our everyday life, hence it is important to prevent their collapse to protect people and urban infrastructures. It is also important to characterize tree wood properties for usages in construction. In order to investigate internal parts of tree trunks non-invasively, ground-penetrating radar (GPR), or in this case, ultra-wideband microwave radar as a general tool, appears to be a very promising technology. Nevertheless, tree trunk tomography using microwave radar is a complicated task due to the circular shape of the trunk and the very complex (heterogeneous and anisotropic) internal structures of the trunk. Microwave sensing of tree trunks is also complicated due to the electromagnetic properties of living wood, which strongly depend on water content, density and temperature of wood. The objective of this study is to describe tree trunk radar cross sections including specific features originating from the particular circumferential data acquisition geometry. In that respect, three experiments were performed: (1) numerical simulations using a finite-difference time-domain software, namely, gprMax 2D, (2) measurements on a simplified laboratory trunk model including plastic and cardboard pipes, sand and air, and (3) measurements over a real tree trunk. The analysis was further deepened by considering: (1) common zero-offset reflection imaging, (2) imaging with a planar perfect electrical conductor (PEC) at the opposite side of the trunk, and (3) imaging with a PEC arc at the opposite side of the trunk. Furthermore, the shape of the reflection curve of a cylindrical target was analytically derived based on the straight-ray propagation approximation. Subsequently, the total internal reflection (TIR) phenomenon occurring in cylindrical objects was observed and analytically described. Both the straight-ray reflection curve and TIR were well observed on the simulated and laboratory radar data. A comparison between all experiments and radar configurations is presented. Future research will focus on the design of an adapted radar antenna for that application to optimize living tree trunk tomography. This research is funded by the Fonds de la Recherche Scientifique (FNRS, Belgium) and benefits from networking activities carried out within the EU COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar".

Decentralized model reference adaptive control of large flexible structures

NASA Technical Reports Server (NTRS)

Lee, Fu-Ming; Fong, I-Kong; Lin, Yu-Hwan

1988-01-01

A decentralized model reference adaptive control (DMRAC) method is developed for large flexible structures (LFS). The development follows that of a centralized model reference adaptive control for LFS that have been shown to be feasible. The proposed method is illustrated using a simply supported beam with collocated actuators and sensors. Results show that the DMRAC can achieve either output regulation or output tracking with adequate convergence, provided the reference model inputs and their time derivatives are integrable, bounded, and approach zero as t approaches infinity.

Agro-ecosystem and socio-economic role of homegarden agroforestry in Jabithenan District, North-Western Ethiopia: implication for climate change adaptation.

PubMed

Linger, Ewuketu

2014-01-01

Homegarden agroforestry is believed to be more diverse and provide multiple services for household than other monocropping system and this is due to the combination of crops, trees and livestock. The aim of this study was to assess socio-economic and agro-ecological role of homegardens in Jabithenan district, North-western Ethiopia. Two sites purposively and two villages randomly from each site were selected. Totally 96 households; in which 48 from homegarden agroforestry user and 48 from non-tree based garden user were selected for this study. Socio-economic data and potential economic and agro-ecosystem role of homegarden agroforestry over non-tree based garden were collected by using semi-structured and structured questionnaires to the households. Homegarden agroforestry significantly (P < 0.05) improved the farmers cash income than non-tree based garden. With insignificant garden size; homegarden agroforestry practice provides good socio-economical and agro-ecological service for farmers which have a higher implication for climate change adaptation than non-tree based garden.

Trees influence preferencial flow and water uptake in tropical savanna

NASA Astrophysics Data System (ADS)

Benegas, Laura; Bargues-Tobella, Aida; Hasselquist, Niles; Malmer, Anders; Ilstedt, Ulrik

2017-04-01

To address potential competition between trees and grasses for soil water, and to disentangle the main process responsible for local soil water dynamics in pasture ecosystems, we conducted a study of the soil water content and water source partitioning of grasses and trees within a pasture in the Copan River catchment, Honduras. We used differences in the 2H/1H (δD) isotopic signature of soil water (δSW) and the local meteoric water line (LMWL; δLMWL) as a relative index of evaporation, following a recent model proposed by Hasselquist et al (under review). The model uses Lc-excess calculated as the absolute value of the difference between measured δD and that predicted by the local meteoric water line (lc-excess = ¦δDM - δDP¦). Lc-excess values close to zero indicate little difference between soil water samples and local precipitation, whereas larger values indicate a greater degree of evaporation .()...(adapted from Landwehr and Coplen, 2006). From the relation between Lc-excess and SWC, we can tease apart different processes by which trees influence local soil water dynamics, where one such processes indicate that if preferential flow, i.e quick flows through macropores that by-pass the soil matrix, is the main pathway for water movement in the soil, then the Lc-excess values of soil water at deeper depths will be closer to zero than those of the surface soil, whereas relatively higher Lc-excess values would indicate increasing dominance of matrix flow. We found that soil underneath trees was wetter than underneath grasses at the dry season and we can relate this with a lack of clear relationship between Lc-excess and SWC and with the treés apparent shift to groundwater sources for root uptake especially in the dry season. Due to the positive correlation between Lc-excess and SWC under trees and due to the lower Lc-excess values found at subsoil below trees during the dry season, we can infer that preferential flow is also facilitated by the trees enhancing its contribution to groundwater recharge. The possible water losses via interception linked with trees on the soil water dynamic was counterbalanced by the positive contribution of trees to preferential flow and groundwater recharge.

Adaptive genetic potential of coniferous forest tree species under climate change: implications for sustainable forest management

NASA Astrophysics Data System (ADS)

Mihai, Georgeta; Birsan, Marius-Victor; Teodosiu, Maria; Dumitrescu, Alexandru; Daia, Mihai; Mirancea, Ionel; Ivanov, Paula; Alin, Alexandru

2017-04-01

Mountain ecosystems are extremely vulnerable to climate change. The real potential for adaptation depends upon the existence of a wide genetic diversity in trees populations, upon the adaptive genetic variation, respectively. Genetic diversity offers the guarantee that forest species can survive, adapt and evolve under the influence of changing environmental conditions. The aim of this study is to evaluate the genetic diversity and adaptive genetic potential of two local species - Norway spruce and European silver fir - in the context of regional climate change. Based on data from a long-term provenance experiments network and climate variables spanning over more than 50 years, we have investigated the impact of climatic factors on growth performance and adaptation of tree species. Our results indicate that climatic and geographic factors significantly affect forest site productivity. Mean annual temperature and annual precipitation amount were found to be statistically significant explanatory variables. Combining the additive genetic model with the analysis of nuclear markers we obtained different images of the genetic structure of tree populations. As genetic indicators we used: gene frequencies, genetic diversity, genetic differentiation, genetic variance, plasticity. Spatial genetic analyses have allowed identifying the genetic centers holding high genetic diversity which will be valuable sources of gene able to buffer the negative effects of future climate change. Correlations between the marginal populations and in the optimal vegetation, between the level of genetic diversity and ecosystem stability, will allow the assessment of future risks arising from current genetic structure. Therefore, the strategies for sustainable forest management have to rely on the adaptive genetic variation and local adaptation of the valuable genetic resources. This work was realized within the framework of the project GENCLIM (Evaluating the adaptive potential of the main coniferous species for a sustainable forest management in the context of climate change), financed by the Executive Agency for Higher Education, Research, Development and Innovation Funding, grant number PN-II-PC-PCCA-2013-4-0695.

Graphical models for optimal power flow

DOE PAGES

Dvijotham, Krishnamurthy; Chertkov, Michael; Van Hentenryck, Pascal; ...

2016-09-13

Optimal power flow (OPF) is the central optimization problem in electric power grids. Although solved routinely in the course of power grid operations, it is known to be strongly NP-hard in general, and weakly NP-hard over tree networks. In this paper, we formulate the optimal power flow problem over tree networks as an inference problem over a tree-structured graphical model where the nodal variables are low-dimensional vectors. We adapt the standard dynamic programming algorithm for inference over a tree-structured graphical model to the OPF problem. Combining this with an interval discretization of the nodal variables, we develop an approximation algorithmmore » for the OPF problem. Further, we use techniques from constraint programming (CP) to perform interval computations and adaptive bound propagation to obtain practically efficient algorithms. Compared to previous algorithms that solve OPF with optimality guarantees using convex relaxations, our approach is able to work for arbitrary tree-structured distribution networks and handle mixed-integer optimization problems. Further, it can be implemented in a distributed message-passing fashion that is scalable and is suitable for “smart grid” applications like control of distributed energy resources. In conclusion, numerical evaluations on several benchmark networks show that practical OPF problems can be solved effectively using this approach.« less

Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

NASA Technical Reports Server (NTRS)

Wada, Ben K. (Editor); Fanson, James L. (Editor); Miura, Koryo (Editor)

1991-01-01

The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

NASA Astrophysics Data System (ADS)

Wada, Ben K.; Fanson, James L.; Miura, Koryo

1991-11-01

The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

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.

Double-Zero-Index Structural Phononic Waveguides

NASA Astrophysics Data System (ADS)

Zhu, Hongfei; Semperlotti, Fabio

2017-12-01

We report on the theoretical and experimental realization of a double-zero-index elastic waveguide and the corresponding acoustic cloaking and supercoupling effects. The proposed waveguide uses geometric tapers in order to induce Dirac-like cones at k → =0 due to accidental degeneracy. The nature of the degeneracy is explored by a k .p perturbation method adapted to thin structural waveguides. The results confirm the linear nature of the dispersion around the degeneracy and the possibility to map the material to effective-medium properties. Effective parameters numerically extracted using boundary medium theory confirm that the phononic waveguide maps into a double-zero-index material. Numerical and experimental results confirm the expected cloaking and supercoupling effects.

Condition Based Maintenance Technology Impact Study: Assessment Methods, Study Design and Interim Results

DTIC Science & Technology

2014-07-01

Unified Theory of Acceptance and Use of Technology, Structuration Model of Technology, UNCLASSIFIED DSTO-TR-2992 UNCLASSIFIED 5 Adaptive...Structuration Theory , Model of Mutual Adaptation, Model of Technology Appropriation, Diffusion/Implementation Model, and Tri-core Model, among others [11...simulation gaming essay/scenario writing genius forecasting role play/acting backcasting swot brainstorming relevance tree/logic chart scenario workshop

Towards a large-scale scalable adaptive heart model using shallow tree meshes

NASA Astrophysics Data System (ADS)

Krause, Dorian; Dickopf, Thomas; Potse, Mark; Krause, Rolf

2015-10-01

Electrophysiological heart models are sophisticated computational tools that place high demands on the computing hardware due to the high spatial resolution required to capture the steep depolarization front. To address this challenge, we present a novel adaptive scheme for resolving the deporalization front accurately using adaptivity in space. Our adaptive scheme is based on locally structured meshes. These tensor meshes in space are organized in a parallel forest of trees, which allows us to resolve complicated geometries and to realize high variations in the local mesh sizes with a minimal memory footprint in the adaptive scheme. We discuss both a non-conforming mortar element approximation and a conforming finite element space and present an efficient technique for the assembly of the respective stiffness matrices using matrix representations of the inclusion operators into the product space on the so-called shallow tree meshes. We analyzed the parallel performance and scalability for a two-dimensional ventricle slice as well as for a full large-scale heart model. Our results demonstrate that the method has good performance and high accuracy.

A short note on the use of the red-black tree in Cartesian adaptive mesh refinement algorithms

NASA Astrophysics Data System (ADS)

Hasbestan, Jaber J.; Senocak, Inanc

2017-12-01

Mesh adaptivity is an indispensable capability to tackle multiphysics problems with large disparity in time and length scales. With the availability of powerful supercomputers, there is a pressing need to extend time-proven computational techniques to extreme-scale problems. Cartesian adaptive mesh refinement (AMR) is one such method that enables simulation of multiscale, multiphysics problems. AMR is based on construction of octrees. Originally, an explicit tree data structure was used to generate and manipulate an adaptive Cartesian mesh. At least eight pointers are required in an explicit approach to construct an octree. Parent-child relationships are then used to traverse the tree. An explicit octree, however, is expensive in terms of memory usage and the time it takes to traverse the tree to access a specific node. For these reasons, implicit pointerless methods have been pioneered within the computer graphics community, motivated by applications requiring interactivity and realistic three dimensional visualization. Lewiner et al. [1] provides a concise review of pointerless approaches to generate an octree. Use of a hash table and Z-order curve are two key concepts in pointerless methods that we briefly discuss next.

Policy tree optimization for adaptive management of water resources systems

NASA Astrophysics Data System (ADS)

Herman, Jonathan; Giuliani, Matteo

2017-04-01

Water resources systems must cope with irreducible uncertainty in supply and demand, requiring policy alternatives capable of adapting to a range of possible future scenarios. Recent studies have developed adaptive policies based on "signposts" or "tipping points" that suggest the need of updating the policy. However, there remains a need for a general method to optimize the choice of the signposts to be used and their threshold values. This work contributes a general framework and computational algorithm to design adaptive policies as a tree structure (i.e., a hierarchical set of logical rules) using a simulation-optimization approach based on genetic programming. Given a set of feature variables (e.g., reservoir level, inflow observations, inflow forecasts), the resulting policy defines both the optimal reservoir operations and the conditions under which such operations should be triggered. We demonstrate the approach using Folsom Reservoir (California) as a case study, in which operating policies must balance the risk of both floods and droughts. Numerical results show that the tree-based policies outperform the ones designed via Dynamic Programming. In addition, they display good adaptive capacity to the changing climate, successfully adapting the reservoir operations across a large set of uncertain climate scenarios.

Adapting a scenario tree model for freedom from disease as surveillance progresses: the Canadian notifiable avian influenza model.

PubMed

Christensen, Jette; El Allaki, Farouk; Vallières, André

2014-05-01

Scenario tree models with temporal discounting have been applied in four continents to support claims of freedom from animal disease. Recently, a second (new) model was developed for the same population and disease. This is a natural development because surveillance is a dynamic process that needs to adapt to changing circumstances - the difficulty is the justification for, documentation of, presentation of and the acceptance of the changes. Our objective was to propose a systematic approach to present changes to an existing scenario tree model for freedom from disease. We used the example of how we adapted the deterministic Canadian Notifiable Avian Influenza scenario tree model published in 2011 to a stochastic scenario tree model where the definition of sub-populations and the estimation of probability of introduction of the pathogen were modified. We found that the standardized approach by Vanderstichel et al. (2013) with modifications provided a systematic approach to make and present changes to an existing scenario tree model. We believe that the new 2013 CanNAISS scenario tree model is a better model than the 2011 model because the 2013 model included more surveillance data. In particular, the new data on Notifiable Avian Influenza in Canada from the last 5 years were used to improve input parameters and model structure. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest.

PubMed

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

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

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest

PubMed Central

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate. PMID:26098916

Adaptive response to land-use history and roost selection by Rafinesque’s big-eared bats

DOE PAGES

Loeb, Susan C.

2017-01-30

Although habitat loss and degradation are major contributors to species declines, some species are able to adapt to changes in land use by selecting different habitats or structures in disturbed areas than they do in more pristine habitats. Bats are particularly vulnerable to changes in land use due to their dependence on specific habitat types and structures. The objective of this study was to determine how selection and use of roost trees, and niche breadth of Rafinesque’s big-eared bats (Corynorhinus rafinesquii) varied with land-use history. I examined use and selection of roosts at 3 bottomland hardwood sites that varied inmore » amount and time since timber harvest. Fortynine transects were established as a means of searching for bats in trees with basal cavity openings and were surveyed 2–9 times. Bats at the most-disturbed sites exhibited the broadest niches, using a greater number of tree species and habitat types, although bats at the least-disturbed site used a broader range of cavity volumes. Cavity characteristics were the primary factors governing roost selection by Rafinesque’s big-eared bats, but selection varied among sites. Probability of use increased with increasing cavity volume for bats at all sites, but bats at the most-disturbed site primarily used trees in the smallest cavity volume class, whereas bats at the least-disturbed site primarily used trees in the largest cavity volume class. Lastly, results of this study suggest that Rafinesque’s bigeared bats can adapt to a range of habitat conditions if trees with large cavities are available. However, future studies need to determine the long-term viability of this species in disturbed habitats.« less

Adaptive response to land-use history and roost selection by Rafinesque’s big-eared bats

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

Loeb, Susan C.

Although habitat loss and degradation are major contributors to species declines, some species are able to adapt to changes in land use by selecting different habitats or structures in disturbed areas than they do in more pristine habitats. Bats are particularly vulnerable to changes in land use due to their dependence on specific habitat types and structures. The objective of this study was to determine how selection and use of roost trees, and niche breadth of Rafinesque’s big-eared bats (Corynorhinus rafinesquii) varied with land-use history. I examined use and selection of roosts at 3 bottomland hardwood sites that varied inmore » amount and time since timber harvest. Fortynine transects were established as a means of searching for bats in trees with basal cavity openings and were surveyed 2–9 times. Bats at the most-disturbed sites exhibited the broadest niches, using a greater number of tree species and habitat types, although bats at the least-disturbed site used a broader range of cavity volumes. Cavity characteristics were the primary factors governing roost selection by Rafinesque’s big-eared bats, but selection varied among sites. Probability of use increased with increasing cavity volume for bats at all sites, but bats at the most-disturbed site primarily used trees in the smallest cavity volume class, whereas bats at the least-disturbed site primarily used trees in the largest cavity volume class. Lastly, results of this study suggest that Rafinesque’s bigeared bats can adapt to a range of habitat conditions if trees with large cavities are available. However, future studies need to determine the long-term viability of this species in disturbed habitats.« less

Competition and time-dependent behavior in spatial iterated prisoner’s dilemma incorporating adaptive zero-determinant strategies

NASA Astrophysics Data System (ADS)

Li, Yong; Xu, Chen; Liu, Jie; Hui, Pak Ming

2016-10-01

We propose and study the competitiveness of a class of adaptive zero-determinant strategies (ZDSs) in a population with spatial structure against four classic strategies in iterated prisoner’s dilemma. Besides strategy updating via a probabilistic mechanism by imitating the strategy of a better performing opponent, players using the ZDSs can also adapt their strategies to take advantage of their local competing environment with another probability. The adapted ZDSs could be extortionate-like to avoid being continually cheated by defectors or to take advantage of unconditional cooperators. The adapted ZDSs could also be a compliance strategy so as to cooperate with the conditionally cooperative players. This flexibility makes adaptive ZDSs more competitive than nonadaptive ZDSs. Results show that adaptive ZDSs can either dominate over other strategies or at least coexist with them when the ZDSs are allowed to adapt more readily than to imitate other strategies. The effectiveness of the adaptive ZDSs relies on how fast they can adapt to the competing environment before they are replaced by other strategies. The adaptive ZDSs generally work well as they could adapt gradually and make use of other strategies for suppressing their enemies. When adaptation happens more readily than imitation for the ZDSs, they outperform other strategies over a wide range of cost-to-benefit ratios.

Synchronization of coupled stochastic complex-valued dynamical networks with time-varying delays via aperiodically intermittent adaptive control

NASA Astrophysics Data System (ADS)

Wang, Pengfei; Jin, Wei; Su, Huan

2018-04-01

This paper deals with the synchronization problem of a class of coupled stochastic complex-valued drive-response networks with time-varying delays via aperiodically intermittent adaptive control. Different from the previous works, the intermittent control is aperiodic and adaptive, and the restrictions on the control width and time delay are removed, which lead to a larger application scope for this control strategy. Then, based on the Lyapunov method and Kirchhoff's Matrix Tree Theorem as well as differential inequality techniques, several novel synchronization conditions are derived for the considered model. Specially, impulsive control is also considered, which can be seen as a special case of the aperiodically intermittent control when the control width tends to zero. And the corresponding synchronization criteria are given as well. As an application of the theoretical results, a class of stochastic complex-valued coupled oscillators with time-varying delays is studied, and the numerical simulations are also given to demonstrate the effectiveness of the control strategies.

Estimating water use by sugar maple trees: considerations when using heat-pulse methods in trees with deep functional sapwood.

PubMed

Pausch, Roman C.; Grote, Edmund E.; Dawson, Todd E.

2000-03-01

Accurate estimates of sapwood properties (including radial depth of functional xylem and wood water content) are critical when using the heat pulse velocity (HPV) technique to estimate tree water use. Errors in estimating the volumetric water content (V(h)) of the sapwood, especially in tree species with a large proportion of sapwood, can cause significant errors in the calculations ofsap velocity and sap flow through tree boles. Scaling to the whole-stand level greatly inflates these errors. We determined the effects of season, tree size and radial wood depth on V(h) of wood cores removed from Acer saccharum Marsh. trees throughout 3 years in upstate New York. We also determined the effects of variation in V(h) on sap velocity and sap flow calculations based on HPV data collected from sap flow gauges inserted at four depths. In addition, we compared two modifications of Hatton's weighted average technique, the zero-step and zero-average methods, for determining sap velocity and sap flow at depths beyond those penetrated by the sap flow gauges. Parameter V(h) varied significantly with time of year (DOY), tree size (S), and radial wood depth (RD), and there were significant DOY x S and DOY x RD interactions. Use of a mean whole-tree V(h) value resulted in differences ranging from -6 to +47% for both sap velocity and sap flow for individual sapwood annuli compared with use of the V(h) value determined at the specific depth where a probe was placed. Whole-tree sap flow was 7% higher when calculated on the basis of the individual V(h) value compared with the mean whole-tree V(h) value. Calculated total sap flow for a tree with a DBH of 48.8 cm was 13 and 19% less using the zero-step and the zero-average velocity techniques, respectively, than the value obtained with Hatton's weighted average technique. Smaller differences among the three methods were observed for a tree with a DBH of 24.4 cm. We conclude that, for Acer saccharum: (1) mean V(h) changes significantly during the year and can range from nearly 50% during winter and early spring, to 20% during the growing season;(2) large trees have a significantly greater V(h) than small trees; (3) overall, V(h) decreases and then increases significantly with radial wood depth, suggesting that radial water movement and storage are highly dynamic; and (4) V(h) estimates can vary greatly and influence subsequent water use calculations depending on whether an average or an individual V(h) value for a wood core is used. For large diameter trees in which sapwood comprises a large fraction of total stem cross-sectional area (where sap flow gauges cannot be inserted across the entire cross-sectional area), the zero-average modification of Hatton's weighted average method reduces the potential for large errors in whole-tree and landscape water balance estimates based on the HPV method.

Policy Tree Optimization for Adaptive Management of Water Resources Systems

NASA Astrophysics Data System (ADS)

Herman, J. D.; Giuliani, M.

2016-12-01

Water resources systems must cope with irreducible uncertainty in supply and demand, requiring policy alternatives capable of adapting to a range of possible future scenarios. Recent studies have developed adaptive policies based on "signposts" or "tipping points", which are threshold values of indicator variables that signal a change in policy. However, there remains a need for a general method to optimize the choice of indicators and their threshold values in a way that is easily interpretable for decision makers. Here we propose a conceptual framework and computational algorithm to design adaptive policies as a tree structure (i.e., a hierarchical set of logical rules) using a simulation-optimization approach based on genetic programming. We demonstrate the approach using Folsom Reservoir, California as a case study, in which operating policies must balance the risk of both floods and droughts. Given a set of feature variables, such as reservoir level, inflow observations and forecasts, and time of year, the resulting policy defines the conditions under which flood control and water supply hedging operations should be triggered. Importantly, the tree-based rule sets are easy to interpret for decision making, and can be compared to historical operating policies to understand the adaptations needed under possible climate change scenarios. Several remaining challenges are discussed, including the empirical convergence properties of the method, and extensions to irreversible decisions such as infrastructure. Policy tree optimization, and corresponding open-source software, provide a generalizable, interpretable approach to designing adaptive policies under uncertainty for water resources systems.

Plasticity in variation of xylem and phloem cell characteristics of Norway spruce under different local conditions

PubMed Central

Gričar, Jožica; Prislan, Peter; de Luis, Martin; Gryc, Vladimír; Hacurová, Jana; Vavrčík, Hanuš; Čufar, Katarina

2015-01-01

There is limited information on intra-annual plasticity of secondary tissues of tree species growing under different environmental conditions. To increase the knowledge about the plasticity of secondary growth, which allows trees to adapt to specific local climatic regimes, we examined climate–radial growth relationships of Norway spruce [Picea abies (L.) H. Karst.] from three contrasting locations in the temperate climatic zone by analyzing tree-ring widths for the period 1932–2010, and cell characteristics in xylem and phloem increments formed in the years 2009–2011. Variation in the structure of xylem and phloem increments clearly shows that plasticity in seasonal dynamics of cambial cell production and cell differentiation exists on xylem and phloem sides. Anatomical characteristics of xylem and phloem cells are predominantly site-specific characteristics, because they varied among sites but were fairly uniform among years in trees from the same site. Xylem and phloem tissues formed in the first part of the growing season seemed to be more stable in structure, indicating their priority over latewood and late phloem for tree performance. Long-term climate and radial growth analyses revealed that growth was in general less dependent on precipitation than on temperature; however, growth sensitivity to local conditions differed among the sites. Only partial dependence of radial growth of spruce on climatic factors on the selected sites confirms its strategy to adapt the structure of wood and phloem increments to function optimally in local conditions. PMID:26442044

The structure, distribution, and biomass of the world's forests

Treesearch

Yude Pan; Richard A. Birdsey; Oliver L. Phillips; Robert B. Jackson

2013-01-01

Forests are the dominant terrestrial ecosystem on Earth. We review the environmental factors controlling their structure and global distribution and evaluate their current and future trajectory. Adaptations of trees to climate and resource gradients, coupled with disturbances and forest dynamics, create complex geographical patterns in forest assemblages and structures...

On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats.

PubMed

Polle, Andrea; Chen, Shaoliang

2015-09-01

Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed. © 2014 John Wiley & Sons Ltd.

Conservation genetics of the European beech in France

Treesearch

A. Ducousso; B. Musch; S. Irola; A. Quenu; A. Hampe; R.J. Petit

2017-01-01

European beech (Fagus sylvatica) is one of the most abundant tree species in Europe. Its genetic structure and diversity have been investigated using both molecular markers and adaptive traits as assessed in field and laboratory experimental tests looking at adaptative traits. A great deal of information also exists on the Quaternary history of the...

A phase cell cluster expansion for Euclidean field theories

NASA Astrophysics Data System (ADS)

Battle, Guy A., III; Federbush, Paul

1982-08-01

We adapt the cluster expansion first used to treat infrared problems for lattice models (a mass zero cluster expansion) to the usual field theory situation. The field is expanded in terms of special block spin functions and the cluster expansion given in terms of the expansion coefficients (phase cell variables); the cluster expansion expresses correlation functions in terms of contributions from finite coupled subsets of these variables. Most of the present work is carried through in d space time dimensions (for φ24 the details of the cluster expansion are pursued and convergence is proven). Thus most of the results in the present work will apply to a treatment of φ34 to which we hope to return in a succeeding paper. Of particular interest in this paper is a substitute for the stability of the vacuum bound appropriate to this cluster expansion (for d = 2 and d = 3), and a new method for performing estimates with tree graphs. The phase cell cluster expansions have the renormalization group incorporated intimately into their structure. We hope they will be useful ultimately in treating four dimensional field theories.

Hydrological states and the resilience of deltaic forested wetlands

NASA Astrophysics Data System (ADS)

Keim, R.; Allen, S. T.

2017-12-01

The flooding regime constitutes a set of chronic disturbances that are largely responsible for ecosystem structure. However, disturbances do not always constitute stresses to plants that survive because of adaptations to flooded conditions. We examine baldcypress-water tupelo forested wetlands in the delta of the Mississippi River as a case study in mechanisms by which hydrologic change shapes wetland ecosystem change, supported by experimental evidence from remote sensing, tree-ring and other field studies, and meta-analysis across the literature. Decreased hydrologic variability caused by water control structures has reduced the frequency of flood events that increase growth of baldcypress and favor its establishment by reducing competition from other species. Hydrologic modifications that lead to semi-permanent, stagnant flooding constitute semi-permanent disturbance that prevents regeneration of any trees, reduces growth of established trees, and reduces stand density by causing mortality of some trees. However, baldcypress trees in low-density stands appear to be generally adapted for long-term survival in stagnant conditions. Thus, initial decreases in stand density after impoundment do not necessarily portend continued conversion away from forest because reduced inter-tree competition is a negative feedback on mortality. Overall, a natural hydrologic regime with high variability in riverine flooding favors denser stands with greater diversity of tree species, and the present, controlled hydrologic regime that has largely eliminated riverine flooding favors open stands. Sea-level rise will increase salinity that quickly leads to forest conversion to marsh, but will also increase stagnant, freshwater flooding further inland. These drivers of hydrologic change reduce carbon assimilation by forests, both by reduced stand-level productivity and decreased forested area.

Uninjured trees - a meaningful guide to white-pine weevil control decisions

Treesearch

William E. Waters

1962-01-01

The white-pine weevil, Pissodes strobi, is a particularly insidious forest pest that can render a stand of host trees virtually worthless. It rarely, if ever, kills a tree; but the crooks, forks, and internal defects that develop in attacked trees over a period of years may reduce the merchantable volume and value of the tree at harvest age to zero. Dollar losses are...

Phylogeographic analyses and evaluation of shortleaf pine population structure in Missouri

Treesearch

Jeff Koppelman; Emily Parsons; Briedi Scott; Jennifer Collantes; Lori S. Eggert; Sedley Josserand; Craig Echt; C. Dana Nelson

2007-01-01

A great expanse of shortleaf pine in Missouri was logged before the mid-20th century, and since that time, seedlings of the species have been planted. Due to large-scale decline in oak trees occupying previous shortleaf pine range, restoration of the shortleaf pine is a priority in Missouri. Restoration can be enhanced through the use of locally adapted trees that have...

Struggle in the flood: tree responses to flooding stress in four tropical floodplain systems

PubMed Central

Parolin, Pia; Wittmann, Florian

2010-01-01

Background and aims In the context of the 200th anniversary of Charles Darwin's birth in 1809, this study discusses the variation in structure and adaptation associated with survival and reproductive success in the face of environmental stresses in the trees of tropical floodplains. Scope We provide a comparative review on the responses to flooding stress in the trees of freshwater wetlands in tropical environments. The four large wetlands we evaluate are: (i) Central Amazonian floodplains in South America, (ii) the Okavango Delta in Africa, (iii) the Mekong floodplains of Asia and (iv) the floodplains of Northern Australia. They each have a predictable ‘flood pulse’. Although flooding height varies between the ecosystems, the annual pulse is a major driving force influencing all living organisms and a source of stress for which specialized adaptations for survival are required. Main points The need for trees to survive an annual flood pulse has given rise to a large variety of adaptations. However, phenological responses to the flood are similar in the four ecosystems. Deciduous and evergreen species respond with leaf shedding, although sap flow remains active for most of the year. Growth depends on adequate carbohydrate supply. Physiological adaptations (anaerobic metabolism, starch accumulation) are also required. Conclusions Data concerning the ecophysiology and adaptations of trees in floodplain forests worldwide are extremely scarce. For successful floodplain conservation, more information is needed, ideally through a globally co-ordinated study using reproducible comparative methods. In the light of climatic change, with increasing drought, decreased groundwater availability and flooding periodicities, this knowledge is needed ever more urgently to facilitate fast and appropriate management responses to large-scale environmental change. PMID:22476061

Spatial Query for Planetary Data

NASA Technical Reports Server (NTRS)

Shams, Khawaja S.; Crockett, Thomas M.; Powell, Mark W.; Joswig, Joseph C.; Fox, Jason M.

2011-01-01

Science investigators need to quickly and effectively assess past observations of specific locations on a planetary surface. This innovation involves a location-based search technology that was adapted and applied to planetary science data to support a spatial query capability for mission operations software. High-performance location-based searching requires the use of spatial data structures for database organization. Spatial data structures are designed to organize datasets based on their coordinates in a way that is optimized for location-based retrieval. The particular spatial data structure that was adapted for planetary data search is the R+ tree.

Adaptation of trees, forests and forestry to climate change

Treesearch

Daniel J. Chmura; Glenn T. Howe; Paul D. Anderson; Bradley J. St Clair

2010-01-01

Ongoing climate change will likely expose trees and forests to new stresses and disturbances during this century. Trees naturally adapt to changes in climate, but their natural adaptive ability may be compromised by the rapid changes projected for this century. In the broad sense, adaptation to climate change also includes the purposeful adaptation of human systems,...

A hierarchical structure for automatic meshing and adaptive FEM analysis

NASA Technical Reports Server (NTRS)

Kela, Ajay; Saxena, Mukul; Perucchio, Renato

1987-01-01

A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.

Pulmonary airways tree segmentation from CT examinations using adaptive volume of interest

NASA Astrophysics Data System (ADS)

Park, Sang Cheol; Kim, Won Pil; Zheng, Bin; Leader, Joseph K.; Pu, Jiantao; Tan, Jun; Gur, David

2009-02-01

Airways tree segmentation is an important step in quantitatively assessing the severity of and changes in several lung diseases such as chronic obstructive pulmonary disease (COPD), asthma, and cystic fibrosis. It can also be used in guiding bronchoscopy. The purpose of this study is to develop an automated scheme for segmenting the airways tree structure depicted on chest CT examinations. After lung volume segmentation, the scheme defines the first cylinder-like volume of interest (VOI) using a series of images depicting the trachea. The scheme then iteratively defines and adds subsequent VOIs using a region growing algorithm combined with adaptively determined thresholds in order to trace possible sections of airways located inside the combined VOI in question. The airway tree segmentation process is automatically terminated after the scheme assesses all defined VOIs in the iteratively assembled VOI list. In this preliminary study, ten CT examinations with 1.25mm section thickness and two different CT image reconstruction kernels ("bone" and "standard") were selected and used to test the proposed airways tree segmentation scheme. The experiment results showed that (1) adopting this approach affectively prevented the scheme from infiltrating into the parenchyma, (2) the proposed method reasonably accurately segmented the airways trees with lower false positive identification rate as compared with other previously reported schemes that are based on 2-D image segmentation and data analyses, and (3) the proposed adaptive, iterative threshold selection method for the region growing step in each identified VOI enables the scheme to segment the airways trees reliably to the 4th generation in this limited dataset with successful segmentation up to the 5th generation in a fraction of the airways tree branches.

Adaptive remodeling of the biliary tree: the essence of liver progenitor cell expansion.

PubMed

Kok, Cindy Yuet-Yin; Miyajima, Atsushi; Itoh, Tohru

2015-07-01

The liver progenitor cell population has long been thought to exist within the liver. However, there are no standardized criteria for defining the liver progenitor cells, and there has been intense debate about the origin of these cells in the adult liver. The characteristics of such cells vary depending on the disease model used and also on the method of analysis. Visualization of three-dimensional biliary structures has revealed that the emergence of liver progenitor cells essentially reflects the adaptive remodeling of the hepatic biliary network in response to liver injury. We propose that the progenitor cell exists as a subpopulation in the biliary tree and show that the appearance of liver progenitor cells in injured parenchyma is reflective of extensive remodeling of the biliary structure. © 2015 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

A splay tree-based approach for efficient resource location in P2P networks.

PubMed

Zhou, Wei; Tan, Zilong; Yao, Shaowen; Wang, Shipu

2014-01-01

Resource location in structured P2P system has a critical influence on the system performance. Existing analytical studies of Chord protocol have shown some potential improvements in performance. In this paper a splay tree-based new Chord structure called SChord is proposed to improve the efficiency of locating resources. We consider a novel implementation of the Chord finger table (routing table) based on the splay tree. This approach extends the Chord finger table with additional routing entries. Adaptive routing algorithm is proposed for implementation, and it can be shown that hop count is significantly minimized without introducing any other protocol overheads. We analyze the hop count of the adaptive routing algorithm, as compared to Chord variants, and demonstrate sharp upper and lower bounds for both worst-case and average case settings. In addition, we theoretically analyze the hop reducing in SChord and derive the fact that SChord can significantly reduce the routing hops as compared to Chord. Several simulations are presented to evaluate the performance of the algorithm and support our analytical findings. The simulation results show the efficiency of SChord.

The zero inflation of standing dead tree carbon stocks

Treesearch

Christopher W. Woodall; David W. MacFarlane

2012-01-01

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

Bayes Forest: a data-intensive generator of morphological tree clones

PubMed Central

Järvenpää, Marko; Åkerblom, Markku; Raumonen, Pasi; Kaasalainen, Mikko

2017-01-01

Abstract Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree “clones” based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research. PMID:29020742

A zero torsional stiffness twist morphing blade as a wind turbine load alleviation device

NASA Astrophysics Data System (ADS)

Lachenal, X.; Daynes, S.; Weaver, P. M.

2013-06-01

This paper presents the design, analysis and realization of a zero stiffness twist morphing wind turbine blade. The morphing blade is designed to actively twist as a means of alleviating the gust loads which reduce the fatigue life of wind turbine blades. The morphing structure exploits an elastic strain energy balance within the blade to enable large twisting deformations with modest actuation requirements. While twist is introduced using the warping of the blade skin, internal pre-stressed members ensure that a constant strain energy balance is achieved throughout the deformation, resulting in a zero torsional stiffness structure. The torsional stability of the morphing blade is characterized by analysing the elastic strain energy in the device. Analytical models of the skin, the pre-stressed components and the complete blade are compared to their respective finite element models as well as experimental results. The load alleviation potential of the adaptive structure is quantified using a two-dimensional steady flow aerodynamic model which is experimentally validated with wind tunnel measurements.

Zero Pearson coefficient for strongly correlated growing trees

NASA Astrophysics Data System (ADS)

Dorogovtsev, S. N.; Ferreira, A. L.; Goltsev, A. V.; Mendes, J. F. F.

2010-03-01

We obtained Pearson’s coefficient of strongly correlated recursive networks growing by preferential attachment of every new vertex by m edges. We found that the Pearson coefficient is exactly zero in the infinite network limit for the recursive trees (m=1) . If the number of connections of new vertices exceeds one (m>1) , then the Pearson coefficient in the infinite networks equals zero only when the degree distribution exponent γ does not exceed 4. We calculated the Pearson coefficient for finite networks and observed a slow power-law-like approach to an infinite network limit. Our findings indicate that Pearson’s coefficient strongly depends on size and details of networks, which makes this characteristic virtually useless for quantitative comparison of different networks.

Zero Pearson coefficient for strongly correlated growing trees.

PubMed

Dorogovtsev, S N; Ferreira, A L; Goltsev, A V; Mendes, J F F

2010-03-01

We obtained Pearson's coefficient of strongly correlated recursive networks growing by preferential attachment of every new vertex by m edges. We found that the Pearson coefficient is exactly zero in the infinite network limit for the recursive trees (m=1). If the number of connections of new vertices exceeds one (m>1), then the Pearson coefficient in the infinite networks equals zero only when the degree distribution exponent gamma does not exceed 4. We calculated the Pearson coefficient for finite networks and observed a slow power-law-like approach to an infinite network limit. Our findings indicate that Pearson's coefficient strongly depends on size and details of networks, which makes this characteristic virtually useless for quantitative comparison of different networks.

Comparing the historic olive trees (Olea europaea L.) of Santa Cruz with contemporaneous trees in the Santa Barbara, CA area: a case study of diversity and structure in an introduced agricultural species conserved in situ

USDA-ARS?s Scientific Manuscript database

Historic populations of crop species outside their centers of origin and diversity, like the domestic olive (Olea europaea L.) in North America, are genetic resources for contemporary agriculture, including genotypes that could be adapted to, local conditions. The primary goal of this study was to d...

Multispectral code excited linear prediction coding and its application in magnetic resonance images.

PubMed

Hu, J H; Wang, Y; Cahill, P T

1997-01-01

This paper reports a multispectral code excited linear prediction (MCELP) method for the compression of multispectral images. Different linear prediction models and adaptation schemes have been compared. The method that uses a forward adaptive autoregressive (AR) model has been proven to achieve a good compromise between performance, complexity, and robustness. This approach is referred to as the MFCELP method. Given a set of multispectral images, the linear predictive coefficients are updated over nonoverlapping three-dimensional (3-D) macroblocks. Each macroblock is further divided into several 3-D micro-blocks, and the best excitation signal for each microblock is determined through an analysis-by-synthesis procedure. The MFCELP method has been applied to multispectral magnetic resonance (MR) images. To satisfy the high quality requirement for medical images, the error between the original image set and the synthesized one is further specified using a vector quantizer. This method has been applied to images from 26 clinical MR neuro studies (20 slices/study, three spectral bands/slice, 256x256 pixels/band, 12 b/pixel). The MFCELP method provides a significant visual improvement over the discrete cosine transform (DCT) based Joint Photographers Expert Group (JPEG) method, the wavelet transform based embedded zero-tree wavelet (EZW) coding method, and the vector tree (VT) coding method, as well as the multispectral segmented autoregressive moving average (MSARMA) method we developed previously.

Kinetic solvers with adaptive mesh in phase space.

PubMed

Arslanbekov, Robert R; Kolobov, Vladimir I; Frolova, Anna A

2013-12-01

An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional kinetic equations by the discrete velocity method. A Cartesian mesh for both configuration (r) and velocity (v) spaces is produced using a "tree of trees" (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed algorithms for solving the full Boltzmann and linear Boltzmann equations with AMPS. Several recent innovations were used to calculate the discrete Boltzmann collision integral with dynamically adaptive v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our AMPS technique has been demonstrated for simulations of hypersonic rarefied gas flows, ion and electron kinetics in weakly ionized plasma, radiation and light-particle transport through thin films, and electron streaming in semiconductors. We have shown that AMPS allows minimizing the number of cells in phase space to reduce the computational cost and memory usage for solving challenging kinetic problems.

A compact and realistic cerebral cortical layout derived from prewhitened resting-state fMRI time series: Cherniak's adjacency rule, size law, and metamodule grouping upheld

PubMed Central

Lewis, Scott M.; Christova, Peka; Jerde, Trenton A.; Georgopoulos, Apostolos P.

2012-01-01

We used hierarchical tree clustering to derive a functional organizational chart of 52 human cortical areas (26 per hemisphere) from zero-lag correlations calculated between single-voxel, prewhitened, resting-state BOLD fMRI time series in 18 subjects. No special “resting-state networks” were identified. There were four major features in the resulting tree (dendrogram). First, there was a strong clustering of homotopic, left-right hemispheric areas. Second, cortical areas were concatenated in multiple, partially overlapping clusters. Third, the arrangement of the areas revealed a layout that closely resembled the actual layout of the cerebral cortex, namely an orderly progression from anterior to posterior. And fourth, the layout of the cortical areas in the tree conformed to principles of efficient, compact layout of components proposed by Cherniak. Since the tree was derived on the basis of the strength of neural correlations, these results document an orderly relation between functional interactions and layout, i.e., between structure and function. PMID:22973198

Clonal growth and fine-scale genetic structure in tanoak (Notholithocarpus densiflorus: Fagaceae)

Treesearch

Richard S. Dodd; Wasima Mayer; Alejandro Nettel; Zara Afzal-Rafii

2013-01-01

The combination of sprouting and reproduction by seed can have important consequences on fine-scale spatial distribution of genetic structure (SGS). SGS is an important consideration for species’ restoration because it determines the minimum distance among seed trees to maximize genetic diversity while not prejudicing locally adapted genotypes. Local environmental...

Micronesian mangrove forest structure and tree responses to a severe typhoon

Treesearch

J. Boone Kauffman; Thomas G. Cole

2010-01-01

Tropical cyclones are common disturbances that have strong effects on mangrove composition and structure. Because there are numerous ecosystem services provided by mangroves, it is important to understand their adaptations and responses to these climatic events. In April 2004, Typhoon Sudal, a category 3-4 cyclone, passed over the state of Yap, Federated States of...

Adaptive root foraging strategies along a boreal-temperate forest gradient.

PubMed

Ostonen, Ivika; Truu, Marika; Helmisaari, Heljä-Sisko; Lukac, Martin; Borken, Werner; Vanguelova, Elena; Godbold, Douglas L; Lõhmus, Krista; Zang, Ulrich; Tedersoo, Leho; Preem, Jens-Konrad; Rosenvald, Katrin; Aosaar, Jürgen; Armolaitis, Kęstutis; Frey, Jane; Kabral, Naima; Kukumägi, Mai; Leppälammi-Kujansuu, Jaana; Lindroos, Antti-Jussi; Merilä, Päivi; Napa, Ülle; Nöjd, Pekka; Parts, Kaarin; Uri, Veiko; Varik, Mats; Truu, Jaak

2017-08-01

The tree root-mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root-mycorrhiza-bacteria continuum along climate and soil C : N gradients. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Utilizing forest tree genetic diversity for an adaptation of forest to climate change

NASA Astrophysics Data System (ADS)

Schueler, Silvio; Lackner, Magdalena; Chakraborty, Debojyoti

2017-04-01

Since climate conditions are considered to be major determinants of tree species' distribution ranges and drivers of local adaptation, anthropogenic climate change (CC) is expected to modify the distribution of tree species, tree species diversity and the forest ecosystems connected to these species. The expected speed of environmental change is significantly larger than the natural migration and adaptation capacity of trees and makes spontaneous adjustment of forest ecosystems improbable. Planting alternative tree species and utilizing the tree species' intrinsic adaptive capacity are considered to be the most promising adaptation strategy. Each year about 900 million seedlings of the major tree species are being planted in Central Europe. At present, the utilization of forest reproductive material is mainly restricted to nationally defined ecoregions (seed/provenance zones), but when seedlings planted today become adult, they might be maladapted, as the climate conditions within ecoregions changed significantly. In the cooperation project SUSTREE, we develop transnational delineation models for forest seed transfer and genetic conservation based on species distribution models and available intra-specific climate-response function. These models are being connected to national registers of forest reproductive material in order support nursery and forest managers by selecting the appropriate seedling material for future plantations. In the long-term, European and national policies as well as regional recommendations for provenances use need to adapted to consider the challenges of climate change.

Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies.

PubMed

Kumar, S; Gadagkar, S R

2000-12-01

The neighbor-joining (NJ) method is widely used in reconstructing large phylogenies because of its computational speed and the high accuracy in phylogenetic inference as revealed in computer simulation studies. However, most computer simulation studies have quantified the overall performance of the NJ method in terms of the percentage of branches inferred correctly or the percentage of replications in which the correct tree is recovered. We have examined other aspects of its performance, such as the relative efficiency in correctly reconstructing shallow (close to the external branches of the tree) and deep branches in large phylogenies; the contribution of zero-length branches to topological errors in the inferred trees; and the influence of increasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency of the NJ method. Results show that the correct reconstruction of deep branches is no more difficult than that of shallower branches. The presence of zero-length branches in realized trees contributes significantly to the overall error observed in the NJ tree, especially in large phylogenies or slowly evolving genes. Furthermore, the tree size does not influence the efficiency of NJ in reconstructing shallow and deep branches in our simulation study, in which the evolutionary process is assumed to be homogeneous in all lineages.

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

PubMed Central

2013-01-01

Background The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing. Results A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years. Conclusions The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers. PMID:23724860

Development of Secondary Woodland in Oak Wood Pastures Reduces the Richness of Rare Epiphytic Lichens

PubMed Central

Paltto, Heidi; Nordberg, Anna; Nordén, Björn; Snäll, Tord

2011-01-01

Wooded pastures with ancient trees were formerly abundant throughout Europe, but during the last century, grazing has largely been abandoned often resulting in dense forests. Ancient trees constitute habitat for many declining and threatened species, but the effects of secondary woodland on the biodiversity associated with these trees are largely unknown. We tested for difference in species richness, occurrence, and abundance of a set of nationally and regionally red-listed epiphytic lichens between ancient oaks located in secondary woodland and ancient oaks located in open conditions. We refined the test of the effect of secondary woodland by also including other explanatory variables. Species occurrence and abundance were modelled jointly using overdispersed zero-inflated Poisson models. The richness of the red-listed lichens on ancient oaks in secondary woodland was half of that compared with oaks growing in open conditions. The species-level analyses revealed that this was mainly the result of lower occupancy of two of the study species. The tree-level abundance of one species was also lower in secondary woodland. Potential explanations for this pattern are that the study lichens are adapted to desiccating conditions enhancing their population persistence by low competition or that open, windy conditions enhance their colonisation rate. This means that the development of secondary woodland is a threat to red-listed epiphytic lichens. We therefore suggest that woody vegetation is cleared and grazing resumed in abandoned oak pastures. Importantly, this will also benefit the vitality of the oaks. PMID:21961041

Hierarchical rendering of trees from precomputed multi-layer z-buffers

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

Max, N.

1996-02-01

Chen and Williams show how precomputed z-buffer images from different fixed viewing positions can be reprojected to produce an image for a new viewpoint. Here images are precomputed for twigs and branches at various levels in the hierarchical structure of a tree, and adaptively combined, depending on the position of the new viewpoint. The precomputed images contain multiple z levels to avoid missing pixels in the reconstruction, subpixel masks for anti-aliasing, and colors and normals for shading after reprojection.

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.

Water availability determines the richness and density of fig trees within Brazilian semideciduous forest landscapes

NASA Astrophysics Data System (ADS)

Coelho, Luís Francisco Mello; Ribeiro, Milton Cezar; Pereira, Rodrigo Augusto Santinelo

2014-05-01

The success of fig trees in tropical ecosystems is evidenced by the great diversity (+750 species) and wide geographic distribution of the genus. We assessed the contribution of environmental variables on the species richness and density of fig trees in fragments of seasonal semideciduous forest (SSF) in Brazil. We assessed 20 forest fragments in three regions in Sao Paulo State, Brazil. Fig tree richness and density was estimated in rectangular plots, comprising 31.4 ha sampled. Both richness and fig tree density were linearly modeled as function of variables representing (1) fragment metrics, (2) forest structure, and (3) landscape metrics expressing water drainage in the fragments. Model selection was performed by comparing the AIC values (Akaike Information Criterion) and the relative weight of each model (wAIC). Both species richness and fig tree density were better explained by the water availability in the fragment (meter of streams/ha): wAICrichness = 0.45, wAICdensity = 0.96. The remaining variables related to anthropic perturbation and forest structure were of little weight in the models. The rainfall seasonality in SSF seems to select for both establishment strategies and morphological adaptations in the hemiepiphytic fig tree species. In the studied SSF, hemiepiphytes established at lower heights in their host trees than reported for fig trees in evergreen rainforests. Some hemiepiphytic fig species evolved superficial roots extending up to 100 m from their trunks, resulting in hectare-scale root zones that allow them to efficiently forage water and soil nutrients. The community of fig trees was robust to variation in forest structure and conservation level of SSF fragments, making this group of plants an important element for the functioning of seasonal tropical forests.

Stable oxygen isotope analysis reveal vegetation influence on soil water movement and ecosystem water fluxes in a semi-arid oak woodland

NASA Astrophysics Data System (ADS)

Piayda, Arndt; Dubbert, Maren; Werner, Christiane; Cuntz, Matthias

2015-04-01

Mechanistically disentangling the role and function of vegetation within the hydrological cycle is one of the key questions in the interdisciplinary field of ecohydrology. The presence of vegetation can have various impacts on soil water relations: transpiration of active vegetation causes great water losses, rainfall is intercepted, soil evaporation can be reduced and infiltration, hydraulic redistribution and translatory flow might be altered. In drylands, covering around 40% of the global land surface, the carbon cycle is closely coupled to water availability due to (seasonal) droughts. Specifically savannah type ecosystems, which cover large areas worldwide, are, due to their bi-layered structure, very suitable to study the effects of distinct vegetation types on the ecosystem water cycle. Oxygen isotope signatures (δ18O) have been used to partition ecosystem evapotranspiration (ET ) because of the distinct isotopic compositions of water transpired by leaves relative to soil evaporated vapor. Recent developments in laser spectroscopy enable measurements of δ18O in the vapor phase with high temporal resolution in the field and bear a novel opportunity to trace water movement within the ecosystem. In the present study, the effects of distinct vegetation layers (i.e. trees and herbaceous vegetation) on soil water infiltration and redistribution as well as ecosystem water fluxes in a Mediterranean cork-oak woodland are disentangled. An irrigation experiment was carried out using δ18O labeled water to quantify the distinct effects of trees and herbaceous vegetation on 1) infiltration and redistribution of water in the soil profile and 2) to disentangle the effects of tree cover on the contribution of unproductive soil evaporation and understory transpiration to total ET . First results proof that stable δ18O isotopes measured onsite with laser spectroscopy is a valuable tool to trace water movement in the soil showing a much higher sensitivity than common TDR-type probes. It was possible to track soil water redistribution even beyond zero net water flux measured with TDR probes. Under shaded conditions beneath tree crowns, infiltration of precipitation reaches much deeper depths due to the limited radiation energy input and thus, reduced evaporative losses, compared to open areas between crowns. As a consequence, the isotopic enrichment back to initial conditions (as observed before the artificial precipitation event) was strongly delayed. Despite the higher water availability beneath tree crowns, transpiration of understory plants and soil evaporation rates were reduced compared to the open area due to the lack of energy. However, transpiration could be maintained much longer and at higher rates after the precipitation event then soil evaporation. These first results support previous findings at this site where a clear difference in understory plant community structure was observed. Beneath tree crowns, favorable water conditions enables a higher occurrence of grasses and nitrogen fixing forbs, whereas in between tree crowns drought adapted native species became dominant.

M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree.

PubMed

Wan, Zhijiang; He, Yishan; Hao, Ming; Yang, Jian; Zhong, Ning

2017-03-29

Understanding the working mechanism of the brain is one of the grandest challenges for modern science. Toward this end, the BigNeuron project was launched to gather a worldwide community to establish a big data resource and a set of the state-of-the-art of single neuron reconstruction algorithms. Many groups contributed their own algorithms for the project, including our mean shift and minimum spanning tree (M-MST). Although M-MST is intuitive and easy to implement, the MST just considers spatial information of single neuron and ignores the shape information, which might lead to less precise connections between some neuron segments. In this paper, we propose an improved algorithm, namely M-AMST, in which a rotating sphere model based on coordinate transformation is used to improve the weight calculation method in M-MST. Two experiments are designed to illustrate the effect of adapted minimum spanning tree algorithm and the adoptability of M-AMST in reconstructing variety of neuron image datasets respectively. In the experiment 1, taking the reconstruction of APP2 as reference, we produce the four difference scores (entire structure average (ESA), different structure average (DSA), percentage of different structure (PDS) and max distance of neurons' nodes (MDNN)) by comparing the neuron reconstruction of the APP2 and the other 5 competing algorithm. The result shows that M-AMST gets lower difference scores than M-MST in ESA, PDS and MDNN. Meanwhile, M-AMST is better than N-MST in ESA and MDNN. It indicates that utilizing the adapted minimum spanning tree algorithm which took the shape information of neuron into account can achieve better neuron reconstructions. In the experiment 2, 7 neuron image datasets are reconstructed and the four difference scores are calculated by comparing the gold standard reconstruction and the reconstructions produced by 6 competing algorithms. Comparing the four difference scores of M-AMST and the other 5 algorithm, we can conclude that M-AMST is able to achieve the best difference score in 3 datasets and get the second-best difference score in the other 2 datasets. We develop a pathway extraction method using a rotating sphere model based on coordinate transformation to improve the weight calculation approach in MST. The experimental results show that M-AMST utilizes the adapted minimum spanning tree algorithm which takes the shape information of neuron into account can achieve better neuron reconstructions. Moreover, M-AMST is able to get good neuron reconstruction in variety of image datasets.

Slant path L- and S-Band tree shadowing measurements

NASA Technical Reports Server (NTRS)

Vogel, Wolfhard J.; Torrence, Geoffrey W.

1994-01-01

This contribution presents selected results from simultaneous L- and S-Band slant-path fade measurements through a pecan, a cottonwood, and a pine tree employing a tower-mounted transmitter and dual-frequency receiver. A single, circularly-polarized antenna was used at each end of the link. The objective was to provide information for personal communications satellite design on the correlation of tree shadowing between frequencies near 1620 and 2500 MHz. Fades were measured along 10 m lateral distance with 5 cm spacing. Instantaneous fade differences between L- and S-Band exhibited normal distribution with means usually near 0 dB and standard deviations from 5.2 to 7.5 dB. The cottonwood tree was an exception, with 5.4 dB higher average fading at S- than at L-Band. The spatial autocorrelation reduced to near zero with lags of about 10 lambda. The fade slope in dB/MHz is normally distributed with zero mean and standard deviation increasing with fade level.

Slant path L- and S-Band tree shadowing measurements

NASA Astrophysics Data System (ADS)

Vogel, Wolfhard J.; Torrence, Geoffrey W.

1994-08-01

This contribution presents selected results from simultaneous L- and S-Band slant-path fade measurements through a pecan, a cottonwood, and a pine tree employing a tower-mounted transmitter and dual-frequency receiver. A single, circularly-polarized antenna was used at each end of the link. The objective was to provide information for personal communications satellite design on the correlation of tree shadowing between frequencies near 1620 and 2500 MHz. Fades were measured along 10 m lateral distance with 5 cm spacing. Instantaneous fade differences between L- and S-Band exhibited normal distribution with means usually near 0 dB and standard deviations from 5.2 to 7.5 dB. The cottonwood tree was an exception, with 5.4 dB higher average fading at S- than at L-Band. The spatial autocorrelation reduced to near zero with lags of about 10 lambda. The fade slope in dB/MHz is normally distributed with zero mean and standard deviation increasing with fade level.

Probabilistic sensitivity analysis for decision trees with multiple branches: use of the Dirichlet distribution in a Bayesian framework.

PubMed

Briggs, Andrew H; Ades, A E; Price, Martin J

2003-01-01

In structuring decision models of medical interventions, it is commonly recommended that only 2 branches be used for each chance node to avoid logical inconsistencies that can arise during sensitivity analyses if the branching probabilities do not sum to 1. However, information may be naturally available in an unconditional form, and structuring a tree in conditional form may complicate rather than simplify the sensitivity analysis of the unconditional probabilities. Current guidance emphasizes using probabilistic sensitivity analysis, and a method is required to provide probabilistic probabilities over multiple branches that appropriately represents uncertainty while satisfying the requirement that mutually exclusive event probabilities should sum to 1. The authors argue that the Dirichlet distribution, the multivariate equivalent of the beta distribution, is appropriate for this purpose and illustrate its use for generating a fully probabilistic transition matrix for a Markov model. Furthermore, they demonstrate that by adopting a Bayesian approach, the problem of observing zero counts for transitions of interest can be overcome.

Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)

PubMed Central

Zinck, John W. R.

2016-01-01

Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation. PMID:27387485

Long-term impacts of prescribed fire on stand structure, growth, mortality, and individual tree vigor in Pinus resinosa forests

Treesearch

Sawyer S. Scherer; Anthony W. D' Amato; Christel C. Kern; Brian J. Palik; Matthew B. Russell

2016-01-01

Prescribed fire is increasingly being viewed as a valuable tool for mitigating the ecological consequences of long-term fire suppression within fire-adapted forest ecosystems. While the use of burning treatments in northern temperate conifer forests has at times received considerable attention, the long-term (>10 years) effects on forest structure and...

Micronesian mangrove forest structure and tree responses to a severe typhoon

Treesearch

J. Boone Kauffman; Thomas G. Cole

2010-01-01

Tropical cyclones are common disturbances that have strong effects on mangrove composition and structure. Because there are numerous ecosystem services provided by mangroves, it is important to understand their adaptations and responses to these climatic events. In April 2004, Typhoon Sudal, a category 3–4 cyclone, passed over the state of Yap, Federated States of...

SVM-based tree-type neural networks as a critic in adaptive critic designs for control.

PubMed

Deb, Alok Kanti; Jayadeva; Gopal, Madan; Chandra, Suresh

2007-07-01

In this paper, we use the approach of adaptive critic design (ACD) for control, specifically, the action-dependent heuristic dynamic programming (ADHDP) method. A least squares support vector machine (SVM) regressor has been used for generating the control actions, while an SVM-based tree-type neural network (NN) is used as the critic. After a failure occurs, the critic and action are retrained in tandem using the failure data. Failure data is binary classification data, where the number of failure states are very few as compared to the number of no-failure states. The difficulty of conventional multilayer feedforward NNs in learning this type of classification data has been overcome by using the SVM-based tree-type NN, which due to its feature to add neurons to learn misclassified data, has the capability to learn any binary classification data without a priori choice of the number of neurons or the structure of the network. The capability of the trained controller to handle unforeseen situations is demonstrated.

Adaptive control based on retrospective cost optimization

NASA Technical Reports Server (NTRS)

Bernstein, Dennis S. (Inventor); Santillo, Mario A. (Inventor)

2012-01-01

A discrete-time adaptive control law for stabilization, command following, and disturbance rejection that is effective for systems that are unstable, MIMO, and/or nonminimum phase. The adaptive control algorithm includes guidelines concerning the modeling information needed for implementation. This information includes the relative degree, the first nonzero Markov parameter, and the nonminimum-phase zeros. Except when the plant has nonminimum-phase zeros whose absolute value is less than the plant's spectral radius, the required zero information can be approximated by a sufficient number of Markov parameters. No additional information about the poles or zeros need be known. Numerical examples are presented to illustrate the algorithm's effectiveness in handling systems with errors in the required modeling data, unknown latency, sensor noise, and saturation.

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

PubMed

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

2017-12-01

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

Combining Vector Quantization and Histogram Equalization.

ERIC Educational Resources Information Center

Cosman, Pamela C.; And Others

1992-01-01

Discussion of contrast enhancement techniques focuses on the use of histogram equalization with a data compression technique, i.e., tree-structured vector quantization. The enhancement technique of intensity windowing is described, and the use of enhancement techniques for medical images is explained, including adaptive histogram equalization.…

Mangrove forests

Treesearch

Ariel E. Lugo; Ernesto Medina

2014-01-01

The mangrove environment is not globally homogeneous, but involves many environmental gradients to which mangrove species must adapt and overcome to maintain the familiar structure and physiognomy associated with the mangrove ecosystem. The stature of mangroves, measured by tree height, decreases along the following environmental gradients from low to high salinity,...

Multiphase Interface Tracking with Fast Semi-Lagrangian Contouring.

PubMed

Li, Xiaosheng; He, Xiaowei; Liu, Xuehui; Zhang, Jian J; Liu, Baoquan; Wu, Enhua

2016-08-01

We propose a semi-Lagrangian method for multiphase interface tracking. In contrast to previous methods, our method maintains an explicit polygonal mesh, which is reconstructed from an unsigned distance function and an indicator function, to track the interface of arbitrary number of phases. The surface mesh is reconstructed at each step using an efficient multiphase polygonization procedure with precomputed stencils while the distance and indicator function are updated with an accurate semi-Lagrangian path tracing from the meshes of the last step. Furthermore, we provide an adaptive data structure, multiphase distance tree, to accelerate the updating of both the distance function and the indicator function. In addition, the adaptive structure also enables us to contour the distance tree accurately with simple bisection techniques. The major advantage of our method is that it can easily handle topological changes without ambiguities and preserve both the sharp features and the volume well. We will evaluate its efficiency, accuracy and robustness in the results part with several examples.

Compression of surface myoelectric signals using MP3 encoding.

PubMed

Chan, Adrian D C

2011-01-01

The potential of MP3 compression of surface myoelectric signals is explored in this paper. MP3 compression is a perceptual-based encoder scheme, used traditionally to compress audio signals. The ubiquity of MP3 compression (e.g., portable consumer electronics and internet applications) makes it an attractive option for remote monitoring and telemedicine applications. The effects of muscle site and contraction type are examined at different MP3 encoding bitrates. Results demonstrate that MP3 compression is sensitive to the myoelectric signal bandwidth, with larger signal distortion associated with myoelectric signals that have higher bandwidths. Compared to other myoelectric signal compression techniques reported previously (embedded zero-tree wavelet compression and adaptive differential pulse code modulation), MP3 compression demonstrates superior performance (i.e., lower percent residual differences for the same compression ratios).

Reducing computation in an i-vector speaker recognition system using a tree-structured universal background model

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

McClanahan, Richard; De Leon, Phillip L.

The majority of state-of-the-art speaker recognition systems (SR) utilize speaker models that are derived from an adapted universal background model (UBM) in the form of a Gaussian mixture model (GMM). This is true for GMM supervector systems, joint factor analysis systems, and most recently i-vector systems. In all of the identified systems, the posterior probabilities and sufficient statistics calculations represent a computational bottleneck in both enrollment and testing. We propose a multi-layered hash system, employing a tree-structured GMM–UBM which uses Runnalls’ Gaussian mixture reduction technique, in order to reduce the number of these calculations. Moreover, with this tree-structured hash, wemore » can trade-off reduction in computation with a corresponding degradation of equal error rate (EER). As an example, we also reduce this computation by a factor of 15× while incurring less than 10% relative degradation of EER (or 0.3% absolute EER) when evaluated with NIST 2010 speaker recognition evaluation (SRE) telephone data.« less

Reducing computation in an i-vector speaker recognition system using a tree-structured universal background model

DOE PAGES

McClanahan, Richard; De Leon, Phillip L.

2014-08-20

The majority of state-of-the-art speaker recognition systems (SR) utilize speaker models that are derived from an adapted universal background model (UBM) in the form of a Gaussian mixture model (GMM). This is true for GMM supervector systems, joint factor analysis systems, and most recently i-vector systems. In all of the identified systems, the posterior probabilities and sufficient statistics calculations represent a computational bottleneck in both enrollment and testing. We propose a multi-layered hash system, employing a tree-structured GMM–UBM which uses Runnalls’ Gaussian mixture reduction technique, in order to reduce the number of these calculations. Moreover, with this tree-structured hash, wemore » can trade-off reduction in computation with a corresponding degradation of equal error rate (EER). As an example, we also reduce this computation by a factor of 15× while incurring less than 10% relative degradation of EER (or 0.3% absolute EER) when evaluated with NIST 2010 speaker recognition evaluation (SRE) telephone data.« less

Nonperturbative study of the four gluon vertex

NASA Astrophysics Data System (ADS)

Binosi, D.; Ibañez, D.; Papavassiliou, J.

2014-09-01

In this paper we study the nonperturbative structure of the SU(3) four-gluon vertex in the Landau gauge, concentrating on contributions quadratic in the metric. We employ an approximation scheme where "one-loop" diagrams are computed using fully dressed gluon and ghost propagators, and tree-level vertices. When a suitable kinematical configuration depending on a single momentum scale p is chosen, only two structures emerge: the tree-level four-gluon vertex, and a tensor orthogonal to it. A detailed numerical analysis reveals that the form factor associated with this latter tensor displays a change of sign (zero-crossing) in the deep infrared, and finally diverges logarithmically. The origin of this characteristic behavior is proven to be entirely due to the masslessness of the ghost propagators forming the corresponding ghost-loop diagram, in close analogy to a similar effect established for the three-gluon vertex. However, in the case at hand, and under the approximations employed, this particular divergence does not affect the form factor proportional to the tree-level tensor, which remains finite in the entire range of momenta, and deviates moderately from its naive tree-level value. It turns out that the kinematic configuration chosen is ideal for carrying out lattice simulations, because it eliminates from the connected Green's function all one-particle reducible contributions, projecting out the genuine one-particle irreducible vertex. Motivated by this possibility, we discuss in detail how a hypothetical lattice measurement of this quantity would compare to the results presented here, and the potential interference from an additional tensorial structure, allowed by Bose symmetry, but not encountered within our scheme.

From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees

Treesearch

Glenn T. Howe; Sally N. Aitken; David B. Neale; Kathleen D. Jermstad; Nicholas C. Wheeler; Tony H.H Chen

2003-01-01

Adaptation to winter cold in temperate and boreal trees involves complex genetic, physiological, and developmental processes. Genecological studies demonstrate the existence of steep genetic clines for cold adaptation traits in relation to environmental (mostly temperature related) gradients. Population differentiation is generally stronger for cold adaptation traits...

Can gas exchange dynamics predict non-structural carbohydrate use under drought stress?

NASA Astrophysics Data System (ADS)

Kannenberg, S.; Phillips, R.

2016-12-01

A recent conceptual framework for understanding tree drought responses characterizes species along a continuum from isohydry to anisohydry, with theory predicting that isohydric and anisohydric trees should display different carbon (C) allocation patterns under drought conditions. We tested the hypothesis that the trade-offs inherent in the isohydry-anisohydry framework (i.e., C starvation vs. hydraulic failure) necessitate different allocation patterns to non-structural carbohydrates (NSCs), growth, and respiration. Specifically, we hypothesized that isohydric trees would decrease NSC stores and growth in the face of reduced incoming photoassimilate, whereas anisohydric trees would maintain assimilation, growth, and NSC pools due to decreased demand for stored metabolic C and enhanced osmoregulatory needs. To test this, we subjected saplings of Liriodendron tulipifera (an isohydric tree) and Quercus alba (an anisohydric tree) to a six week drought in the greenhouse, and measured assimilation, leaf water potential (midday and predawn), growth, leaf dark respiration and NSCs (both sugars and starch in aboveground and belowground tissues) in control and droughted plants. Overall, we confirmed that the isohydric and anisohydric species used NSCs differently during drought. In most tissues, both species had similar responses of NSCs to drought: starch NSCs were maintained or decreased while sugar NSCs tended to increase. Stem NSCs were a notable exception, as L. tulipifera decreased total NSC to almost zero while NSCs in Q. alba remained constant. This depletion of stem NSC in L. tulipifera was offset by increases in other tissues, however, resulting in no net change to total NSC during the drought. In contrast, Q. alba increased total NSC. Interestingly, Q. alba also decreased assimilation and growth, indicating a potential trade-off between NSC and biomass allocation. Our results show that NSCs in different tissues may have contrasting uses as storage or osmoregulatory compounds. Collectively, our work also demonstrates that NSC dynamics may be coupled to hydraulic strategies and proposes a link between a tree's degree of isohydry, C allocation patterns, and potential mechanisms of tree mortality.

Stem girdling indicates prioritized carbon allocation to the root system at the expense of radial stem growth in Norway spruce under drought conditions

PubMed Central

Oberhuber, Walter; Gruber, Andreas; Lethaus, Gina; Winkler, Andrea; Wieser, Gerhard

2017-01-01

The early culmination of maximum radial growth (RG) in late spring has been found in several coniferous species in a dry inner Alpine environment. We hypothesized that an early decrease in RG is an adaptation to cope with drought stress, which might require an early switch of carbon (C) allocation to belowground organs. To test this hypothesis, we experimentally subjected six-year-old Norway spruce saplings (tree height: 1.35 m; n = 80 trees) to two levels of soil water availability (watered versus drought conditions) and manipulated tree C status by physically blocking phloem transport at three girdling dates (GD). The influence of C availability and drought on tree growth (radial and shoot growth; root biomass) in response to girdling was analyzed in both treatments. Non-structural carbohydrates (NSCs, soluble sugars and starch) were measured in the stem, root and current leader to evaluate changes in tree C status due to girdling. The main finding was a significant increase in RG of the girdled trees compared to the controls above the girdling zone (UZ). At all girdling dates the RG increase was significantly more intense in the drought-stressed compared with watered trees (c. 3.3 and 1.9-fold higher compared with controls in the drought-stressed and watered trees, respectively), most likely indicating that an early switch of C allocation to belowground occurs as an adaptation to maintain tree water status under drought conditions. Reactivation of the cambium after the cessation of its regular activity was detected in UZ in drought-stressed trees, while below the girdling zone no xylem formation was found and the NSC content was strikingly reduced. Irrespective of water availability, girdling before growth onset significantly reduced the progression of bud break (P < 0.05) and the length of the current leader shoot by −47% (P < 0.01) indicating a reduction in xylem hydraulic conductance, which was corroborated by significantly reduced xylem sap flow (P < 0.001). Based on our findings, we conclude that during the growing season drought stress prioritizes an early switch of C allocation to the root system as an adaptation to maintain adequate tree water status in drought-prone environments. PMID:28392608

Analysing the mechanical performance and growth adaptation of Norway spruce using a non-linear finite-element model and experimental data.

PubMed

Lundström, T; Jonas, T; Volkwein, A

2008-01-01

Thirteen Norway spruce [Picea abies (L.) Karst.] trees of different size, age, and social status, and grown under varying conditions, were investigated to see how they react to complex natural static loading under summer and winter conditions, and how they have adapted their growth to such combinations of load and tree state. For this purpose a non-linear finite-element model and an extensive experimental data set were used, as well as a new formulation describing the degree to which the exploitation of the bending stress capacity is uniform. The three main findings were: material and geometric non-linearities play important roles when analysing tree deflections and critical loads; the strengths of the stem and the anchorage mutually adapt to the local wind acting on the tree crown in the forest canopy; and the radial stem growth follows a mechanically high-performance path because it adapts to prevailing as well as acute seasonal combinations of the tree state (e.g. frozen or unfrozen stem and anchorage) and load (e.g. wind and vertical and lateral snow pressure). Young trees appeared to adapt to such combinations in a more differentiated way than older trees. In conclusion, the mechanical performance of the Norway spruce studied was mostly very high, indicating that their overall growth had been clearly influenced by the external site- and tree-specific mechanical stress.

Maximal tree size of few-qubit states

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Organizing Books and Authors by Multilayer SOM.

PubMed

Zhang, Haijun; Chow, Tommy W S; Wu, Q M Jonathan

2016-12-01

This paper introduces a new framework for the organization of electronic books (e-books) and their corresponding authors using a multilayer self-organizing map (MLSOM). An author is modeled by a rich tree-structured representation, and an MLSOM-based system is used as an efficient solution to the organizational problem of structured data. The tree-structured representation formulates author features in a hierarchy of author biography, books, pages, and paragraphs. To efficiently tackle the tree-structured representation, we used an MLSOM algorithm that serves as a clustering technique to handle e-books and their corresponding authors. A book and author recommender system is then implemented using the proposed framework. The effectiveness of our approach was examined in a large-scale data set containing 3868 authors along with the 10500 e-books that they wrote. We also provided visualization results of MLSOM for revealing the relevance patterns hidden from presented author clusters. The experimental results corroborate that the proposed method outperforms other content-based models (e.g., rate adapting poisson, latent Dirichlet allocation, probabilistic latent semantic indexing, and so on) and offers a promising solution to book recommendation, author recommendation, and visualization.

Zero-stress states of human pulmonary arteries and veins.

PubMed

Huang, W; Yen, R T

1998-09-01

The zero-stress states of the pulmonary arteries and veins from order 3 to order 9 were determined in six normal human lungs within 15 h postmortem. The zero-stress state of each vessel was obtained by cutting the vessel transversely into a series of short rings, then cutting each ring radially, which caused the ring to spring open into a sector. Each sector was characterized by its opening angle. The mean opening angle varied between 92 and 163 degrees in the arterial tree and between 89 and 128 degrees in the venous tree. There was a tendency for opening angles to increase as the sizes of the arteries and veins increased. We computed the residual strains based on the experimental measurements and estimated the residual stresses according to Hooke's law. We found that the inner wall of a vessel at the state in which the internal pressure, external pressure, and longitudinal stress are all zero was under compression and the outer wall was in tension, and that the magnitude of compressive stress was greater than the magnitude of tensile stress.

Why Be a Shrub? A Basic Model and Hypotheses for the Adaptive Values of a Common Growth Form

PubMed Central

Götmark, Frank; Götmark, Elin; Jensen, Anna M.

2016-01-01

Shrubs are multi-stemmed short woody plants, more widespread than trees, important in many ecosystems, neglected in ecology compared to herbs and trees, but currently in focus due to their global expansion. We present a novel model based on scaling relationships and four hypotheses to explain the adaptive significance of shrubs, including a review of the literature with a test of one hypothesis. Our model describes advantages for a small shrub compared to a small tree with the same above-ground woody volume, based on larger cross-sectional stem area, larger area of photosynthetic tissue in bark and stem, larger vascular cambium area, larger epidermis (bark) area, and larger area for sprouting, and faster production of twigs and canopy. These components form our Hypothesis 1 that predicts higher growth rate for a small shrub than a small tree. This prediction was supported by available relevant empirical studies (14 publications). Further, a shrub will produce seeds faster than a tree (Hypothesis 2), multiple stems in shrubs insure future survival and growth if one or more stems die (Hypothesis 3), and three structural traits of short shrub stems improve survival compared to tall tree stems (Hypothesis 4)—all hypotheses have some empirical support. Multi-stemmed trees may be distinguished from shrubs by more upright stems, reducing bending moment. Improved understanding of shrubs can clarify their recent expansion on savannas, grasslands, and alpine heaths. More experiments and other empirical studies, followed by more elaborate models, are needed to understand why the shrub growth form is successful in many habitats. PMID:27507981

Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change.

PubMed

Housset, Johann M; Nadeau, Simon; Isabel, Nathalie; Depardieu, Claire; Duchesne, Isabelle; Lenz, Patrick; Girardin, Martin P

2018-04-01

Local adaptation in tree species has been documented through a long history of common garden experiments where functional traits (height, bud phenology) are used as proxies for fitness. However, the ability to identify genes or genomic regions related to adaptation to climate requires the evaluation of traits that precisely reflect how and when climate exerts selective constraints. We combine dendroecology with association genetics to establish a link between genotypes, phenotypes and interannual climatic fluctuations. We illustrate this approach by examining individual tree responses embedded in the annual rings of 233 Pinus strobus trees growing in a common garden experiment representing 38 populations from the majority of its range. We found that interannual variability in growth was affected by low temperatures during spring and autumn, and by summer heat and drought. Among-population variation in climatic sensitivity was significantly correlated with the mean annual temperature of the provenance, suggesting local adaptation. Genotype-phenotype associations using these new tree-ring phenotypes validated nine candidate genes identified in a previous genetic-environment association study. Combining dendroecology with association genetics allowed us to assess tree vulnerability to past climate at fine temporal scales and provides avenues for future genomic studies on functional adaptation in forest trees. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Adaptive Window Zero-Crossing-Based Instantaneous Frequency Estimation

NASA Astrophysics Data System (ADS)

Sekhar, S. Chandra; Sreenivas, TV

2004-12-01

We address the problem of estimating instantaneous frequency (IF) of a real-valued constant amplitude time-varying sinusoid. Estimation of polynomial IF is formulated using the zero-crossings of the signal. We propose an algorithm to estimate nonpolynomial IF by local approximation using a low-order polynomial, over a short segment of the signal. This involves the choice of window length to minimize the mean square error (MSE). The optimal window length found by directly minimizing the MSE is a function of the higher-order derivatives of the IF which are not available a priori. However, an optimum solution is formulated using an adaptive window technique based on the concept of intersection of confidence intervals. The adaptive algorithm enables minimum MSE-IF (MMSE-IF) estimation without requiring a priori information about the IF. Simulation results show that the adaptive window zero-crossing-based IF estimation method is superior to fixed window methods and is also better than adaptive spectrogram and adaptive Wigner-Ville distribution (WVD)-based IF estimators for different signal-to-noise ratio (SNR).

Spectral properties of plant leaves pertaining to urban landscape design of broad-spectrum solar ultraviolet radiation reduction

NASA Astrophysics Data System (ADS)

Yoshimura, Haruka; Zhu, Hui; Wu, Yunying; Ma, Ruijun

2010-03-01

Human exposure to harmful ultraviolet (UV) radiation has important public health implications. Actual human exposure to solar UV radiation depends on ambient UV irradiance, and the latter is influenced by ground reflection. In urban areas with higher reflectivity, UV exposure occurs routinely. To discover the solar UV radiation regulation mechanism of vegetation, the spectral reflectance and transmittance of plant leaves were measured with a spectrophotometer. Typically, higher plants have low leaf reflectance (around 5%) and essentially zero transmittance throughout the UV region regardless of plant species and seasonal change. Accordingly, incident UV radiation decreases to 5% by being reflected and is reduced to zero by passing through a leaf. Therefore, stratified structures of vegetation are working as another terminator of UV rays, protecting whole terrestrial ecosystems, while vegetation at waterfronts contributes to protect aquatic ecosystems. It is possible to protect the human population from harmful UV radiation by urban landscape design of tree shade and the botanical environment. Even thin but uniformly distributed canopy is effective in attenuating UV radiation. To intercept diffuse radiation, UV screening by vertical structures such as hedges should be considered. Reflectivity of vegetation is around 2%, as foliage surfaces reduce incident UV radiation via reflection, while also eliminating it by transmittance. Accordingly, vegetation reduces incident UV radiation to around 2% by reflection. Vegetation influence on ambient UV radiation is broad-spectrum throughout the UV region. Only trees provide cool UV protective shade. Urban landscapes aimed at abating urban heat islands integrated with a reduction of human UV over-exposure would contribute to mitigation of climate change.

Effective Tree Scattering and Opacity at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; O'Neill, Peggy E.; Lang, Roger H.; Joseph, Alicia T.; Cosh, Michael H.; Jackson, Thomas J.

2011-01-01

This paper investigates vegetation effects at L-band by using a first-order radiative transfer (RT) model and truck-based microwave measurements over natural conifer stands to assess the applicability of the tau-omega) model over trees. The tau-omega model is a zero-order RT solution that accounts for vegetation effects with effective vegetation parameters (vegetation opacity and single-scattering albedo), which represent the canopy as a whole. This approach inherently ignores multiple-scattering effects and, therefore, has a limited validity depending on the level of scattering within the canopy. The fact that the scattering from large forest components such as branches and trunks is significant at L-band requires that zero-order vegetation parameters be evaluated (compared) along with their theoretical definitions to provide a better understanding of these parameters in the retrieval algorithms as applied to trees. This paper compares the effective vegetation opacities, computed from multi-angular pine tree brightness temperature data, against the results of two independent approaches that provide theoretical and measured optical depths. These two techniques are based on forward scattering theory and radar corner reflector measurements, respectively. The results indicate that the effective vegetation opacity values are smaller than but of similar magnitude to both radar and theoretical estimates. The effective opacity of the zero-order model is thus set equal to the theoretical opacity and an explicit expression for the effective albedo is then obtained from the zero- and first- order RT model comparison. The resultant albedo is found to have a similar magnitude as the effective albedo value obtained from brightness temperature measurements. However, it is less than half of that estimated using the theoretical calculations (0.5 - 0.6 for tree canopies at L-band). This lower observed albedo balances the scattering darkening effect of the large theoretical albedo with a first-order multiple-scattering contribution. The retrieved effective albedo is different from theoretical definitions and not the albedo of single forest elements anymore, but it becomes a global parameter, which depends on all the processes taking place within the canopy, including multiple-scattering.

Adaptive forest management for drinking water protection under climate change

NASA Astrophysics Data System (ADS)

Koeck, R.; Hochbichler, E.

2012-04-01

Drinking water resources drawn from forested catchment areas are prominent for providing water supply on our planet. Despite the fact that source waters stemming from forested watersheds have generally lower water quality problems than those stemming from agriculturally used watersheds, it has to be guaranteed that the forest stands meet high standards regarding their water protection functionality. For fulfilling these, forest management concepts have to be applied, which are adaptive regarding the specific forest site conditions and also regarding climate change scenarios. In the past century forest management in the alpine area of Austria was mainly based on the cultivation of Norway spruce, by the way neglecting specific forest site conditions, what caused in many cases highly vulnerable mono-species forest stands. The GIS based forest hydrotope model (FoHyM) provides a framework for forest management, which defines the most crucial parameters in a spatial explicit form. FoHyM stratifies the spacious drinking water protection catchments into forest hydrotopes, being operational units for forest management. The primary information layer of FoHyM is the potential natural forest community, which reflects the specific forest site conditions regarding geology, soil types, elevation above sea level, exposition and inclination adequately and hence defines the specific forest hydrotopes. For each forest hydrotope, the adequate tree species composition and forest stand structure for drinking water protection functionality was deduced, based on the plant-sociological information base provided by FoHyM. The most important overall purpose for the related elaboration of adaptive forest management concepts and measures was the improvement of forest stand stability, which can be seen as the crucial parameter for drinking water protection. Only stable forest stands can protect the fragile soil and humus layers and hence prevent erosion process which could endanger the water resources. Forest stands which are formed by a tree species set which conforms to the potential natural forest community are more stable than the currently wide-spread mono-species Norway spruce plantations, especially in times of climate change, where e.g. bark beetle infestations threat spruce with increased intensity. FoHyM also provides the relevant ecological boundary conditions for any estimation of climate change adaptations. The adaptation of the tree species distribution within each forest hydrotope to climate change conditions was fulfilled by the integration of climate change scenarios and the estimation of the eco-physiological characteristics of related tree species. Hence it was possible to define the tree species distribution related to a specific climate change scenario for each forest hydrotope. The silvicultural concepts and measures to accomplish the defined tree species distribution and forest stand structure for each forest hydrotope were defined and elaborated by taking the specific requirements of drinking water protection areas into account, what e.g. comprised the prohibition of the clear cut technique and the application of continuous cover forest management concepts. The overall purpose of these adaptive silvicultural concepts and techniques which were based on the application of FoHyM was the improvement of the water protection functionality of forest stands within drinking water protection zones.

ZeroCal: Automatic MAC Protocol Calibration

NASA Astrophysics Data System (ADS)

Meier, Andreas; Woehrle, Matthias; Zimmerling, Marco; Thiele, Lothar

Sensor network MAC protocols are typically configured for an intended deployment scenario once and for all at compile time. This approach, however, leads to suboptimal performance if the network conditions deviate from the expectations. We present ZeroCal, a distributed algorithm that allows nodes to dynamically adapt to variations in traffic volume. Using ZeroCal, each node autonomously configures its MAC protocol at runtime, thereby trying to reduce the maximum energy consumption among all nodes. While the algorithm is readily usable for any asynchronous low-power listening or low-power probing protocol, we validate and demonstrate the effectiveness of ZeroCal on X-MAC. Extensive testbed experiments and simulations indicate that ZeroCal quickly adapts to traffic variations. We further show that ZeroCal extends network lifetime by 50% compared to an optimal configuration with identical and static MAC parameters at all nodes.

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model.

PubMed

Ingram, T; Harmon, L J; Shurin, J B

2012-09-01

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

PubMed

Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Adaptation, migration or extirpation: climate change outcomes for tree populations

PubMed Central

Aitken, Sally N; Yeaman, Sam; Holliday, Jason A; Wang, Tongli; Curtis-McLane, Sierra

2008-01-01

Abstract Species distribution models predict a wholesale redistribution of trees in the next century, yet migratory responses necessary to spatially track climates far exceed maximum post-glacial rates. The extent to which populations will adapt will depend upon phenotypic variation, strength of selection, fecundity, interspecific competition, and biotic interactions. Populations of temperate and boreal trees show moderate to strong clines in phenology and growth along temperature gradients, indicating substantial local adaptation. Traits involved in local adaptation appear to be the product of small effects of many genes, and the resulting genotypic redundancy combined with high fecundity may facilitate rapid local adaptation despite high gene flow. Gene flow with preadapted alleles from warmer climates may promote adaptation and migration at the leading edge, while populations at the rear will likely face extirpation. Widespread species with large populations and high fecundity are likely to persist and adapt, but will likely suffer adaptational lag for a few generations. As all tree species will be suffering lags, interspecific competition may weaken, facilitating persistence under suboptimal conditions. Species with small populations, fragmented ranges, low fecundity, or suffering declines due to introduced insects or diseases should be candidates for facilitated migration. PMID:25567494

Demographic analysis of tree colonization in a 20-year-old right-of-way.

PubMed

Mercier, C; Brison, J; Bouchard, A

2001-12-01

Past tree colonization dynamics of a powerline-right-of-way (ROW) corridor in the Haut-Saint-Laurent region of Quebec was studied based on the present age distribution of its tree populations. This colonization study spans 20 years, from 1977 (ROW clearance) to 1996. The sampled quadrats were classified into six vegetation types. Tree colonization dynamics were interpreted in each type, and three distinct patterns were identified. (1) Communities adapted to acidic conditions were heavily colonized by Acer rubrum, at least for the last 12 years. (2) Communities adapted to mesic or to hydric conditions were more intensely colonized in the period 1985-1987 than in the following 9 years; this past success in tree colonization may have been caused by herbicide treatments, which could have facilitated tree establishment by damaging the herbaceous and shrub vegetation. (3) Cattail, vine-raspberry, and reed-dominated communities contained few tree individuals, with almost all trees establishing between 1979 and 1990; those three vegetation types appear as the most resistant to tree invasion in the ROW studied. This study supports the need for an integrated approach in ROW vegetation management, in which the selection of vegetation treatment methods would depend on the tree colonization dynamics in each vegetation type. Minimizing disturbances inflicted on ROW herbaceous and shrub covers should be the central strategy because disturbances jeopardize natural resistance to future tree invasion, except in communities adapted to acidic conditions where the existing vegetation does not prevent invasion by A. rubrum. Many trees are surviving the successive cutting operations by producing new sprouts each time, particularly in communities adapted to mesic and hydric conditions. In these cases, mechanical cutting should be replaced by a one-time stump-killing operation, to avoid repeated and unsuccessful treatments of the same individuals over time.

Silvicultural management and the manipulation of rare alleles

Treesearch

Paul G. Schaberg; Gary J. Hawley; Donald H. DeHayes; Samuel E. Nijensohn

2004-01-01

Because rare alleles provide a means for adaptation to environmental change they are often considered important to long-term forest health. Through the selective removal of trees (and genes), silvicultural management may alter the genetic structure of forests, with rare alleles perhaps being uniquely vulnerable to manipulation due to their low frequencies or...

Variation of mobile carbon reserves in trees at the alpine treeline ecotone is under environmental control.

PubMed

Fajardo, Alex; Piper, Frida I; Pfund, Laura; Körner, Christian; Hoch, Günter

2012-09-01

In low temperature-adapted plants, including treeline trees, light-saturated photosynthesis is considerably less sensitive to temperature than growth. As a consequence, all plants tested so far show increased nonstructural carbohydrate (NSC) tissue concentrations when exposed to low temperatures. Reduced carbon supply is thus an unlikely cause for low temperature range limits of plants. For altitudinal treeline trees there is, however, a possibility that high NSC genotypes have been selected. Here, we explored this possibility using afforestations with single-provenance conifers along elevational gradients in the Southern Chilean Andes and the Swiss Alps. Tree growth was measured at each of four approximately equidistant elevations at and below the treeline. Additionally, at the same elevations, needle, branch and stem sapwood tissues were collected to determine NSC concentrations. Overall, growth decreased and NSC concentrations increased with elevation. Along with previous empirical and experimental studies, the findings of this study provide no indication of NSC reduction at the treeline; NSC increased in most species (each represented by one common population) towards their upper climatic limit. The disparity between carbon acquisition and structural carbon investment at low temperature (accumulation of NSC) thus does occur even among genotypes not adapted to treeline environments. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Assisted migration of forest populations for adapting trees to climate change

Treesearch

Cuauhtémoc Sáenz-Romero; Roberto A. Lindig-Cisneros; Dennis G. Joyce; Jean Beaulieu; J. Bradley St. Clair; Barry C. Jaquish

2016-01-01

We present evidence that climatic change is an ongoing process and that forest tree populations are genetically differentiated for quantitative traits because of adaptation to specific habitats. We discuss in detail indications that the shift of suitable climatic habitat for forest tree species and populations, as a result of rapid climatic change, is likely to cause...

Adapting and Evaluating a Tree of Life Group for Women with Learning Disabilities

ERIC Educational Resources Information Center

Randle-Phillips, Cathy; Farquhar, Sarah; Thomas, Sally

2016-01-01

Background: This study describes how a specific narrative therapy approach called 'the tree of life' was adapted to run a group for women with learning disabilities. The group consisted of four participants and ran for five consecutive weeks. Materials and Methods: Participants each constructed a tree to represent their lives and presented their…

A device adaptive inflow boundary condition for Wigner equations of quantum transport

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

Jiang, Haiyan; Lu, Tiao; Cai, Wei, E-mail: wcai@uncc.edu

2014-02-01

In this paper, an improved inflow boundary condition is proposed for Wigner equations in simulating a resonant tunneling diode (RTD), which takes into consideration the band structure of the device. The original Frensley inflow boundary condition prescribes the Wigner distribution function at the device boundary to be the semi-classical Fermi–Dirac distribution for free electrons in the device contacts without considering the effect of the quantum interaction inside the quantum device. The proposed device adaptive inflow boundary condition includes this effect by assigning the Wigner distribution to the value obtained from the Wigner transform of wave functions inside the device atmore » zero external bias voltage, thus including the dominant effect on the electron distribution in the contacts due to the device internal band energy profile. Numerical results on computing the electron density inside the RTD under various incident waves and non-zero bias conditions show much improvement by the new boundary condition over the traditional Frensley inflow boundary condition.« less

Trait shifts associated with the subshrub life-history strategy in a tropical savanna.

PubMed

Giroldo, A B; Scariot, A; Hoffmann, W A

2017-10-01

Over the past 10 million years, tropical savanna environments have selected for small growth forms within woody plant lineages. The result has been the evolution of subshrubs (geoxyles), presumably as an adaptation to frequent fire. To evaluate the traits associated with the shift from tree to subshrub growth forms, we compared seed biomass, germination, survival, resprouting, biomass allocation, and photosynthesis between congeneric trees and subshrubs, and quantified phylogenetic conservatism. Despite large differences in adult morphology between trees and subshrub species, the differences are modest in seedlings, and most of the variation in traits was explained by genus, indicating considerable phylogenic conservatism. Regardless, tree seedlings invested more heavily in aboveground growth, compared to subshrubs, which is consistent with the adult strategy of savanna trees, which depend on a large resistant-fire stem. Subshrub seedlings also invest in greater non-structural carbohydrate reserves, likely as an adaptation to the high fire frequencies typical of tropical savannas. The modest differences as seedlings suggest that selective pressures during early development may not have contributed substantially to the evolution of the subshrub growth form and that the distinct allocation and life history must arise later in life. This is consistent with the interpretation that the subshrub growth form arose as a life-history strategy in which maturity is reached at a small stem size, allowing them to reproduce despite repeated fire-induced topkill. The convergent evolution of subshrubs within multiple tree lineages reaffirms the importance of fire in the origin and diversification of the flora of mesic savannas.

Contributions of a global network of tree diversity experiments to sustainable forest plantations.

PubMed

Verheyen, Kris; Vanhellemont, Margot; Auge, Harald; Baeten, Lander; Baraloto, Christopher; Barsoum, Nadia; Bilodeau-Gauthier, Simon; Bruelheide, Helge; Castagneyrol, Bastien; Godbold, Douglas; Haase, Josephine; Hector, Andy; Jactel, Hervé; Koricheva, Julia; Loreau, Michel; Mereu, Simone; Messier, Christian; Muys, Bart; Nolet, Philippe; Paquette, Alain; Parker, John; Perring, Mike; Ponette, Quentin; Potvin, Catherine; Reich, Peter; Smith, Andy; Weih, Martin; Scherer-Lorenzen, Michael

2016-02-01

The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and disadvantages of mixed species plantations. The network currently consists of 18 experiments, distributed over 36 sites and five ecoregions. With plantations 1-15 years old, TreeDivNet can already provide relevant data for forest policy and management. In this paper, we highlight some early results on the carbon sequestration and pest resistance potential of more diverse plantations. Finally, suggestions are made for new, innovative experiments in understudied regions to complement the existing network.

Threshold-adaptive canny operator based on cross-zero points

NASA Astrophysics Data System (ADS)

Liu, Boqi; Zhang, Xiuhua; Hong, Hanyu

2018-03-01

Canny edge detection[1] is a technique to extract useful structural information from different vision objects and dramatically reduce the amount of data to be processed. It has been widely applied in various computer vision systems. There are two thresholds have to be settled before the edge is segregated from background. Usually, by the experience of developers, two static values are set as the thresholds[2]. In this paper, a novel automatic thresholding method is proposed. The relation between the thresholds and Cross-zero Points is analyzed, and an interpolation function is deduced to determine the thresholds. Comprehensive experimental results demonstrate the effectiveness of proposed method and advantageous for stable edge detection at changing illumination.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase.

PubMed

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross 'Olivière' x 'Arbequina' were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding.

Plasticity in Vegetative Growth over Contrasted Growing Sites of an F1 Olive Tree Progeny during Its Juvenile Phase

PubMed Central

Ben Sadok, Inès; Martinez, Sebastien; Moutier, Nathalie; Garcia, Gilbert; Leon, Lorenzo; Belaj, Angelina; De La Rosa, Raúl; Khadari, Bouchaib; Costes, Evelyne

2015-01-01

Climatic changes impact fruit tree growth and severely limit their production. Investigating the tree ability to cope with environmental variations is thus necessary to adapt breeding and management strategies in order to ensure sustainable production. In this study, we assessed the genetic parameters and genotype by environment interaction (GxE) during the early tree growth. One hundred and twenty olive seedlings derived from the cross ‘Olivière’ x ‘Arbequina’ were examined across two sites with contrasted environments, accounting for ontogenetic trends over three years. Models including the year of growth, branching order, environment, genotype effects, and their interactions were built with variance function and covariance structure of residuals when necessary. After selection of a model, broad sense heritabilities were estimated. Despite strong environmental effect on most traits, no GxE was found. Moreover, the internal structure of traits co-variation was similar in both sites. Ontogenetic growth variation, related to (i) the overall tree form and (ii) the growth and branching habit at growth unit scale, was not altered by the environment. Finally, a moderate to strong genetic control was identified for traits at the whole tree scale and at internode scale. Among all studied traits, the maximal internode length exhibited the highest heritability (H2 = 0.74). Considering the determinant role of this trait in tree architecture and its stability across environments, this study consolidates its relevance for breeding. PMID:26062090

Drought, tree mortality, and wildfire in forests adapted to frequent fire

Treesearch

Scott L Stephens; Brandon M Collins; Christopher J Fettig; Mark A Finney; Chad M Hoffman; Eric E Knapp; Malcolm P North; Hugh Safford; Rebecca B Wayman

2018-01-01

Massive tree mortality has occurred rapidly in frequent-fire-adapted forests of the Sierra Nevada, California. This mortality is a product of acute drought compounded by the long-established removal of a key ecosystem process: frequent, low- to moderate-intensity fire. The recent tree mortality has many implications for the future of these forests and the ecological...

Restoration over time and sustainability of Schinus terebinthifolius Raddi.

PubMed

Álvares-Carvalho, S V; Silva-Mann, R; Gois, I B; Melo, M F V; Oliveira, A S; Ferreira, R A; Gomes, L J

2017-05-31

The success of recovery programs on degraded areas is dependent on the genetic material to be used, which should present heterozygosity and genetic diversity in native and recovered populations. This study was carried out to evaluate the model efficiency to enable the recovery of a degraded area of the Lower São Francisco, Sergipe, Brazil. The target species for this study was Schinus terebinthifolius Raddi. Three populations were analyzed, the recovered area, seed-tree source population, and native tree population border established to the recovered area. The random amplified polymorphic DNA (RAPD) markers were used for diversity analysis. Genetic structure was estimated to evaluate the level of genetic variability existent in each population. There was no correlation between the spatial distribution and the genetic distances for all trees of the recovered area. The heterozygosity present in the recovered population was higher than the native tree population. The seed-tree source population presents genetic bottlenecks. Three clusters were suggested (ΔK = 3) with non-genetic structure. High intra-population genetic variability and inter-population differentiation are present. However, gene flow may also introduce potentially adaptive alleles in the populations of the recovered area, and the native population is necessary to ensure the sustainability and maintenance of the populations by allelic exchange.

Trees as methane sources: A case study of West Siberian South taiga

NASA Astrophysics Data System (ADS)

Churkina, A. I.; Mochenov, S. Yu; Sabrekov, S. F.; Glagolev, M. V.; Il’yasov, D. V.; Terentieva, I. E.; Maksyutov, S. S.

2018-03-01

Within this study, we were measuring methane emission from the tree trunks, leaves and branches in the seasonally flooded forest and in the forested bogs (pine-shrub-sphagnum ecosystems or “ryams”) in south taiga zone of Western Siberia. Our results suggest that the tree trunks may act as a methane conductor from the soil to the atmosphere bypassing the methanotrophically active zones of soil. The tree methane flux depends on a trunk diameter and an ecosystem type. The average methane emission from tree trunks was 0.0061±0.0003 mg CH4·m-2·h-1 per unit of ground area. The methane emission from branches and leaves was zero.

The applicability of ordinary least squares to consistently short distances between taxa in phylogenetic tree construction and the normal distribution test consequences.

PubMed

Roux, C Z

2009-05-01

Short phylogenetic distances between taxa occur, for example, in studies on ribosomal RNA-genes with slow substitution rates. For consistently short distances, it is proved that in the completely singular limit of the covariance matrix ordinary least squares (OLS) estimates are minimum variance or best linear unbiased (BLU) estimates of phylogenetic tree branch lengths. Although OLS estimates are in this situation equal to generalized least squares (GLS) estimates, the GLS chi-square likelihood ratio test will be inapplicable as it is associated with zero degrees of freedom. Consequently, an OLS normal distribution test or an analogous bootstrap approach will provide optimal branch length tests of significance for consistently short phylogenetic distances. As the asymptotic covariances between branch lengths will be equal to zero, it follows that the product rule can be used in tree evaluation to calculate an approximate simultaneous confidence probability that all interior branches are positive.

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor.

PubMed

Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben; Paina, Cristiana; Rudi, Heidi; Rognli, Odd-Arne; Fjellheim, Siri; Sandve, Simen R

2013-09-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence (P < 0.05). Genome-wide heterogeneity in substitution rates was also observed, reflecting divergent genome evolution processes within these grasses. Our results provide evidence for a link between adaptation to cold habitats and adaptive evolution of LTI stress responses in early Pooideae evolution and shed light on a poorly understood chapter in the evolutionary history of some of the world's most important temperate crops. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Indirect learning control for nonlinear dynamical systems

NASA Technical Reports Server (NTRS)

Ryu, Yeong Soon; Longman, Richard W.

1993-01-01

In a previous paper, learning control algorithms were developed based on adaptive control ideas for linear time variant systems. The learning control methods were shown to have certain advantages over their adaptive control counterparts, such as the ability to produce zero tracking error in time varying systems, and the ability to eliminate repetitive disturbances. In recent years, certain adaptive control algorithms have been developed for multi-body dynamic systems such as robots, with global guaranteed convergence to zero tracking error for the nonlinear system euations. In this paper we study the relationship between such adaptive control methods designed for this specific class of nonlinear systems, and the learning control problem for such systems, seeking to converge to zero tracking error in following a specific command repeatedly, starting from the same initial conditions each time. The extension of these methods from the adaptive control problem to the learning control problem is seen to be trivial. The advantages and disadvantages of using learning control based on such adaptive control concepts for nonlinear systems, and the use of other currently available learning control algorithms are discussed.

A domain-specific compiler for a parallel multiresolution adaptive numerical simulation environment

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

Rajbhandari, Samyam; Kim, Jinsung; Krishnamoorthy, Sriram

This paper describes the design and implementation of a layered domain-specific compiler to support MADNESS---Multiresolution ADaptive Numerical Environment for Scientific Simulation. MADNESS is a high-level software environment for the solution of integral and differential equations in many dimensions, using adaptive and fast harmonic analysis methods with guaranteed precision. MADNESS uses k-d trees to represent spatial functions and implements operators like addition, multiplication, differentiation, and integration on the numerical representation of functions. The MADNESS runtime system provides global namespace support and a task-based execution model including futures. MADNESS is currently deployed on massively parallel supercomputers and has enabled many science advances.more » Due to the highly irregular and statically unpredictable structure of the k-d trees representing the spatial functions encountered in MADNESS applications, only purely runtime approaches to optimization have previously been implemented in the MADNESS framework. This paper describes a layered domain-specific compiler developed to address some performance bottlenecks in MADNESS. The newly developed static compile-time optimizations, in conjunction with the MADNESS runtime support, enable significant performance improvement for the MADNESS framework.« less

Tree die-off in response to global change-type drought: Mortality insights from a decade of plant water potential measurements

USGS Publications Warehouse

Breshears, D.D.; Myers, O.B.; Meyer, Clifton W.; Barnes, F.J.; Zou, C.B.; Allen, Craig D.; McDowell, N.G.; Pockman, W. T.

2009-01-01

Global climate change is projected to produce warmer, longer, and more frequent droughts, referred to here as “global change-type droughts”, which have the potential to trigger widespread tree die-off. However, drought-induced tree mortality cannot be predicted with confidence, because long-term field observations of plant water stress prior to, and culminating in, mortality are rare, precluding the development and testing of mechanisms. Here, we document plant water stress in two widely distributed, co-occurring species, piñon pine (Pinus edulis) and juniper (Juniperus monosperma), over more than a decade, leading up to regional-scale die-off of piñon pine trees in response to global change-related drought. Piñon leaf water potentials remained substantially below their zero carbon assimilation point for at least 10 months prior to dying, in contrast to those of juniper, which rarely dropped below their zero-assimilation point. These data suggest that piñon mortality was driven by protracted water stress, leading to carbon starvation and associated increases in susceptibility to other disturbances (eg bark beetles), a finding that should help to improve predictions of mortality during drought.

Defining old growth for fire-adapted forests of the Western United States

Treesearch

Merrill R. Kaufmann; Daniel Binkley; Peter Z. Fule; Johnson Marlin; Scott L. Stephens; Thomas W. Swetnam

2007-01-01

There are varying definitions of old-growth forests because of differences in environment and differing fire influence across the Intermountain West. Two general types of forests reflect the role of fire: 1) forests shaped by natural changes in structure and species makeup-plant succession-that are driven by competitive differences among species and individual trees...

Tree Changes or Wholesale Changes: The Role of Adult Education in Transitions in Regional Life

ERIC Educational Resources Information Center

Townsend, Robert; Delves, Melinda

2009-01-01

Regional adult education and training providers have been required in recent decades to adapt to funding structures rather than engage with their local communities. This has meant providing education programs that are funded based on national or State and Territory based policy frameworks, often linked to human capital development. Adult education…

Design and testing of botanical thermotropic actuator mechanisms in thermally adaptive building coverings

NASA Astrophysics Data System (ADS)

Barrett, Ronald M.; Barrett, Ronald P.; Barrett, Cassandra M.

2017-09-01

This paper lays out the inspiration, operational principles, analytical modeling and coupon testing of a new class of thermally adaptive building coverings. The fundamental driving concepts for these coverings are derived from various families of thermotropic plant structures. Certain plant cellular structures like those in Mimosa pudica (Sensitive Plant), Rhododendron leaves or Albizia julibrissin (Mimosa Tree), exhibit actuation physiology which depends on changes in cellular turgor pressures to generate motion. This form of cellular action via turgor pressure manipulation is an inspiration for a new field of thermally adaptive building coverings which use various forms of cellular foam to aid or enable actuation much like plant cells are used to move leaves. When exposed to high solar loading, the structures use the inherent actuation capability of pockets of air trapped in closed cell foam as actuators to curve plates upwards and outwards. When cold, these same structures curve back towards the building forming large convex pockets of dead air to insulate the building. This paper describes basic classical laminated plate theory models comparing theory and experiment of such coupons containing closed-cell foam actuators. The study concludes with a global description of the effectiveness of this class of thermally adaptive building coverings.

Trees wanted--dead or alive! Host selection and population dynamics in tree-killing bark beetles.

PubMed

Kausrud, Kyrre L; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between "endemic" and "epidemic" regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.

Adaptability of 14 tree species to two hydrol humic latosol soils in Hawaii.

Treesearch

Craig O. Whitesell; Jr. Myron O. Ishennrood

1971-01-01

Tree species capable of thriving on soils in high rainfall areas are needed in Hawaii for reforestation. The soils are highly leached and infertile.Two native and 12 introduced tree species were planted at two sites to determine adaptability. Survival, growth, vigor, and form were appraised 1 to 7 years after planting. Performance varied-both within and between species...

Molecular and Metabolic Adaptations of Lactococcus lactis at Near-Zero Growth Rates

PubMed Central

Ercan, Onur; Wels, Michiel; Smid, Eddy J.

2014-01-01

This paper describes the molecular and metabolic adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state by using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentations during retentostat cultivation, which appeared to be controlled at the level of transcription of the corresponding pyruvate dissipation-encoding genes. During retentostat cultivation, cells continued to consume several amino acids but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in L. lactis KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero-growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end products) study provides molecular understanding of the adaptation of L. lactis to conditions supporting low growth rates and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates toward gene regulation patterns involved in zero-growth adaptation. PMID:25344239

Structuration of lipid bases with fully hydrogenated crambe oil and sorbitan monostearate for obtaining zero-trans/low sat fats.

PubMed

Stahl, Marcella Aparecida; Buscato, Monise Helen Masuchi; Grimaldi, Renato; Cardoso, Lisandro Pavie; Ribeiro, Ana Paula Badan

2018-05-01

Several studies have shown that excessive intake of trans and saturated fatty acids is associated with an increased risk of cardiovascular disease. In this context, the food industry has sought alternatives for the development of healthy lipid bases, with higher levels of unsaturated fatty acids, adapting to current legislation. The incorporation of structuring agents into liquid oils has proven to be a potential alternative for obtaining semi-plastic lipid bases with reduced levels of saturated fatty acids. Thus, the objective of this study was to produce zero trans fat bases with lower saturated fatty acids levels. Palm oil (PO) was used as a zero trans-lipid base reference because of its technological functionality. Blends containing different proportions of high oleic sunflower oil (HOSO) and PO were prepared as follows: control 100: 0; 80:20; 60:40; 40:60; 20:80; and 100: 0 PO: HOSO (w/w%), respectively. Then, 3% of fully hydrogenated crambe oil (FHCO) and 3% sorbitan monostearate (SMS) were added to the blends as structuring agents, forming the structured (S) blends. The addition of HOSO to the PO decreased the saturated fatty acids by up to 30.6%, with consequent increase of unsaturated fatty acids, especially oleic acid. The joint action of the SMS and the FCHO allowed for obtaining structured blends with plastic and spreadability characteristics, as well as modifications throughout the crystallization process of the original blends. Copyright © 2018 Elsevier Ltd. All rights reserved.

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill

PubMed Central

González-Martínez, Santiago C.; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G.; Verdú, Miguel; Pausas, Juli G.

2017-01-01

Background and Aims The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Methods Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Key Results Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. Conclusions An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. PMID:28159988

An O(log sup 2 N) parallel algorithm for computing the eigenvalues of a symmetric tridiagonal matrix

NASA Technical Reports Server (NTRS)

Swarztrauber, Paul N.

1989-01-01

An O(log sup 2 N) parallel algorithm is presented for computing the eigenvalues of a symmetric tridiagonal matrix using a parallel algorithm for computing the zeros of the characteristic polynomial. The method is based on a quadratic recurrence in which the characteristic polynomial is constructed on a binary tree from polynomials whose degree doubles at each level. Intervals that contain exactly one zero are determined by the zeros of polynomials at the previous level which ensures that different processors compute different zeros. The exact behavior of the polynomials at the interval endpoints is used to eliminate the usual problems induced by finite precision arithmetic.

Water relations and photosynthetic performance in Larix sibirica growing in the forest-steppe ecotone of northern Mongolia.

PubMed

Dulamsuren, Choimaa; Hauck, Markus; Bader, Martin; Osokhjargal, Dalaikhuu; Oyungerel, Shagjjav; Nyambayar, Suran; Runge, Michael; Leuschner, Christoph

2009-01-01

Shoot water relations were studied in Siberian larch (Larix sibirica Ledeb.) trees growing at the borderline between taiga and steppe in northern Mongolia. Larix sibirica is the main tree species in these forests covering 80% of Mongolia's forested area. Minimum shoot water potentials (Psi(m)) close to the point of zero turgor (Psi(0)) repeatedly recorded throughout the growing season suggest that the water relations in L. sibirica were often critical. The Psi(m) varied in close relation to the atmospheric vapor pressure deficit, whereas Psi(0) was correlated with monthly precipitation. Young larch trees growing at the forest line to the steppe were more susceptible to drought than mature trees at the same sites. Furthermore, isolated trees growing on the steppe exhibited lower Psi(m) and recovered to a lower degree from drought overnight than the trees at the forest line. Indications of drought stress in L. sibirica were obtained in two study areas in Mongolia's forest-steppe ecotone: one in the mountain taiga of the western Khentey in northernmost Mongolia, the other in the forest-steppe at the southern distribution limit of L. sibirica on Mt. Bogd Uul, southern Khentey. Larix sibirica growing in riverine taiga with contact to the groundwater table was better water-supplied than the larch trees growing at the forest line to the steppe. Larch trees from the interior of light taiga forests on north-facing slopes, however, exhibited more critical water relations than the trees at the forest line. Frequent drought stress in mature trees and even more in young larch trees at the forest-steppe borderline suggests that L. sibirica does not have the potential to encroach on the steppe under the present climate, except in a sequence of exceptionally moist and cool years. A regression of the present borderline between forest and steppe is likely to occur, as average temperatures are increasing everywhere and precipitation is decreasing regionally in Mongolia's taiga forest region. Higher stomatal conductance concomitant to lower Psi(m) in trees of northern-slope forests compared to trees from the forest line to the steppe may be the result of a recent increase in drought intensity that affects better drought-adapted trees at the forest edge less than the trees in the forest interior. We conclude that drought is a key factor explaining the forest-steppe borderline in northern Mongolia. The proportion of forests within the present vegetation pattern of forests on north-facing slopes and the grasslands on south-facing slopes in Mongolia's forest-steppe ecotone is not likely to increase under the present climate, but may decrease with increasing aridity due to global warming.

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster.

PubMed

Santos-del-Blanco, L; Climent, J; González-Martínez, S C; Pannell, J R

2012-11-01

The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted across a broad geographical range of the Mediterranean conifer species Pinus pinaster. In particular, the study investigates whether this monoecious species varies genetically among populations in terms of whether individuals start to reproduce through their male function, their female function or both sexual functions simultaneously. Whether differences among populations could be attributed to local adaptation across a climatic gradient is then considered. Male and female reproduction and growth were measured during early stages of sexual maturity of a P. pinaster common garden comprising 23 populations sampled across the species range. Generalized linear mixed models were used to assess genetic variability of early reproductive life-history traits. Environmental correlations with reproductive life-history traits were tested after controlling for neutral genetic structure provided by 12 nuclear simple sequence repeat markers. Trees tended to reproduce first through their male function, at a size (height) that varied little among source populations. The transition to female reproduction was slower, showed higher levels of variability and was negatively correlated with vegetative growth traits. Several female reproductive traits were correlated with a gradient of growth conditions, even after accounting for neutral genetic structure, with populations from more unfavourable sites tending to commence female reproduction at a lower individual size. The study represents the first report of genetic variability among populations for differences in the threshold size for first reproduction between male and female sexual functions in a tree species. The relatively uniform size at which individuals begin reproducing through their male function probably represents the fact that pollen dispersal is also relatively invariant among sites. However, the genetic variability in the timing of female reproduction probably reflects environment-dependent costs of cone production. The results also suggest that early sex allocation in this species might evolve under constraints that do not apply to other conifers.

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster

PubMed Central

Santos-del-Blanco, L.; Climent, J.; González-Martínez, S. C.; Pannell, J. R.

2012-01-01

Background and Aims The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted across a broad geographical range of the Mediterranean conifer species Pinus pinaster. In particular, the study investigates whether this monoecious species varies genetically among populations in terms of whether individuals start to reproduce through their male function, their female function or both sexual functions simultaneously. Whether differences among populations could be attributed to local adaptation across a climatic gradient is then considered. Methods Male and female reproduction and growth were measured during early stages of sexual maturity of a P. pinaster common garden comprising 23 populations sampled across the species range. Generalized linear mixed models were used to assess genetic variability of early reproductive life-history traits. Environmental correlations with reproductive life-history traits were tested after controlling for neutral genetic structure provided by 12 nuclear simple sequence repeat markers. Key Results Trees tended to reproduce first through their male function, at a size (height) that varied little among source populations. The transition to female reproduction was slower, showed higher levels of variability and was negatively correlated with vegetative growth traits. Several female reproductive traits were correlated with a gradient of growth conditions, even after accounting for neutral genetic structure, with populations from more unfavourable sites tending to commence female reproduction at a lower individual size. Conclusions The study represents the first report of genetic variability among populations for differences in the threshold size for first reproduction between male and female sexual functions in a tree species. The relatively uniform size at which individuals begin reproducing through their male function probably represents the fact that pollen dispersal is also relatively invariant among sites. However, the genetic variability in the timing of female reproduction probably reflects environment-dependent costs of cone production. The results also suggest that early sex allocation in this species might evolve under constraints that do not apply to other conifers. PMID:23002272

Semantic Segmentation of Forest Stands of Pure Species as a Global Optimization Problem

NASA Astrophysics Data System (ADS)

Dechesne, C.; Mallet, C.; Le Bris, A.; Gouet-Brunet, V.

2017-05-01

Forest stand delineation is a fundamental task for forest management purposes, that is still mainly manually performed through visual inspection of geospatial (very) high spatial resolution images. Stand detection has been barely addressed in the literature which has mainly focused, in forested environments, on individual tree extraction and tree species classification. From a methodological point of view, stand detection can be considered as a semantic segmentation problem. It offers two advantages. First, one can retrieve the dominant tree species per segment. Secondly, one can benefit from existing low-level tree species label maps from the literature as a basis for high-level object extraction. Thus, the semantic segmentation issue becomes a regularization issue in a weakly structured environment and can be formulated in an energetical framework. This papers aims at investigating which regularization strategies of the literature are the most adapted to delineate and classify forest stands of pure species. Both airborne lidar point clouds and multispectral very high spatial resolution images are integrated for that purpose. The local methods (such as filtering and probabilistic relaxation) are not adapted for such problem since the increase of the classification accuracy is below 5%. The global methods, based on an energy model, tend to be more efficient with an accuracy gain up to 15%. The segmentation results using such models have an accuracy ranging from 96% to 99%.

D Semantic Labeling of ALS Data Based on Domain Adaption by Transferring and Fusing Random Forest Models

NASA Astrophysics Data System (ADS)

Wu, J.; Yao, W.; Zhang, J.; Li, Y.

2018-04-01

Labeling 3D point cloud data with traditional supervised learning methods requires considerable labelled samples, the collection of which is cost and time expensive. This work focuses on adopting domain adaption concept to transfer existing trained random forest classifiers (based on source domain) to new data scenes (target domain), which aims at reducing the dependence of accurate 3D semantic labeling in point clouds on training samples from the new data scene. Firstly, two random forest classifiers were firstly trained with existing samples previously collected for other data. They were different from each other by using two different decision tree construction algorithms: C4.5 with information gain ratio and CART with Gini index. Secondly, four random forest classifiers adapted to the target domain are derived through transferring each tree in the source random forest models with two types of operations: structure expansion and reduction-SER and structure transfer-STRUT. Finally, points in target domain are labelled by fusing the four newly derived random forest classifiers using weights of evidence based fusion model. To validate our method, experimental analysis was conducted using 3 datasets: one is used as the source domain data (Vaihingen data for 3D Semantic Labelling); another two are used as the target domain data from two cities in China (Jinmen city and Dunhuang city). Overall accuracies of 85.5 % and 83.3 % for 3D labelling were achieved for Jinmen city and Dunhuang city data respectively, with only 1/3 newly labelled samples compared to the cases without domain adaption.

Biological Races in Humans

PubMed Central

Templeton, Alan R.

2013-01-01

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race. PMID:23684745

Tree-oriented interactive processing with an application to theorem-proving, appendix E

NASA Technical Reports Server (NTRS)

Hammerslag, David; Kamin, Samuel N.; Campbell, Roy H.

1985-01-01

The concept of unstructured structure editing and ted, an editor for unstructured trees, is described. Ted is used to manipulate hierarchies of information in an unrestricted manner. The tool was implemented and applied to the problem of organizing formal proofs. As a proof management tool, it maintains the validity of a proof and its constituent lemmas independently from the methods used to validate the proof. It includes an adaptable interface which may be used to invoke theorem provers and other aids to proof construction. Using ted, a user may construct, maintain, and verify formal proofs using a variety of theorem provers, proof checkers, and formatters.

Kinetic solvers with adaptive mesh in phase space

NASA Astrophysics Data System (ADS)

Arslanbekov, Robert R.; Kolobov, Vladimir I.; Frolova, Anna A.

2013-12-01

An adaptive mesh in phase space (AMPS) methodology has been developed for solving multidimensional kinetic equations by the discrete velocity method. A Cartesian mesh for both configuration (r) and velocity (v) spaces is produced using a “tree of trees” (ToT) data structure. The r mesh is automatically generated around embedded boundaries, and is dynamically adapted to local solution properties. The v mesh is created on-the-fly in each r cell. Mappings between neighboring v-space trees is implemented for the advection operator in r space. We have developed algorithms for solving the full Boltzmann and linear Boltzmann equations with AMPS. Several recent innovations were used to calculate the discrete Boltzmann collision integral with dynamically adaptive v mesh: the importance sampling, multipoint projection, and variance reduction methods. We have developed an efficient algorithm for calculating the linear Boltzmann collision integral for elastic and inelastic collisions of hot light particles in a Lorentz gas. Our AMPS technique has been demonstrated for simulations of hypersonic rarefied gas flows, ion and electron kinetics in weakly ionized plasma, radiation and light-particle transport through thin films, and electron streaming in semiconductors. We have shown that AMPS allows minimizing the number of cells in phase space to reduce the computational cost and memory usage for solving challenging kinetic problems.

Dynamics of a temperate deciduous forest under landscape-scale management: Implications for adaptability to climate change

Treesearch

Matthew G. Olson; Benjamin O. Knapp; John M. Kabrick

2017-01-01

Landscape forest management is an approach to meeting diverse objectives that collectively span multiple spatial scales. It is critical that we understand the long-term effects of landscape management on the structure and composition of forest tree communities to ensure that these practices are sustainable. Furthermore, it is increasingly important to also consider...

Vulnerability and resilience to droughts in South-West USA: carbon allocation and impact on wood and evaporative anatomy

NASA Astrophysics Data System (ADS)

Guerin, M. F.; von Arx, G.; McDowell, N. G.; Pockman, W.; Andreu-Hayles, L.; Gentine, P.

2015-12-01

Survival and distribution of conifers across the globe will depend on their adaptive potential to the new climatic conditions (warmer, more droughts, heat waves). Recent studies predicting forest evolution have mainly focused on understanding tree mortality processes (hydraulic failure, carbon starvation, biotic stresses). These explicit causes of mortality are also the result of unsuccessful adaptation on a longer period. Using a 7 years drought-irrigation experiment in New Mexico, USA, we investigated the response to water availability on structure-function interactions at the tree level. Bridging dendrology and physiology on multiple individuals of local Pinion pine, we observe a structural dynamics in i) wood anatomy ii) evaporative anatomy and a resulting functional dynamics in i) leaf water potential and ii) water use efficiency on multiple time scales (daily to interannual). These results emphasize the tight coupling between carbon allocation and the surface hydrologic cycle on longer time scales and its impact on resilience and mortality, which is not included in current generation land-surface models. figure: Wood anatomy obtained from a 5.2mm core of a Pinion Edulis from the experimental site - illustrating the variability of the water transport capacities accross years

Photoperiodic growth control in perennial trees.

PubMed

Azeez, Abdul; Sane, Aniruddha P

2015-01-01

Plants have to cope with changing seasons and adverse environmental conditions. Being sessile, plants have developed elaborate mechanisms for their survival that allow them to sense and adapt to the environment and reproduce successfully. A major adaptive trait for the survival of trees of temperate and boreal forests is the induction of growth cessation in anticipation of winters. In the last few years enormous progress has been made to elucidate the molecular mechanisms underlying SDs induced growth cessation in model perennial tree hybrid aspen (Populus tremula × P. tremuloides). In this review we discuss the molecular mechanism underlying photoperiodic control of growth cessation and adaptive responses.

EM Adaptive LASSO—A Multilocus Modeling Strategy for Detecting SNPs Associated with Zero-inflated Count Phenotypes

PubMed Central

Mallick, Himel; Tiwari, Hemant K.

2016-01-01

Count data are increasingly ubiquitous in genetic association studies, where it is possible to observe excess zero counts as compared to what is expected based on standard assumptions. For instance, in rheumatology, data are usually collected in multiple joints within a person or multiple sub-regions of a joint, and it is not uncommon that the phenotypes contain enormous number of zeroes due to the presence of excessive zero counts in majority of patients. Most existing statistical methods assume that the count phenotypes follow one of these four distributions with appropriate dispersion-handling mechanisms: Poisson, Zero-inflated Poisson (ZIP), Negative Binomial, and Zero-inflated Negative Binomial (ZINB). However, little is known about their implications in genetic association studies. Also, there is a relative paucity of literature on their usefulness with respect to model misspecification and variable selection. In this article, we have investigated the performance of several state-of-the-art approaches for handling zero-inflated count data along with a novel penalized regression approach with an adaptive LASSO penalty, by simulating data under a variety of disease models and linkage disequilibrium patterns. By taking into account data-adaptive weights in the estimation procedure, the proposed method provides greater flexibility in multi-SNP modeling of zero-inflated count phenotypes. A fast coordinate descent algorithm nested within an EM (expectation-maximization) algorithm is implemented for estimating the model parameters and conducting variable selection simultaneously. Results show that the proposed method has optimal performance in the presence of multicollinearity, as measured by both prediction accuracy and empirical power, which is especially apparent as the sample size increases. Moreover, the Type I error rates become more or less uncontrollable for the competing methods when a model is misspecified, a phenomenon routinely encountered in practice. PMID:27066062

EM Adaptive LASSO-A Multilocus Modeling Strategy for Detecting SNPs Associated with Zero-inflated Count Phenotypes.

PubMed

Mallick, Himel; Tiwari, Hemant K

2016-01-01

Count data are increasingly ubiquitous in genetic association studies, where it is possible to observe excess zero counts as compared to what is expected based on standard assumptions. For instance, in rheumatology, data are usually collected in multiple joints within a person or multiple sub-regions of a joint, and it is not uncommon that the phenotypes contain enormous number of zeroes due to the presence of excessive zero counts in majority of patients. Most existing statistical methods assume that the count phenotypes follow one of these four distributions with appropriate dispersion-handling mechanisms: Poisson, Zero-inflated Poisson (ZIP), Negative Binomial, and Zero-inflated Negative Binomial (ZINB). However, little is known about their implications in genetic association studies. Also, there is a relative paucity of literature on their usefulness with respect to model misspecification and variable selection. In this article, we have investigated the performance of several state-of-the-art approaches for handling zero-inflated count data along with a novel penalized regression approach with an adaptive LASSO penalty, by simulating data under a variety of disease models and linkage disequilibrium patterns. By taking into account data-adaptive weights in the estimation procedure, the proposed method provides greater flexibility in multi-SNP modeling of zero-inflated count phenotypes. A fast coordinate descent algorithm nested within an EM (expectation-maximization) algorithm is implemented for estimating the model parameters and conducting variable selection simultaneously. Results show that the proposed method has optimal performance in the presence of multicollinearity, as measured by both prediction accuracy and empirical power, which is especially apparent as the sample size increases. Moreover, the Type I error rates become more or less uncontrollable for the competing methods when a model is misspecified, a phenomenon routinely encountered in practice.

Root architecture and wind-firmness of mature Pinus pinaster.

PubMed

Danjon, Frédéric; Fourcaud, Thierry; Bert, Didier

2005-11-01

This study aims to link three-dimensional coarse root architecture to tree stability in mature timber trees with an average of 1-m rooting depth. Undamaged and uprooted trees were sampled in a stand damaged by a storm. Root architecture was measured by three-dimensional (3-D) digitizing. The distribution of root volume by root type and in wind-oriented sectors was analysed. Mature Pinus pinaster root systems were organized in a rigid 'cage' composed of a taproot, the zone of rapid taper of horizontal surface roots and numerous sinkers and deep roots, imprisoning a large mass of soil and guyed by long horizontal surface roots. Key compartments for stability exhibited strong selective leeward or windward reinforcement. Uprooted trees showed a lower cage volume, a larger proportion of oblique and intermediate depth horizontal roots and less wind-oriented root reinforcement. Pinus pinaster stability on moderately deep soils is optimized through a typical rooting pattern and a considerable structural adaptation to the prevailing wind and soil profile.

Efficient Delaunay Tessellation through K-D Tree Decomposition

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

Morozov, Dmitriy; Peterka, Tom

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

Epigenetic regulation of adaptive responses of forest tree species to the environment

PubMed Central

Bräutigam, Katharina; Vining, Kelly J; Lafon-Placette, Clément; Fossdal, Carl G; Mirouze, Marie; Marcos, José Gutiérrez; Fluch, Silvia; Fraga, Mario Fernández; Guevara, M Ángeles; Abarca, Dolores; Johnsen, Øystein; Maury, Stéphane; Strauss, Steven H; Campbell, Malcolm M; Rohde, Antje; Díaz-Sala, Carmen; Cervera, María-Teresa

2013-01-01

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change. PMID:23467802

Trees Wanted—Dead or Alive! Host Selection and Population Dynamics in Tree-Killing Bark Beetles

PubMed Central

Kausrud, Kyrre L.; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr.

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between “endemic” and “epidemic” regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics. PMID:21647433

Comparative height crown allometry and mechanical design in 22 tree species of Kuala Belalong rainforest, Brunei, Borneo.

PubMed

Osunkoya, Olusegun O; Omar-Ali, Kharunnisa; Amit, Norratna; Dayan, Juita; Daud, Dayanawati S; Sheng, Tan K

2007-12-01

In rainforests, trunk size, strength, crown position, and geometry of a tree affect light interception and the likelihood of mechanical failure. Allometric relationships of tree diameter, wood density, and crown architecture vs. height are described for a diverse range of rainforest trees in Brunei, northern Borneo. The understory species follow a geometric model in their diameter-height relationship (slope, β = 1.08), while the stress-elasticity models prevail (β = 1.27-1.61) for the midcanopy and canopy/emergent species. These relationships changed with ontogeny, especially for the understory species. Within species, the tree stability safety factor (SSF) and relative crown width decreased exponentially with increasing tree height. These trends failed to emerge in across-species comparisons and were reversed at a common (low) height. Across species, the relative crown depth decreased with maximum potential height and was indistinguishable at a common (low) height. Crown architectural traits influence SSF more than structural property of wood density. These findings emphasize the importance of applying a common reference size in comparative studies and suggest that forest trees (especially the understory group) may adapt to low light by having deeper rather than wider crowns due to an efficient distribution and geometry of their foliage.

Genomics of Tropical Fruit Tree Crops

USDA-ARS?s Scientific Manuscript database

The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

Convergence of bark investment according to fire and climate structures ecosystem vulnerability to future change.

PubMed

Pellegrini, Adam F A; Anderegg, William R L; Paine, C E Timothy; Hoffmann, William A; Kartzinel, Tyler; Rabin, Sam S; Sheil, Douglas; Franco, Augusto C; Pacala, Stephen W

2017-03-01

Fire regimes in savannas and forests are changing over much of the world. Anticipating the impact of these changes requires understanding how plants are adapted to fire. In this study, we test whether fire imposes a broad selective force on a key fire-tolerance trait, bark thickness, across 572 tree species distributed worldwide. We show that investment in thick bark is a pervasive adaptation in frequently burned areas across savannas and forests in both temperate and tropical regions where surface fires occur. Geographic variability in bark thickness is largely explained by annual burned area and precipitation seasonality. Combining environmental and species distribution data allowed us to assess vulnerability to future climate and fire conditions: tropical rainforests are especially vulnerable, whereas seasonal forests and savannas are more robust. The strong link between fire and bark thickness provides an avenue for assessing the vulnerability of tree communities to fire and demands inclusion in global models. © 2017 John Wiley & Sons Ltd/CNRS.

Structural Analysis Of CD59 Of Chinese Tree Shrew: A New Reference Molecule For Human Immune System Specific CD59 Drug Discovery.

PubMed

Panda, Subhamay; Kumari, Leena; Panda, Santamay

2017-11-17

Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquires shared common as well as unique characteristics, and hence offers a genetic basis for employing this animal as a prospective model for biomedical research. CD59 glycoprotein, commonly referred to as MAC-inhibitory protein (MAC-IP), membrane inhibitor of reactive lysis (MIRL), or protectin, is encoded by the CD59 gene in human beings. It is the member of the LY6/uPAR/alpha-neurotoxin protein family. With this initial point the objective of this study was to determine a comparative composite based structure of CD59 of Chinese tree shrew. The additional objective of this study was to examine the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the assistance of several bioinformatical analytical tools. CD59 Amino acid sequence of Chinese tree shrew collected from the online database system of National Centre for Biotechnology Information. SignalP 4.0 online server was employed for detection of signal peptide instance within the protein sequence of CD59. Molecular model structure of CD59 protein was generated by the Iterative Threading ASSEmbly Refinement (I-TASSER) suite. The confirmation for three-dimensional structural model was evaluated by structure validation tools. Location of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of Chimera tool. Electrostatic potential analysis was carried out with the adaptive Poisson-Boltzmann solver package. Subsequently validated model was used for the functionally critical amino acids and active site prediction. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) was determined using the COACH program. Analysis of Ramachandran plot for Chinese tree shrew depicted that overall, 100% of the residues in homology model were observed in allowed and favored regions, sequentially leading to the validation of the standard of generated protein structural model. In case of CD59 of Chinese tree shrew, the total score of G-factor was found to be -0.66 that was generally larger than the acceptable value. This approach suggests the significance and acceptability of the modeled structure of CD59 of Chinese tree shrew. The molecular model data in cooperation to other relevant post model analysis data put forward molecular insight to protecting activity of CD59 protein molecule of Chinese tree shrew. In the present study, we have proposed the first molecular model structure of uncharted CD59 of Chinese tree shrew by significantly utilizing the comparative composite modeling approach. Therefore, the development of a structural model of the CD59 protein was carried out and analyzed further for deducing molecular enrichment technique. The collaborative effort of molecular model and other relevant data of post model analysis carry forward molecular understanding to protecting activity of CD59 functions towards better insight of features of this natural lead compound. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Blacks Mountain Experimental Forest: bark beetle responses to differences in forest structure and the application of prescribed fire in interior ponderosa pine

Treesearch

Christopher J. Fettig; Robert R. Borys; Stephen R. McKelvey; Christopher P. Dabney

2008-01-01

Mechanical thinning and the application of prescribed fire are commonly used tools in the restoration of fire-adapted forest ecosystems. However, few studies have explored their effects on subsequent amounts of bark beetle caused tree mortality in interior ponderosa pine, Pinus ponderosa Dougl. ex P. & C. Laws. var. ponderosa. In...

Automatic segmentation of airway tree based on local intensity filter and machine learning technique in 3D chest CT volume.

PubMed

Meng, Qier; Kitasaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Ueno, Junji; Mori, Kensaku

2017-02-01

Airway segmentation plays an important role in analyzing chest computed tomography (CT) volumes for computerized lung cancer detection, emphysema diagnosis and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3D airway tree structure from a CT volume is quite a challenging task. Several researchers have proposed automated airway segmentation algorithms basically based on region growing and machine learning techniques. However, these methods fail to detect the peripheral bronchial branches, which results in a large amount of leakage. This paper presents a novel approach for more accurate extraction of the complex airway tree. This proposed segmentation method is composed of three steps. First, Hessian analysis is utilized to enhance the tube-like structure in CT volumes; then, an adaptive multiscale cavity enhancement filter is employed to detect the cavity-like structure with different radii. In the second step, support vector machine learning will be utilized to remove the false positive (FP) regions from the result obtained in the previous step. Finally, the graph-cut algorithm is used to refine the candidate voxels to form an integrated airway tree. A test dataset including 50 standard-dose chest CT volumes was used for evaluating our proposed method. The average extraction rate was about 79.1 % with the significantly decreased FP rate. A new method of airway segmentation based on local intensity structure and machine learning technique was developed. The method was shown to be feasible for airway segmentation in a computer-aided diagnosis system for a lung and bronchoscope guidance system.

Adaptive Dynamic Programming for Discrete-Time Zero-Sum Games.

PubMed

Wei, Qinglai; Liu, Derong; Lin, Qiao; Song, Ruizhuo

2018-04-01

In this paper, a novel adaptive dynamic programming (ADP) algorithm, called "iterative zero-sum ADP algorithm," is developed to solve infinite-horizon discrete-time two-player zero-sum games of nonlinear systems. The present iterative zero-sum ADP algorithm permits arbitrary positive semidefinite functions to initialize the upper and lower iterations. A novel convergence analysis is developed to guarantee the upper and lower iterative value functions to converge to the upper and lower optimums, respectively. When the saddle-point equilibrium exists, it is emphasized that both the upper and lower iterative value functions are proved to converge to the optimal solution of the zero-sum game, where the existence criteria of the saddle-point equilibrium are not required. If the saddle-point equilibrium does not exist, the upper and lower optimal performance index functions are obtained, respectively, where the upper and lower performance index functions are proved to be not equivalent. Finally, simulation results and comparisons are shown to illustrate the performance of the present method.

Zero-knowledge cooperation in dilemma games.

PubMed

Huck, Steffen; Normann, Hans Theo; Oechssler, Jorg

2003-01-07

We consider a very simple adaptive rule that induces cooperative behavior in a large class of dilemma games. The rule has a Pavlovian flavor and can be described as win-continue, lose-reverse. It assumes no knowledge about the underlying structure of the environment (the "rules of the game") and requires very little cognitive effort. Both features make it an appealing candidate for explaining the emergence of cooperative behavior in non-human species. Copyright 2003 Elsevier Science Ltd.

Development of a photogrammetric method of measuring tree taper outside bark

Treesearch

David R. Larsen

2006-01-01

A photogrammetric method is presented for measuring tree diameters outside bark using calibrated control ground-based digital photographs. The method was designed to rapidly collect tree taper information from subject trees for the development of tree taper equations. Software that is commercially available, but designed for a different purpose, can be readily adapted...

Adaptive responses and disruptive effects: how major wildfire influences kinship-based social interactions in a forest marsupial.

PubMed

Banks, Sam C; Blyton, Michaela D J; Blair, David; McBurney, Lachlan; Lindenmayer, David B

2012-02-01

Environmental disturbance is predicted to play a key role in the evolution of animal social behaviour. This is because disturbance affects key factors underlying social systems, such as demography, resource availability and genetic structure. However, because natural disturbances are unpredictable there is little information on their effects on social behaviour in wild populations. Here, we investigated how a major wildfire affected cooperation (sharing of hollow trees) by a hollow-dependent marsupial. We based two alternative social predictions on the impacts of fire on population density, genetic structure and resources. We predicted an adaptive social response from previous work showing that kin selection in den-sharing develops as competition for den resources increases. Thus, kin selection should occur in burnt areas because the fire caused loss of the majority of hollow-bearing trees, but no detectable mortality. Alternatively, fire may have a disruptive social effect, whereby postfire home range-shifts 'neutralize' fine-scale genetic structure, thereby removing opportunities for kin selection between neighbours. Both predictions occurred: the disruptive social effect in burnt habitat and the adaptive social response in adjacent unburnt habitat. The latter followed a massive demographic influx to unburnt 'refuge' habitat that increased competition for dens, leading to a density-related kin selection response. Our results show remarkable short-term plasticity of animal social behaviour and demonstrate how the social effects of disturbance extend into undisturbed habitat owing to landscape-scale demographic shifts. We predicted long-term changes in kinship-based cooperative behaviour resulting from the genetic and resource impacts of forecast changes to fire regimes in these forests. © 2011 Blackwell Publishing Ltd.

Climate-related genetic variation in a threatened tree species, Pinus albicaulis

Treesearch

Marcus V. Warwell; Ruth G. Shaw

2017-01-01

PREMISE OF THE STUDY: With ongoing climate change, understanding of intraspecific adaptive variation is critical for conservation and restoration of plant species. Such information is especially scarce for threatened and endangered tree species, such as Pinus albicaulis Engelm. Therefore, our principal aims were to assess adaptive variation and characterize its...

The red-cockaded woodpecker cavity tree: A very special pine

Treesearch

Richard N. Conner; D. Craig Rudolph; Daniel Saenz; Robert H. Johnson

2004-01-01

The adaptation of red-cockaded woodpeckers (Picoides borealis) to fire-maintained southern pine ecosystems has included the development of behaviors that permit the species to use living pines for their cavity trees. Their adaptation to pine ecosystems has also involved a major adjustment in the species' breeding system to cooperative breeding,...

How oaks respond to water limitation

Treesearch

Michael F. Allen

2015-01-01

Oaks are extremely resilient trees. They have persisted since the mid-Cretaceous, with life forms ranging from shrubs to large trees, from evergreen to deciduous. They have two distinct, but critical, adaptations to drought that make this "mesic" taxon adaptable to dry hot environments. First, they form both arbuscular and ectotrophic mycorrhizae, with a high...

Planning the future's forests with assisted migration

Treesearch

Mary I. Williams; R. Kasten Dumroese

2014-01-01

Studies show that changes in climate may exceed plant adaptation and migration. The mismatch in rates between climate change and plant adaptation and migration will pose significant challenges for practitioners that select, grow, and outplant native tree species. Native tree species and populations that are planted today must meet the climatic challenges that they will...

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests.

PubMed

Wills, Christopher; Harms, Kyle E; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S; Erickson, David; Kress, W John; Hubbell, Stephen P; Gunatilleke, C V Savitri; Gunatilleke, I A U Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species' gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees' lifetimes.

Retinal optical coherence tomography image enhancement via shrinkage denoising using double-density dual-tree complex wavelet transform

PubMed Central

Mayer, Markus A.; Boretsky, Adam R.; van Kuijk, Frederik J.; Motamedi, Massoud

2012-01-01

Abstract. Image enhancement of retinal structures, in optical coherence tomography (OCT) scans through denoising, has the potential to aid in the diagnosis of several eye diseases. In this paper, a locally adaptive denoising algorithm using double-density dual-tree complex wavelet transform, a combination of the double-density wavelet transform and the dual-tree complex wavelet transform, is applied to reduce speckle noise in OCT images of the retina. The algorithm overcomes the limitations of commonly used multiple frame averaging technique, namely the limited number of frames that can be recorded due to eye movements, by providing a comparable image quality in significantly less acquisition time equal to an order of magnitude less time compared to the averaging method. In addition, improvements of image quality metrics and 5 dB increase in the signal-to-noise ratio are attained. PMID:23117804

Retinal optical coherence tomography image enhancement via shrinkage denoising using double-density dual-tree complex wavelet transform.

PubMed

Chitchian, Shahab; Mayer, Markus A; Boretsky, Adam R; van Kuijk, Frederik J; Motamedi, Massoud

2012-11-01

ABSTRACT. Image enhancement of retinal structures, in optical coherence tomography (OCT) scans through denoising, has the potential to aid in the diagnosis of several eye diseases. In this paper, a locally adaptive denoising algorithm using double-density dual-tree complex wavelet transform, a combination of the double-density wavelet transform and the dual-tree complex wavelet transform, is applied to reduce speckle noise in OCT images of the retina. The algorithm overcomes the limitations of commonly used multiple frame averaging technique, namely the limited number of frames that can be recorded due to eye movements, by providing a comparable image quality in significantly less acquisition time equal to an order of magnitude less time compared to the averaging method. In addition, improvements of image quality metrics and 5 dB increase in the signal-to-noise ratio are attained.

Tropical Tree Trait Diversity Enhances Forest Biomass Resilience in a Dynamic Global Vegetation Model

NASA Astrophysics Data System (ADS)

Sakschewski, B.; Kirsten, T.; von Bloh, W.; Poorter, L.; Pena-Claros, M.; Boit, A.

2016-12-01

Functional diversity of ecosystems has been found to increase ecosystem functions and therefore enhance ecosystem resilience against environmental stressors. However, global carbon-cycle and biosphere models still classify the global vegetation into a relatively small number of distinct plant functional types (PFT) with constant features over space and time. Therefore, those models might underestimate the resilience and adaptive capacity of natural vegetation under climate change by ignoring positive effects that functional diversity might bring about. We diversified a set a of selected tree traits in a dynamic global vegetation model (LPJmL). In the new subversion, called LPJmL-FIT, Amazon region biomass stocks and forest structure appear significantly more resilient against climate change. Enhanced tree trait diversity enables the simulated rainforests to adjust to new environmental conditions via ecological sorting. These results may stimulate a new debate on the value of biodiversity for climate change mitigation.

Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges

PubMed Central

Griffin, Philippa C.; Hoffmann, Ary A.

2014-01-01

Background and Aims While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone. Methods Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses. Key Results Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5–1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group. Conclusions The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations. PMID:24607721

Speed tracking and synchronization of multiple motors using ring coupling control and adaptive sliding mode control.

PubMed

Li, Le-Bao; Sun, Ling-Ling; Zhang, Sheng-Zhou; Yang, Qing-Quan

2015-09-01

A new control approach for speed tracking and synchronization of multiple motors is developed, by incorporating an adaptive sliding mode control (ASMC) technique into a ring coupling synchronization control structure. This control approach can stabilize speed tracking of each motor and synchronize its motion with other motors' motion so that speed tracking errors and synchronization errors converge to zero. Moreover, an adaptive law is exploited to estimate the unknown bound of uncertainty, which is obtained in the sense of Lyapunov stability theorem to minimize the control effort and attenuate chattering. Performance comparisons with parallel control, relative coupling control and conventional PI control are investigated on a four-motor synchronization control system. Extensive simulation results show the effectiveness of the proposed control scheme. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

The control of the controller: molecular mechanisms for robust perfect adaptation and temperature compensation.

PubMed

Ni, Xiao Yu; Drengstig, Tormod; Ruoff, Peter

2009-09-02

Organisms have the property to adapt to a changing environment and keep certain components within a cell regulated at the same level (homeostasis). "Perfect adaptation" describes an organism's response to an external stepwise perturbation by regulating some of its variables/components precisely to their original preperturbation values. Numerous examples of perfect adaptation/homeostasis have been found, as for example, in bacterial chemotaxis, photoreceptor responses, MAP kinase activities, or in metal-ion homeostasis. Two concepts have evolved to explain how perfect adaptation may be understood: In one approach (robust perfect adaptation), the adaptation is a network property, which is mostly, but not entirely, independent of rate constant values; in the other approach (nonrobust perfect adaptation), a fine-tuning of rate constant values is needed. Here we identify two classes of robust molecular homeostatic mechanisms, which compensate for environmental variations in a controlled variable's inflow or outflow fluxes, and allow for the presence of robust temperature compensation. These two classes of homeostatic mechanisms arise due to the fact that concentrations must have positive values. We show that the concept of integral control (or integral feedback), which leads to robust homeostasis, is associated with a control species that has to work under zero-order flux conditions and does not necessarily require the presence of a physico-chemical feedback structure. There are interesting links between the two identified classes of homeostatic mechanisms and molecular mechanisms found in mammalian iron and calcium homeostasis, indicating that homeostatic mechanisms may underlie similar molecular control structures.

Adaptive feedforward control of non-minimum phase structural systems

NASA Astrophysics Data System (ADS)

Vipperman, J. S.; Burdisso, R. A.

1995-06-01

Adaptive feedforward control algorithms have been effectively applied to stationary disturbance rejection. For structural systems, the ideal feedforward compensator is a recursive filter which is a function of the transfer functions between the disturbance and control inputs and the error sensor output. Unfortunately, most control configurations result in a non-minimum phase control path; even a collocated control actuator and error sensor will not necessarily produce a minimum phase control path in the discrete domain. Therefore, the common practice is to choose a suitable approximation of the ideal compensator. In particular, all-zero finite impulse response (FIR) filters are desirable because of their inherent stability for adaptive control approaches. However, for highly resonant systems, large order filters are required for broadband applications. In this work, a control configuration is investigated for controlling non-minimum phase lightly damped structural systems. The control approach uses low order FIR filters as feedforward compensators in a configuration that has one more control actuator than error sensors. The performance of the controller was experimentally evaluated on a simply supported plate under white noise excitation for a two-input, one-output (2I1O) system. The results show excellent error signal reduction, attesting to the effectiveness of the method.

Automation of Hessian-Based Tubularity Measure Response Function in 3D Biomedical Images.

PubMed

Dzyubak, Oleksandr P; Ritman, Erik L

2011-01-01

The blood vessels and nerve trees consist of tubular objects interconnected into a complex tree- or web-like structure that has a range of structural scale 5 μm diameter capillaries to 3 cm aorta. This large-scale range presents two major problems; one is just making the measurements, and the other is the exponential increase of component numbers with decreasing scale. With the remarkable increase in the volume imaged by, and resolution of, modern day 3D imagers, it is almost impossible to make manual tracking of the complex multiscale parameters from those large image data sets. In addition, the manual tracking is quite subjective and unreliable. We propose a solution for automation of an adaptive nonsupervised system for tracking tubular objects based on multiscale framework and use of Hessian-based object shape detector incorporating National Library of Medicine Insight Segmentation and Registration Toolkit (ITK) image processing libraries.

ADAPT

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

Reynolds, John; Jankovsky, Zachary; Metzroth, Kyle G

2018-04-04

The purpose of the ADAPT code is to generate Dynamic Event Trees (DET) using a user specified set of simulators. ADAPT can utilize any simulation tool which meets a minimal set of requirements. ADAPT is based on the concept of DET which uses explicit modeling of the deterministic dynamic processes that take place during a nuclear reactor plant system (or other complex system) evolution along with stochastic modeling. When DET are used to model various aspects of Probabilistic Risk Assessment (PRA), all accident progression scenarios starting from an initiating event are considered simultaneously. The DET branching occurs at user specifiedmore » times and/or when an action is required by the system and/or the operator. These outcomes then decide how the dynamic system variables will evolve in time for each DET branch. Since two different outcomes at a DET branching may lead to completely different paths for system evolution, the next branching for these paths may occur not only at separate times, but can be based on different branching criteria. The computational infrastructure allows for flexibility in ADAPT to link with different system simulation codes, parallel processing of the scenarios under consideration, on-line scenario management (initiation as well as termination), analysis of results, and user friendly graphical capabilities. The ADAPT system is designed for a distributed computing environment; the scheduler can track multiple concurrent branches simultaneously. The scheduler is modularized so that the DET branching strategy can be modified (e.g. biasing towards the worst-case scenario/event). Independent database systems store data from the simulation tasks and the DET structure so that the event tree can be constructed and analyzed later. ADAPT is provided with a user-friendly client which can easily sort through and display the results of an experiment, precluding the need for the user to manually inspect individual simulator runs.« less

phyloXML: XML for evolutionary biology and comparative genomics

PubMed Central

Han, Mira V; Zmasek, Christian M

2009-01-01

Background Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. Results We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. Conclusion PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at . PMID:19860910

Potential Effects of Drought on Tree Dieback in Great Britain and Implications for Forest Management in Adaptation to Climate Change

NASA Astrophysics Data System (ADS)

Yu, Jianjun; Berry, Pam

2017-04-01

The drought and heat stress has alerted the composition, structure and biogeography of forests globally, whilst the projected severe and widespread droughts are potentially increasing. This challenges the sustainable forest management to better cope with future climate and maintain the forest ecosystem functions and services. Many studies have investigated the climate change impacts on forest ecosystem but less considered the climate extremes like drought. In this study, we implement a dynamic ecosystem model based on a version of LPJ-GUESS parameterized with European tree species and apply to Great Britain at a finer spatial resolution of 5*5 km. The model runs for the baseline from 1961 to 2011 and projects to the latter 21st century using 100 climate scenarios generated from MaRIUS project to tackle the climate model uncertainty. We will show the potential impacts of climate change on forest ecosystem and vegetation transition in Great Britain by comparing the modelled conditions in the 2030s and the 2080s relative to the baseline. In particular, by analyzing the modelled tree mortality, we will show the tree dieback patterns in response to drought for various species, and assess their drought vulnerability across Great Britain. We also use species distribution modelling to project the suitable climate space for selected tree species using the same climate scenarios. Aided by these two modelling approaches and based on the corresponding modelling results, we will discuss the implications for adaptation strategy for forest management, especially in extreme drought conditions. The gained knowledge and lessons for Great Britain are considered to be transferable in many other regions.

Cold adaptation recorded in tree rings highlights risks associated with climate change and assisted migration.

PubMed

Montwé, David; Isaac-Renton, Miriam; Hamann, Andreas; Spiecker, Heinrich

2018-04-23

With lengthening growing seasons but increased temperature variability under climate change, frost damage to plants may remain a risk and could be exacerbated by poleward planting of warm-adapted seed sources. Here, we study cold adaptation of tree populations in a wide-ranging coniferous species in western North America to inform limits to seed transfer. Using tree-ring signatures of cold damage from common garden trials designed to study genetic population differentiation, we find opposing geographic clines for spring frost and fall frost damage. Provenances from northern regions are sensitive to spring frosts, while the more productive provenances from central and southern regions are more susceptible to fall frosts. Transferring the southern, warm-adapted genotypes northward causes a significant loss of growth and a permanent rank change after a spring frost event. We conclude that cold adaptation should remain an important consideration when implementing seed transfers designed to mitigate harmful effects of climate change.

Safety assurance of non-deterministic flight controllers in aircraft applications

NASA Astrophysics Data System (ADS)

Noriega, Alfonso

Loss of control is a serious problem in aviation that primarily affects General Aviation. Technological advancements can help mitigate the problem, but the FAA certification process makes certain solutions economically unfeasible. This investigation presents the design of a generic adaptive autopilot that could potentially lead to a single certification for use in several makes and models of aircraft. The autopilot consists of a conventional controller connected in series with a robust direct adaptive model reference controller. In this architecture, the conventional controller is tuned once to provide outer-loop guidance and navigation to a reference model. The adaptive controller makes unknown aircraft behave like the reference model, allowing the conventional controller to successfully provide navigation without the need for retuning. A strong theoretical foundation is presented as an argument for the safety and stability of the controller. The stability proof of direct adaptive controllers require that the plant being controlled has no unstable transmission zeros and has a nonzero high frequency gain. Because most conventional aircraft do not readily meet these requirements, a process known as sensor blending was used. Sensor blending consists of using a linear combination of the plant's outputs that has no unstable transmission zeros and has a nonzero high frequency gain to drive the adaptive controller. Although this method does not present a problem for regulators, it can lead to a steady state error in tracking applications. The sensor blending theory was expanded to take advantage of the system's dynamics to allow for zero steady state error tracking. This method does not need knowledge of the specific system's dynamics, but instead uses the structure of the A and B matrices to perform the blending for the general case. The generic adaptive autopilot was tested in two high-fidelity nonlinear simulators of two typical General Aviation aircraft. The results show that the autopilot was able to adapt appropriately to the different aircraft and was able to perform three-dimensional navigation and an ILS approach, without any modification to the controller. The autopilot was tested in moderate atmospheric turbulence, using consumer-grade sensors and actuators currently available in General Aviation aircraft. The generic adaptive autopilot was shown to be robust to atmospheric turbulence and sensor and actuator random noise. In both aircraft simulators, the autopilot adapted successfully to changes in airspeed, altitude, and configuration. This investigation proves the feasibility of a generic autopilot using direct adaptive controller. The autopilot does not need a priori information of the specific aircraft's dynamics to maintain its safety and stability arguments. Real-time parameter estimation of the aircraft dynamics are not needed. Recommendations for future work are provided.

Identification and characterization of toll-like receptors (TLRs) in the Chinese tree shrew (Tupaia belangeri chinensis).

PubMed

Yu, Dandan; Wu, Yong; Xu, Ling; Fan, Yu; Peng, Li; Xu, Min; Yao, Yong-Gang

2016-07-01

In mammals, the toll-like receptors (TLRs) play a major role in initiating innate immune responses against pathogens. Comparison of the TLRs in different mammals may help in understanding the TLR-mediated responses and developing of animal models and efficient therapeutic measures for infectious diseases. The Chinese tree shrew (Tupaia belangeri chinensis), a small mammal with a close relationship to primates, is a viable experimental animal for studying viral and bacterial infections. In this study, we characterized the TLRs genes (tTLRs) in the Chinese tree shrew and identified 13 putative TLRs, which are orthologs of mammalian TLR1-TLR9 and TLR11-TLR13, and TLR10 was a pseudogene in tree shrew. Positive selection analyses using the Maximum likelihood (ML) method showed that tTLR8 and tTLR9 were under positive selection, which might be associated with the adaptation to the pathogen challenge. The mRNA expression levels of tTLRs presented an overall low and tissue-specific pattern, and were significantly upregulated upon Hepatitis C virus (HCV) infection. tTLR4 and tTLR9 underwent alternative splicing, which leads to different transcripts. Phylogenetic analysis and TLR structure prediction indicated that tTLRs were evolutionarily conserved, which might reflect an ancient mechanism and structure in the innate immune response system. Taken together, TLRs had both conserved and unique features in the Chinese tree shrew. Copyright © 2016 Elsevier Ltd. All rights reserved.

An efficient Adaptive Mesh Refinement (AMR) algorithm for the Discontinuous Galerkin method: Applications for the computation of compressible two-phase flows

NASA Astrophysics Data System (ADS)

Papoutsakis, Andreas; Sazhin, Sergei S.; Begg, Steven; Danaila, Ionut; Luddens, Francky

2018-06-01

We present an Adaptive Mesh Refinement (AMR) method suitable for hybrid unstructured meshes that allows for local refinement and de-refinement of the computational grid during the evolution of the flow. The adaptive implementation of the Discontinuous Galerkin (DG) method introduced in this work (ForestDG) is based on a topological representation of the computational mesh by a hierarchical structure consisting of oct- quad- and binary trees. Adaptive mesh refinement (h-refinement) enables us to increase the spatial resolution of the computational mesh in the vicinity of the points of interest such as interfaces, geometrical features, or flow discontinuities. The local increase in the expansion order (p-refinement) at areas of high strain rates or vorticity magnitude results in an increase of the order of accuracy in the region of shear layers and vortices. A graph of unitarian-trees, representing hexahedral, prismatic and tetrahedral elements is used for the representation of the initial domain. The ancestral elements of the mesh can be split into self-similar elements allowing each tree to grow branches to an arbitrary level of refinement. The connectivity of the elements, their genealogy and their partitioning are described by linked lists of pointers. An explicit calculation of these relations, presented in this paper, facilitates the on-the-fly splitting, merging and repartitioning of the computational mesh by rearranging the links of each node of the tree with a minimal computational overhead. The modal basis used in the DG implementation facilitates the mapping of the fluxes across the non conformal faces. The AMR methodology is presented and assessed using a series of inviscid and viscous test cases. Also, the AMR methodology is used for the modelling of the interaction between droplets and the carrier phase in a two-phase flow. This approach is applied to the analysis of a spray injected into a chamber of quiescent air, using the Eulerian-Lagrangian approach. This enables us to refine the computational mesh in the vicinity of the droplet parcels and accurately resolve the coupling between the two phases.

Adaptive fine root foraging patterns in climate experiments and natural gradients

NASA Astrophysics Data System (ADS)

Ostonen, Ivika; Truu, Marika; Parts, Kaarin; Truu, Jaak

2017-04-01

Site based manipulative experiments and studies along climatic gradients have long been keystones of ecological research. We aimed to compare the response of ectomycorrhizal (EcM) and fine roots in manipulative studies and along climate gradient to describe the universal trends in root traits and to raise hypotheses about general mechanisms in fine root system adaptation of forest trees in global change. The root traits from two climate manipulation experiments - Bangor FACE and FAHM in Estonia, manipulated by CO2 concentration and relative air humidity in silver birch forest ecosystems, respectively and the data for three most ubiquitous tree species - Norway spruce (Picea abies), Scots pine (Pinus sylvestris) and silver birch (Betula pendula) stands along natural gradient encompassing different climate and forest zones in Northern Europe were analysed. There are two main strategies in response of fine root system of trees: A) an extensive increase in absorptive root biomass, surface area and length, or B) a greater reliance on root-associated EcM fungi and bacterial communities with a smaller investment to absorptive root biomass. Trees in all studies tended to increase the EcM root biomass and the proportion of EcM root biomass of total fine root biomass towards harsh (northern boreal forests) or changed conditions (stress created by the increase in CO2 concentration or relative air humidity). We envisage a role of trilateral relation between the morphological traits of absorptive fine roots, exploration types of colonising EcM fungi and rhizosphere and bulk soil bacterial community structure. A significant change in EcM absorptive fine root biomass in all experiments and for all studied tree species coincided with changes in absorptive root morphology, being longer and thinner root tips with higher root tissue density in poor/treated sites. These changes were associated with significant shifts in community structure of dominating EcM fungi as well as soil and rhizosphere bacterial communities. We suggest a multidimensional concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in root-mycorhizosphere along environmental gradients and in climate experiments.

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests

PubMed Central

Wills, Christopher; Harms, Kyle E.; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S.; Erickson, David; Kress, W. John; Hubbell, Stephen P.; Gunatilleke, C. V. Savitri; Gunatilleke, I. A. U. Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species’ gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees’ lifetimes. PMID:27305092

Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

PubMed

Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

2017-04-01

The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Tree Species for Plantations in the Grantic Uplands of Puerto Rico

Treesearch

T. F. Geary; C. B. Briscoe

1972-01-01

Thirty-two tree species were tested for adaptability in Puerto Rico's humid, granitic uplands, a region of sandy, well drained, erosive soils. Based on adaptability and potential wood uses the following species are recommended for timber plantations: Honduras pine for most landowners; mahoe for those willing to speculate on development of a demand for this cabinet...

Planning the future's forests with assisted migration [Chapter 8

Treesearch

Mary I. Williams; R. Kasten Dumroese

2016-01-01

If the climate changes faster than the adaptation or migration capability of plants (Zhu et al. 2012; Gray and Hamann 2013), foresters and other land managers will face an overwhelming challenge. Growing trees that survive may become more important than growing perfectly formed trees (Hebda 2008) and may require selection of adapted plant materials and/or assisting the...

Is local best? Examining the evidence for local adaptation in trees and its scale

Treesearch

David Boshier; Linda Broadhurst; Jonathan Cornelius; Leonardo Gallo; Jarkko Koskela; Judy Loo; Gillian Petrokofsky; Brad St. Clair

2015-01-01

Background: Although the importance of using local provenance planting stock for woodland production, habitat conservation and restoration remains contentious, the concept is easy to understand, attractive and easy to ‘sell’. With limited information about the extent and scale of adaptive variation in native trees, discussion about suitable...

Patterns of Cross-Continental Variation in Tree Seed Mass in the Canadian Boreal Forest

PubMed Central

Liu, Jushan; Bai, Yuguang; Lamb, Eric G.; Simpson, Dale; Liu, Guofang; Wei, Yongsheng; Wang, Deli; McKenney, Daniel W.; Papadopol, Pia

2013-01-01

Seed mass is an adaptive trait affecting species distribution, population dynamics and community structure. In widely distributed species, variation in seed mass may reflect both genetic adaptation to local environments and adaptive phenotypic plasticity. Acknowledging the difficulty in separating these two aspects, we examined the causal relationships determining seed mass variation to better understand adaptability and/or plasticity of selected tree species to spatial/climatic variation. A total of 504, 481 and 454 seed collections of black spruce (Picea mariana (Mill.) B.S.P.), white spruce (Picea glauca (Moench) Voss) and jack pine (Pinus banksiana Lamb) across the Canadian Boreal Forest, respectively, were selected. Correlation analyses were used to determine how seed mass vary with latitude, longitude, and altitude. Structural Equation Modeling was used to examine how geographic and climatic variables influence seed mass. Climatic factors explained a large portion of the variation in seed mass (34, 14 and 29%, for black spruce, white spruce and jack pine, respectively), indicating species-specific adaptation to long term climate conditions. Higher annual mean temperature and winter precipitation caused greater seed mass in black spruce, but annual precipitation was the controlling factor for white spruce. The combination of factors such as growing season temperature and evapotranspiration, temperature seasonality and annual precipitation together determined seed mass of jack pine. Overall, sites with higher winter temperatures were correlated with larger seeds. Thus, long-term climatic conditions, at least in part, determined spatial variation in seed mass. Black spruce and Jack pine, species with relatively more specific habitat requirements and less plasticity, had more variation in seed mass explained by climate than did the more plastic species white spruce. As traits such as seed mass are related to seedling growth and survival, they potentially influence forest species composition in a changing climate and should be included in future modeling of vegetation shifts. PMID:23593392

Non-serotinous woody plants behave as aerial seed bank species when a late-summer wildfire coincides with a mast year.

PubMed

Pounden, Edith; Greene, David F; Michaletz, Sean T

2014-10-01

Trees which lack obvious fire-adaptive traits such as serotinous seed-bearing structures or vegetative resprouting are assumed to be at a dramatic disadvantage in recolonization via sexual recruitment after fire, because seed dispersal is invariably quite constrained. We propose an alternative strategy in masting tree species with woody cones or cone-like structures: that the large clusters of woody tissue in a mast year will sufficiently impede heat transfer that a small fraction of seeds can survive the flaming front passage; in a mast year, this small fraction would be a very large absolute number.In Kootenay National Park in British Columbia, we examined regeneration by Engelmann spruce (Picea engelmannii), a non-serotinous conifer, after two fires, both of which coincided with mast years. Coupling models of seed survivorship within cones and seed maturation schedule to a spatially realistic recruitment model, we show that (1) the spatial pattern of seedlings on a 630 m transect from the forest edge into the burn was best explained if there was in situ seed dissemination by burnt trees; (2) in areas several hundred meters from any living trees, recruitment density was well correlated with local prefire cone density; and (3) spruce was responding exactly like its serotinous codominant, lodgepole pine (Pinus contorta).We conclude that non-serotinous species can indeed behave like aerial seed bank species in mast years if the fire takes place late in the seed maturation period. Using the example of the circumpolar boreal forest, while the joint probability of a mast year and a late-season fire will make this type of event rare (we estimate P = 0.1), nonetheless, it would permit a species lacking obvious fire-adapted traits to occasionally establish a widespread and abundant cohort on a large part of the landscape.

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers

PubMed Central

2010-01-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species. PMID:21637482

A new drought tipping point for conifer mortality

NASA Astrophysics Data System (ADS)

Kolb, Thomas E.

2015-03-01

(Huang et al 2015 Environ. Res. Lett. 10 024011) present a method for predicting mortality of ponderosa pine (Pinus ponderosa) and pinyon pine (Pinus edulis) in the Southwestern US during severe drought based on the relationship between the standardized precipitation-evapotranspiration index (SPEI) and annual tree ring growth. Ring growth was zero when SPEI for September to July was -1.64. The threshold SPEI of -1.64 was successful in distinguishing areas with high tree mortality during recent severe drought from areas with low mortality, and is proposed to be a tipping point of drought severity leading to tree mortality. Below, I discuss this work in more detail.

Structural zeroes and zero-inflated models.

PubMed

He, Hua; Tang, Wan; Wang, Wenjuan; Crits-Christoph, Paul

2014-08-01

In psychosocial and behavioral studies count outcomes recording the frequencies of the occurrence of some health or behavior outcomes (such as the number of unprotected sexual behaviors during a period of time) often contain a preponderance of zeroes because of the presence of 'structural zeroes' that occur when some subjects are not at risk for the behavior of interest. Unlike random zeroes (responses that can be greater than zero, but are zero due to sampling variability), structural zeroes are usually very different, both statistically and clinically. False interpretations of results and study findings may result if differences in the two types of zeroes are ignored. However, in practice, the status of the structural zeroes is often not observed and this latent nature complicates the data analysis. In this article, we focus on one model, the zero-inflated Poisson (ZIP) regression model that is commonly used to address zero-inflated data. We first give a brief overview of the issues of structural zeroes and the ZIP model. We then given an illustration of ZIP with data from a study on HIV-risk sexual behaviors among adolescent girls. Sample codes in SAS and Stata are also included to help perform and explain ZIP analyses.

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

Treesearch

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

2017-01-01

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

A window of opportunity for climate-change adaptation: Easing tree mortality by reducing forest basal area

USGS Publications Warehouse

Bradford, John B.; Bell, David M.

2017-01-01

Increasing aridity as a result of climate change is expected to exacerbate tree mortality. Reducing forest basal area – the cross-sectional area of tree stems within a given ground area – can decrease tree competition, which may reduce drought-induced tree mortality. However, neither the magnitude of expected mortality increases, nor the potential effectiveness of basal area reduction, has been quantified in dryland forests such as those of the drought-prone Southwest US. We used thousands of repeatedly measured forest plots to show that unusually warm and dry conditions are related to high tree mortality rates and that mortality is positively related to basal area. Those relationships suggest that while increasing high temperature extremes forecasted by climate models may lead to elevated tree mortality during the 21st century, future tree mortality might be partly ameliorated by reducing stand basal area. This adaptive forest management strategy may provide a window of opportunity for forest managers and policy makers to guide forest transitions to species and/or genotypes more suited to future climates.

Did the late spring frost in 2007 and 2011 affect tree-ring width and earlywood vessel size in Pedunculate oak (Quercus robur) in northern Poland?

PubMed

Puchałka, Radosław; Koprowski, Marcin; Przybylak, Julia; Przybylak, Rajmund; Dąbrowski, Henryk P

2016-08-01

Trees are sensitive to extreme weather and environmental conditions. This sensitivity is visible in tree-ring widths and cell structure. In our study, we hypothesized that the sudden frost noted at the beginning of May in both 2007 and 2011 affected cambial activity and, consequently, the number and size of vessels in the tree rings. It was decided to test this hypothesis after damage to leaves was observed. The applied response function model did not show any significant relationships between spring temperature and growth. However, this method uses average values for long periods and sometimes misses the short-term effects. This is why we decided to study each ring separately, comparing them with rings unaffected by the late frost. Our study showed that the short-term effect of sudden frost in late spring did not affect tree rings and selected cell parameters. The most likely reasons for this are (i) cambial activity producing the earlywood vessels before the occurrence of the observed leaf damage, (ii) the forest micro-climate protecting the trees from the harsh frost and (iii) the temperature decline being too short-lived an event to affect the oaks. On the other hand, the visible damage may be occasional and not affect cambium activity and tree vitality at all. We conclude that oak is well-adapted to this phenomenon.

Within-twig leaf distribution patterns differ among plant life-forms in a subtropical Chinese forest.

PubMed

Meng, Fengqun; Cao, Rui; Yang, Dongmei; Niklas, Karl J; Sun, Shucun

2013-07-01

In theory, plants can alter the distribution of leaves along the lengths of their twigs (i.e., within-twig leaf distribution patterns) to optimize light interception in the context of the architectures of their leaves, branches and canopies. We hypothesized that (i) among canopy tree species sharing similar light environments, deciduous trees will have more evenly spaced within-twig leaf distribution patterns compared with evergreen trees (because deciduous species tend to higher metabolic demands than evergreen species and hence require more light), and that (ii) shade-adapted evergreen species will have more evenly spaced patterns compared with sun-adapted evergreen ones (because shade-adapted species are generally light-limited). We tested these hypotheses by measuring morphological traits (i.e., internode length, leaf area, lamina mass per area, LMA; and leaf and twig inclination angles to the horizontal) and physiological traits (i.e., light-saturated net photosynthetic rates, Amax; light saturation points, LSP; and light compensation points, LCP), and calculated the 'evenness' of within-twig leaf distribution patterns as the coefficient of variation (CV; the higher the CV, the less evenly spaced leaves) of within-twig internode length for 9 deciduous canopy tree species, 15 evergreen canopy tree species, 8 shade-adapted evergreen shrub species and 12 sun-adapted evergreen shrub species in a subtropical broad-leaved rainforest in eastern China. Coefficient of variation was positively correlated with large LMA and large leaf and twig inclination angles, which collectively specify a typical trait combination adaptive to low light interception, as indicated by both ordinary regression and phylogenetic generalized least squares analyses. These relationships were also valid within the evergreen tree species group (which had the largest sample size). Consistent with our hypothesis, in the canopy layer, deciduous species (which were characterized by high LCP, LSP and Amax) had more even leaf distribution patterns than evergreen species (which had low LCP, LSP and Amax); shade-adapted evergreen species had more even leaf distribution patterns than sun-adapted evergreen species. We propose that the leaf distribution pattern (i.e., 'evenness' CV, which is an easily measured functional trait) can be used to distinguish among life-forms in communities similar to the one examined in this study.

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

PubMed

Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

2006-06-06

To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.

Adaptive Sniping for Volatile and Stable Continuous Double Auction Markets

NASA Astrophysics Data System (ADS)

Toft, I. E.; Bagnall, A. J.

This paper introduces a new adaptive sniping agent for the Continuous Double Auction. We begin by analysing the performance of the well known Kaplan sniper in two extremes of market conditions. We generate volatile and stable market conditions using the well known Zero Intelligence-Constrained agent and a new zero-intelligence agent Small Increment (SI). ZI-C agents submit random but profitable bids/offers and cause high volatility in prices and individual trader performance. Our new zero-intelligence agent, SI, makes small random adjustments to the outstanding bid/offer and hence is more cautious than ZI-C. We present results for SI in self-play and then analyse Kaplan in volatile and stable markets. We demonstrate that the non-adaptive Kaplan sniper can be configured to suit either market conditions, but no single configuration is performs well across both market types. We believe that in a dynamic auction environment where current or future market conditions cannot be predicted a viable sniping strategy should adapt its behaviour to suit prevailing market conditions. To this end, we propose the Adaptive Sniper (AS) agent for the CDA. AS traders classify sniping opportunities using a statistical model of market activity and adjust their classification thresholds using a Widrow-Hoff adapted search. Our AS agent requires little configuration, and outperforms the original Kaplan sniper in volatile and stable markets, and in a mixed trader type scenario that includes adaptive strategies from the literature.

Maximum height in a conifer is associated with conflicting requirements for xylem design.

PubMed

Domec, Jean-Christophe; Lachenbruch, Barbara; Meinzer, Frederick C; Woodruff, David R; Warren, Jeffrey M; McCulloh, Katherine A

2008-08-19

Despite renewed interest in the nature of limitations on maximum tree height, the mechanisms governing ultimate and species-specific height limits are not yet understood, but they likely involve water transport dynamics. Tall trees experience increased risk of xylem embolism from air-seeding because tension in their water column increases with height because of path-length resistance and gravity. We used morphological measurements to estimate the hydraulic properties of the bordered pits between tracheids in Douglas-fir trees along a height gradient of 85 m. With increasing height, the xylem structural modifications that satisfied hydraulic requirements for avoidance of runaway embolism imposed increasing constraints on water transport efficiency. In the branches and trunks, the pit aperture diameter of tracheids decreases steadily with height, whereas torus diameter remains relatively constant. The resulting increase in the ratio of torus to pit aperture diameter allows the pits to withstand higher tensions before air-seeding but at the cost of reduced pit aperture conductance. Extrapolations of vertical trends for trunks and branches show that water transport across pits will approach zero at a heights of 109 m and 138 m, respectively, which is consistent with historic height records of 100-127 m for this species. Likewise, the twig water potential corresponding to the threshold for runaway embolism would be attained at a height of approximately 107 m. Our results suggest that the maximum height of Douglas-fir trees may be limited in part by the conflicting requirements for water transport and water column safety.

Long-distance gene flow and adaptation of forest trees to rapid climate change

PubMed Central

Kremer, Antoine; Ronce, Ophélie; Robledo-Arnuncio, Juan J; Guillaume, Frédéric; Bohrer, Gil; Nathan, Ran; Bridle, Jon R; Gomulkiewicz, Richard; Klein, Etienne K; Ritland, Kermit; Kuparinen, Anna; Gerber, Sophie; Schueler, Silvio

2012-01-01

Forest trees are the dominant species in many parts of the world and predicting how they might respond to climate change is a vital global concern. Trees are capable of long-distance gene flow, which can promote adaptive evolution in novel environments by increasing genetic variation for fitness. It is unclear, however, if this can compensate for maladaptive effects of gene flow and for the long-generation times of trees. We critically review data on the extent of long-distance gene flow and summarise theory that allows us to predict evolutionary responses of trees to climate change. Estimates of long-distance gene flow based both on direct observations and on genetic methods provide evidence that genes can move over spatial scales larger than habitat shifts predicted under climate change within one generation. Both theoretical and empirical data suggest that the positive effects of gene flow on adaptation may dominate in many instances. The balance of positive to negative consequences of gene flow may, however, differ for leading edge, core and rear sections of forest distributions. We propose future experimental and theoretical research that would better integrate dispersal biology with evolutionary quantitative genetics and improve predictions of tree responses to climate change. PMID:22372546

Long-distance gene flow and adaptation of forest trees to rapid climate change.

PubMed

Kremer, Antoine; Ronce, Ophélie; Robledo-Arnuncio, Juan J; Guillaume, Frédéric; Bohrer, Gil; Nathan, Ran; Bridle, Jon R; Gomulkiewicz, Richard; Klein, Etienne K; Ritland, Kermit; Kuparinen, Anna; Gerber, Sophie; Schueler, Silvio

2012-04-01

Forest trees are the dominant species in many parts of the world and predicting how they might respond to climate change is a vital global concern. Trees are capable of long-distance gene flow, which can promote adaptive evolution in novel environments by increasing genetic variation for fitness. It is unclear, however, if this can compensate for maladaptive effects of gene flow and for the long-generation times of trees. We critically review data on the extent of long-distance gene flow and summarise theory that allows us to predict evolutionary responses of trees to climate change. Estimates of long-distance gene flow based both on direct observations and on genetic methods provide evidence that genes can move over spatial scales larger than habitat shifts predicted under climate change within one generation. Both theoretical and empirical data suggest that the positive effects of gene flow on adaptation may dominate in many instances. The balance of positive to negative consequences of gene flow may, however, differ for leading edge, core and rear sections of forest distributions. We propose future experimental and theoretical research that would better integrate dispersal biology with evolutionary quantitative genetics and improve predictions of tree responses to climate change. © 2012 Blackwell Publishing Ltd/CNRS.

Computerized Adaptive Test vs. decision trees: Development of a support decision system to identify suicidal behavior.

PubMed

Delgado-Gomez, D; Baca-Garcia, E; Aguado, D; Courtet, P; Lopez-Castroman, J

2016-12-01

Several Computerized Adaptive Tests (CATs) have been proposed to facilitate assessments in mental health. These tests are built in a standard way, disregarding useful and usually available information not included in the assessment scales that could increase the precision and utility of CATs, such as the history of suicide attempts. Using the items of a previously developed scale for suicidal risk, we compared the performance of a standard CAT and a decision tree in a support decision system to identify suicidal behavior. We included the history of past suicide attempts as a class for the separation of patients in the decision tree. The decision tree needed an average of four items to achieve a similar accuracy than a standard CAT with nine items. The accuracy of the decision tree, obtained after 25 cross-validations, was 81.4%. A shortened test adapted for the separation of suicidal and non-suicidal patients was developed. CATs can be very useful tools for the assessment of suicidal risk. However, standard CATs do not use all the information that is available. A decision tree can improve the precision of the assessment since they are constructed using a priori information. Copyright © 2016 Elsevier B.V. All rights reserved.

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...

Conformal amplitude hierarchy and the Poincaré disk

NASA Astrophysics Data System (ADS)

Shimada, Hirohiko

2018-02-01

The amplitude for the singlet channels in the 4-point function of the fundamental field in the conformal field theory of the 2d O(n) model is studied as a function of n. For a generic value of n, the 4-point function has infinitely many amplitudes, whose landscape can be very spiky as the higher amplitude changes its sign many times at the simple poles, which generalize the unique pole of the energy operator amplitude at n = 0. In the stadard parameterization of n by angle in unit of π, we find that the zeros and poles happen at the rational angles, forming a hierarchical tree structure inherent in the Poincaré disk. Some relation between the amplitude and the Farey path, a piecewise geodesic that visits these zeros and poles, is suggested. In this hierarchy, the symmetry of the congruence subgroup Γ(2) of SL(2, ℤ) naturally arises from the two clearly distinct even/odd classes of the rational angles, in which one respectively gets the truncated operator algebras and the logarithmic 4-point functions.

Manipulating the transmission through valve structure composed of zero-index metamaterial

NASA Astrophysics Data System (ADS)

Wang, Yongxing; Sun, Zhouzhou; Xu, Ping

2017-11-01

We propose a valve structure composed of zero-index metamaterial to manipulate the electromagnetic wave conveniently and effectively through regulating the phase of reflected waves. Both the structure and characteristics of zero-index metamaterial need not to be changed when manipulating the transmission, which maintains the stability of zero-index metamaterial. Moreover, the good performance of tuning the electromagnetic wave is not limited by the shape and size of our proposed structure. By using our proposed valve structure, we demonstrate the realization of the tunable curved anisotropic ɛ-near-zero material waveguide with irregular shape, arbitrarily sized isotropic ɛ-near-zero material waveguide with high transmittance and the curved isotropic impedance matched ɛ-near-zero material waveguide without polarization limitations.

Iterative Adaptive Dynamic Programming for Solving Unknown Nonlinear Zero-Sum Game Based on Online Data.

PubMed

Zhu, Yuanheng; Zhao, Dongbin; Li, Xiangjun

2017-03-01

H ∞ control is a powerful method to solve the disturbance attenuation problems that occur in some control systems. The design of such controllers relies on solving the zero-sum game (ZSG). But in practical applications, the exact dynamics is mostly unknown. Identification of dynamics also produces errors that are detrimental to the control performance. To overcome this problem, an iterative adaptive dynamic programming algorithm is proposed in this paper to solve the continuous-time, unknown nonlinear ZSG with only online data. A model-free approach to the Hamilton-Jacobi-Isaacs equation is developed based on the policy iteration method. Control and disturbance policies and value are approximated by neural networks (NNs) under the critic-actor-disturber structure. The NN weights are solved by the least-squares method. According to the theoretical analysis, our algorithm is equivalent to a Gauss-Newton method solving an optimization problem, and it converges uniformly to the optimal solution. The online data can also be used repeatedly, which is highly efficient. Simulation results demonstrate its feasibility to solve the unknown nonlinear ZSG. When compared with other algorithms, it saves a significant amount of online measurement time.

The Atlantic-Mediterranean watershed, river basins and glacial history shape the genetic structure of Iberian poplars.

PubMed

Macaya-Sanz, D; Heuertz, M; López-de-Heredia, U; De-Lucas, A I; Hidalgo, E; Maestro, C; Prada, A; Alía, R; González-Martínez, S C

2012-07-01

Recent phylogeographic studies have elucidated the effects of Pleistocene glaciations and of Pre-Pleistocene events on populations from glacial refuge areas. This study investigates those effects in riparian trees (Populus spp.), whose particular features may convey enhanced resistance to climate fluctuations. We analysed the phylogeographic structure of 44 white (Populus alba), 13 black (Populus nigra) and two grey (Populus x canescens) poplar populations in the Iberian Peninsula using plastid DNA microsatellites and sequences. We also assessed fine-scale spatial genetic structure and the extent of clonality in four white and one grey poplar populations using nuclear microsatellites and we determined quantitative genetic differentiation (Q(ST) ) for growth traits in white poplar. Black poplar displayed higher regional diversity and lower differentiation than white poplar, reflecting its higher cold-tolerance. The dependence of white poplar on phreatic water was evidenced by strong differentiation between the Atlantic and Mediterranean drainage basins and among river basins, and by weaker isolation by distance within than among river basins. Our results suggest confinement to the lower river courses during glacial periods and moderate interglacial gene exchange along coastlines. In northern Iberian river basins, white poplar had lower diversity, fewer private haplotypes and larger clonal assemblies than in southern basins, indicating a stronger effect of glaciations in the north. Despite strong genetic structure and frequent asexual propagation in white poplar, some growth traits displayed adaptive divergence between drainage and river basins (Q(ST) >F(ST)), highlighting the remarkable capacity of riparian tree populations to adapt to regional environmental conditions. © 2012 Blackwell Publishing Ltd.

Adaptive Cluster Sampling for Forest Inventories

Treesearch

Francis A. Roesch

1993-01-01

Adaptive cluster sampling is shown to be a viable alternative for sampling forests when there are rare characteristics of the forest trees which are of interest and occur on clustered trees. The ideas of recent work in Thompson (1990) have been extended to the case in which the initial sample is selected with unequal probabilities. An example is given in which the...

Photosynthetic temperature responses of tree species in Rwanda: evidence of pronounced negative effects of high temperature in montane rainforest climax species

NASA Astrophysics Data System (ADS)

Vårhammar, Angelica; Wallin, Göran; McLean, Christopher M.; Dusenge, Mirindi Eric; Medlyn, Belinda E.; Hasper, Thomas B.; Nsabimana, Donat; Uddling, Johan

2015-04-01

The sensitivity of photosynthetic metabolism to temperature has been identified as a key uncertainty for projecting the magnitude of the terrestrial feedback on future climate change. While temperature responses of photosynthetic capacities have been comparatively well investigated in temperate species, the responses of tropical tree species remain unexplored. We compared the responses of seedlings of native cold-adapted tropical montane rainforest tree species to exotic warm-adapted plantation species, all growing in an intermediate temperature common garden in Rwanda. Leaf gas exchange responses to CO2 at different temperatures (20 - 40 C) were used to assess the temperature responses of biochemical photosynthetic capacities. Analyses revealed a lower optimum temperature for photosynthetic electron transport rates than for Rubisco carboxylation rates, along with lower electron transport optima in the native cold-adapted than in the exotic warm-adapted species. The photosynthetic optimum temperatures were generally exceeded by daytime peak leaf temperatures, in particular in the native montane rainforest climax species. This study thus provides evidence of pronounced negative effects of high temperature in tropical trees and indicates high susceptibility of montane rainforest climax species to future global warming. (Reference: New Phytologist, in press)

Generation of dark hollow beam via coherent combination based on adaptive optics.

PubMed

Zheng, Yi; Wang, Xiaohua; Shen, Feng; Li, Xinyang

2010-12-20

A novel method for generating a dark hollow beam (DHB) is proposed and studied both theoretically and experimentally. A coherent combination technique for laser arrays is implemented based on adaptive optics (AO). A beam arraying structure and an active segmented mirror are designed and described. Piston errors are extracted by a zero-order interference detection system with the help of a custom-made photo-detectors array. An algorithm called the extremum approach is adopted to calculate feedback control signals. A dynamic piston error is imported by LiNbO₃ to test the capability of the AO servo. In a closed loop the stable and clear DHB is obtained. The experimental results confirm the feasibility of the concept.

Physiological processes during winter dormancy and their ecological significance

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

Havranek, W.M.; Tranquillini, W.

1995-07-01

Lengthy and severe winters require that trees in the forests of boreal and mountain zones undergo winter dormancy. Physiologically, a high resistance to subfreezing temperatures and concomitant dehydration are necessary. To accomplish this dormancy, both physiological and structural changes are needed at the cellular level that require induction by endogenous and photoperiodic control early in autumn. Endogenous rhythmicity promotes cold hardening in early autumn and the persistence of hardiness throughout the winter. Numerous physiological functions are maintained at a reduced level, or become completely inhibited during true winter dormancy. Winter hardiness also includes the capability to minimize water loss effectivelymore » when water uptake is severely impeded or impossible. Anatomical features such as tracheids act to minimize xylem embolism during frequent freeze-thaw cycles, and {open_quotes}crown{close_quotes} tissues enable buds to stay in a dehydrated and, thus, more resistant state during winter. Both these structural features are adaptations that contribute to the dominance of conifers in cold climates. Interestingly, deciduous tree species rather than evergreen conifers dominate in the most severe winter climates, although it is not clear whether limitations during winter, during the summer growth period, or during both are most limiting to conifer tree ecology. Additional work that evaluates the importance of winter and summer growth restriction, and their interaction, is needed before a comprehensive understanding of conifer tree ecophysiology will be possible.« less

Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances.

PubMed

Du, Baoguo; Kreuzwieser, Jürgen; Dannenmann, Michael; Junker, Laura Verena; Kleiber, Anita; Hess, Moritz; Jansen, Kirstin; Eiblmeier, Monika; Gessler, Arthur; Kohnle, Ulrich; Ensminger, Ingo; Rennenberg, Heinz; Wildhagen, Henning

2018-01-01

The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats.

Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances

PubMed Central

Du, Baoguo; Kreuzwieser, Jürgen; Dannenmann, Michael; Junker, Laura Verena; Kleiber, Anita; Hess, Moritz; Jansen, Kirstin; Eiblmeier, Monika; Gessler, Arthur; Kohnle, Ulrich; Ensminger, Ingo; Rennenberg, Heinz

2018-01-01

The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats. PMID:29566035

SETs: stand evaluation tools: II. tree value conversion standards for hardwood sawtimber

Treesearch

Joseph J. Mendel; Paul S. DeBald; Martin E. Dale

1976-01-01

Tree quatity index tables are presented for 12 important hardwood species of the oak-hickory forest. From these, tree value conversion standards are developed for each species, log grade, merchantable height, and diameter at breast height. The method of calculating tree value conversion standards and adapting them to different conditions is explained. A computer...

Reflections on Using an Adaptive Leadership Approach to Respond to the Needs of Pregnant and Postpartum Women

ERIC Educational Resources Information Center

Laszewski, Audrey

2017-01-01

The concept of "adaptive leadership" refers to principles that allow professionals and organizations to respond effectively in challenging circumstances. This article presents the personal reflections of a ZERO TO THREE Fellow on selected adaptive leadership principles in action. The author explains how adaptive leadership tools informed…

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

PubMed Central

Krehbiel, B.; Ericsson, S. A.; Wilson, C.; Caetano, A. R.; Paiva, S. R.

2017-01-01

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events. PMID:28459870

A parallel algorithm for computing the eigenvalues of a symmetric tridiagonal matrix

NASA Technical Reports Server (NTRS)

Swarztrauber, Paul N.

1993-01-01

A parallel algorithm, called polysection, is presented for computing the eigenvalues of a symmetric tridiagonal matrix. The method is based on a quadratic recurrence in which the characteristic polynomial is constructed on a binary tree from polynomials whose degree doubles at each level. Intervals that contain exactly one zero are determined by the zeros of polynomials at the previous level which ensures that different processors compute different zeros. The signs of the polynomials at the interval endpoints are determined a priori and used to guarantee that all zeros are found. The use of finite-precision arithmetic may result in multiple zeros; however, in this case, the intervals coalesce and their number determines exactly the multiplicity of the zero. For an N x N matrix the eigenvalues can be determined in O(log-squared N) time with N-squared processors and O(N) time with N processors. The method is compared with a parallel variant of bisection that requires O(N-squared) time on a single processor, O(N) time with N processors, and O(log N) time with N-squared processors.

Computing the structural influence matrix for biological systems.

PubMed

Giordano, Giulia; Cuba Samaniego, Christian; Franco, Elisa; Blanchini, Franco

2016-06-01

We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.

A window of opportunity for climate-change adaptation: easing tree mortality by reducing forest basal area

Treesearch

John B Bradford; David M Bell

2016-01-01

Increasing aridity as a result of climate change is expected to exacerbate tree mortality. Reducing forest basal area – the cross-sectional area of tree stems within a given ground area – can decrease tree competition, which may reduce drought-induced tree mortality. However, neither the magnitude of expected mortality increases, nor the potential effectiveness of...

Genome hypermethylation in Pinus silvestris of Chernobyl--a mechanism for radiation adaptation?

PubMed

Kovalchuk, Olga; Burke, Paula; Arkhipov, Andrey; Kuchma, Nikolaj; James, S Jill; Kovalchuk, Igor; Pogribny, Igor

2003-08-28

Adaptation is a complex process by which populations of organisms respond to long-term environmental stresses by permanent genetic change. Here we present data from the natural "open-field" radiation adaptation experiment after the Chernobyl accident and provide the first evidence of the involvement of epigenetic changes in adaptation of a eukaryote-Scots pine (Pinus silvestris), to chronic radiation exposure. We have evaluated global genome methylation of control and radiation-exposed pine trees using a method based on cleavage by a methylation-sensitive HpaII restriction endonuclease that leaves a 5' guanine overhang and subsequent single nucleotide extension with labeled [3H] dCTP. We have found that genomic DNA of exposed pine trees was considerably hypermethylated. Moreover, hypermethylation appeared to be dependent upon the radiation dose absorbed by the trees. Such hypermethylation may be viewed as a defense strategy of plants that prevents genome instability and reshuffling of the hereditary material, allowing survival in an extreme environment. Further studies are clearly needed to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of radiation stress and adaptive response.

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

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

Treesearch

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

2006-01-01

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

Environmental versus geographical determinants of genetic structure in two subalpine conifers.

PubMed

Mosca, Elena; González-Martínez, Santiago C; Neale, David B

2014-01-01

Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Zero torque gear head wrench

NASA Technical Reports Server (NTRS)

Mcdougal, A. R.; Norman, R. M. (Inventor)

1976-01-01

A gear head wrench particularly suited for use in applying torque to bolts without transferring torsional stress to bolt-receiving structures is introduced. The wrench is characterized by a coupling including a socket, for connecting a bolt head with a torque multiplying gear train, provided within a housing having an annulus concentrically related to the socket and adapted to be coupled with a spacer interposed between the bolt head and the juxtaposed surface of the bolt-receiving structure for applying a balancing counter-torque to the spacer as torque is applied to the bolt head whereby the bolt-receiving structure is substantially isolated from torsional stress. As a result of the foregoing, the operator of the wrench is substantially isolated from any forces which may be imposed.

Stay tuned: active amplification tunes tree cricket ears to track temperature-dependent song frequency.

PubMed

Mhatre, Natasha; Pollack, Gerald; Mason, Andrew

2016-04-01

Tree cricket males produce tonal songs, used for mate attraction and male-male interactions. Active mechanics tunes hearing to conspecific song frequency. However, tree cricket song frequency increases with temperature, presenting a problem for tuned listeners. We show that the actively amplified frequency increases with temperature, thus shifting mechanical and neuronal auditory tuning to maintain a match with conspecific song frequency. Active auditory processes are known from several taxa, but their adaptive function has rarely been demonstrated. We show that tree crickets harness active processes to ensure that auditory tuning remains matched to conspecific song frequency, despite changing environmental conditions and signal characteristics. Adaptive tuning allows tree crickets to selectively detect potential mates or rivals over large distances and is likely to bestow a strong selective advantage by reducing mate-finding effort and facilitating intermale interactions. © 2016 The Author(s).

Quantifying pruning impacts on olive tree architecture and annual canopy growth by using UAV-based 3D modelling.

PubMed

Jiménez-Brenes, F M; López-Granados, F; de Castro, A I; Torres-Sánchez, J; Serrano, N; Peña, J M

2017-01-01

Tree pruning is a costly practice with important implications for crop harvest and nutrition, pest and disease control, soil protection and irrigation strategies. Investigations on tree pruning usually involve tedious on-ground measurements of the primary tree crown dimensions, which also might generate inconsistent results due to the irregular geometry of the trees. As an alternative to intensive field-work, this study shows a innovative procedure based on combining unmanned aerial vehicle (UAV) technology and advanced object-based image analysis (OBIA) methodology for multi-temporal three-dimensional (3D) monitoring of hundreds of olive trees that were pruned with three different strategies (traditional, adapted and mechanical pruning). The UAV images were collected before pruning, after pruning and a year after pruning, and the impacts of each pruning treatment on the projected canopy area, tree height and crown volume of every tree were quantified and analyzed over time. The full procedure described here automatically identified every olive tree on the orchard and computed their primary 3D dimensions on the three study dates with high accuracy in the most cases. Adapted pruning was generally the most aggressive treatment in terms of the area and volume (the trees decreased by 38.95 and 42.05% on average, respectively), followed by trees under traditional pruning (33.02 and 35.72% on average, respectively). Regarding the tree heights, mechanical pruning produced a greater decrease (12.15%), and these values were minimal for the other two treatments. The tree growth over one year was affected by the pruning severity and by the type of pruning treatment, i.e., the adapted-pruning trees experienced higher growth than the trees from the other two treatments when pruning intensity was low (<10%), similar to the traditionally pruned trees at moderate intensity (10-30%), and lower than the other trees when the pruning intensity was higher than 30% of the crown volume. Combining UAV-based images and an OBIA procedure allowed measuring tree dimensions and quantifying the impacts of three different pruning treatments on hundreds of trees with minimal field work. Tree foliage losses and annual canopy growth showed different trends as affected by the type and severity of the pruning treatments. Additionally, this technology offers valuable geo-spatial information for designing site-specific crop management strategies in the context of precision agriculture, with the consequent economic and environmental benefits.

[Spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest].

PubMed

Shao, Fang-Li; Yu, Xin-Xiao; Song, Si-Ming; Zhao, Yang

2011-11-01

This paper analyzed the spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest in a 4 hm2 plot of Mulan Paddock, based on the diameter distribution and the spatial structure parameters mingling degree, neighborhood comparison, and angle index. In the forest, the diameter distribution of the stands presented as an inverse 'J' curve, the average mingling degree was 0.4, with the individuals at weak and zero mingling degree reached 51.6%, and the average mingling degree of P. davidiana and B. platyphylla was 0.25 and 0.39, respectively. The neighborhood comparison based on the diameter at breast height (DBH) and tree height was almost the same, suggesting that the P. davidiana and B. platyphylla were in the transition state from subdominant to middle. The horizontal distribution pattern had a close relation to the minimum measured DBH, being clustered when the DBH was > or = 1 cm and < 6 cm, and random when the DBH was > or = 6 cm.

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

Treesearch

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

2005-01-01

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

Emergent gravity from a mass deformation in warped spacetime

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

Gherghetta, Tony; Peloso, Marco; Poppitz, Erich

2005-11-15

We consider a deformation of five-dimensional warped gravity with bulk and boundary mass terms to quadratic order in the action. We show that massless zero modes occur for special choices of the masses. The tensor zero mode is a smooth deformation of the Randall-Sundrum graviton wave function and can be localized anywhere in the bulk. There is also a vector zero mode with similar localization properties, which is decoupled from conserved sources at tree level. Interestingly, there are no scalar modes, and the model is ghost-free at the linearized level. When the tensor zero mode is localized near the IRmore » brane, the dual interpretation is a composite graviton describing an emergent (induced) theory of gravity at the IR scale. In this case Newton's law of gravity changes to a new power law below the millimeter scale, with an exponent that can even be irrational.« less

Tests of a habitat suitability model for black-capped chickadees

USGS Publications Warehouse

Schroeder, Richard L.

1990-01-01

The black-capped chickadee (Parus atricapillus) Habitat Suitability Index (HSI) model provides a quantitative rating of the capability of a habitat to support breeding, based on measures related to food and nest site availability. The model assumption that tree canopy volume can be predicted from measures of tree height and canopy closure was tested using data from foliage volume studies conducted in the riparian cottonwood habitat along the South Platte River in Colorado. Least absolute deviations (LAD) regression showed that canopy cover and over story tree height yielded volume predictions significantly lower than volume estimated by more direct methods. Revisions to these model relations resulted in improved predictions of foliage volume. The relation between the HSI and estimates of black-capped chickadee population densities was examined using LAD regression for both the original model and the model with the foliage volume revisions. Residuals from these models were compared to residuals from both a zero slope model and an ideal model. The fit model for the original HSI differed significantly from the ideal model, whereas the fit model for the original HSI did not differ significantly from the ideal model. However, both the fit model for the original HSI and the fit model for the revised HSI did not differ significantly from a model with a zero slope. Although further testing of the revised model is needed, its use is recommended for more realistic estimates of tree canopy volume and habitat suitability.

Multigenerational memory and adaptive adhesion in early bacterial biofilm communities.

PubMed

Lee, Calvin K; de Anda, Jaime; Baker, Amy E; Bennett, Rachel R; Luo, Yun; Lee, Ernest Y; Keefe, Joshua A; Helali, Joshua S; Ma, Jie; Zhao, Kun; Golestanian, Ramin; O'Toole, George A; Wong, Gerard C L

2018-04-24

Using multigenerational, single-cell tracking we explore the earliest events of biofilm formation by Pseudomonas aeruginosa During initial stages of surface engagement (≤20 h), the surface cell population of this microbe comprises overwhelmingly cells that attach poorly (∼95% stay <30 s, well below the ∼1-h division time) with little increase in surface population. If we harvest cells previously exposed to a surface and direct them to a virgin surface, we find that these surface-exposed cells and their descendants attach strongly and then rapidly increase the surface cell population. This "adaptive," time-delayed adhesion requires determinants we showed previously are critical for surface sensing: type IV pili (TFP) and cAMP signaling via the Pil-Chp-TFP system. We show that these surface-adapted cells exhibit damped, coupled out-of-phase oscillations of intracellular cAMP levels and associated TFP activity that persist for multiple generations, whereas surface-naïve cells show uncorrelated cAMP and TFP activity. These correlated cAMP-TFP oscillations, which effectively impart intergenerational memory to cells in a lineage, can be understood in terms of a Turing stochastic model based on the Pil-Chp-TFP framework. Importantly, these cAMP-TFP oscillations create a state characterized by a suppression of TFP motility coordinated across entire lineages and lead to a drastic increase in the number of surface-associated cells with near-zero translational motion. The appearance of this surface-adapted state, which can serve to define the historical classification of "irreversibly attached" cells, correlates with family tree architectures that facilitate exponential increases in surface cell populations necessary for biofilm formation.

The molecular basis for tree growth habit in Prunus persica (peach)

USDA-ARS?s Scientific Manuscript database

The large size and spreading growth habit of trees requires excessive labor, land space, and pesticides. Genetically improving tree shapes so they can be planted at higher density and/or more readily adapted to mechanization would increase productivity and be more environmentally friendly. Current...

I-AUV Docking and Panel Intervention at Sea

PubMed Central

Palomeras, Narcís; Peñalver, Antonio; Massot-Campos, Miquel; Negre, Pep Lluís; Fernández, José Javier; Ridao, Pere; Sanz, Pedro J.; Oliver-Codina, Gabriel

2016-01-01

The use of commercially available autonomous underwater vehicles (AUVs) has increased during the last fifteen years. While they are mainly used for routine survey missions, there is a set of applications that nowadays can be only addressed by manned submersibles or work-class remotely operated vehicles (ROVs) equipped with teleoperated arms: the intervention applications. To allow these heavy vehicles controlled by human operators to perform intervention tasks, underwater structures like observatory facilities, subsea panels or oil-well Christmas trees have been adapted, making them more robust and easier to operate. The TRITON Spanish founded project proposes the use of a light-weight intervention AUV (I-AUV) to carry out intervention applications simplifying the adaptation of these underwater structures and drastically reducing the operational cost. To prove this concept, the Girona 500 I-AUV is used to autonomously dock into an adapted subsea panel and once docked perform an intervention composed of turning a valve and plugging in/unplugging a connector. The techniques used for the autonomous docking and manipulation as well as the design of an adapted subsea panel with a funnel-based docking system are presented in this article together with the results achieved in a water tank and at sea. PMID:27754348

I-AUV Docking and Panel Intervention at Sea.

PubMed

Palomeras, Narcís; Peñalver, Antonio; Massot-Campos, Miquel; Negre, Pep Lluís; Fernández, José Javier; Ridao, Pere; Sanz, Pedro J; Oliver-Codina, Gabriel

2016-10-12

The use of commercially available autonomous underwater vehicles (AUVs) has increased during the last fifteen years. While they are mainly used for routine survey missions, there is a set of applications that nowadays can be only addressed by manned submersibles or work-class remotely operated vehicles (ROVs) equipped with teleoperated arms: the intervention applications. To allow these heavy vehicles controlled by human operators to perform intervention tasks, underwater structures like observatory facilities, subsea panels or oil-well Christmas trees have been adapted, making them more robust and easier to operate. The TRITON Spanish founded project proposes the use of a light-weight intervention AUV (I-AUV) to carry out intervention applications simplifying the adaptation of these underwater structures and drastically reducing the operational cost. To prove this concept, the Girona 500 I-AUV is used to autonomously dock into an adapted subsea panel and once docked perform an intervention composed of turning a valve and plugging in/unplugging a connector. The techniques used for the autonomous docking and manipulation as well as the design of an adapted subsea panel with a funnel-based docking system are presented in this article together with the results achieved in a water tank and at sea.

Leaf phenological characters of main tree species in urban forest of Shenyang.

PubMed

Xu, Sheng; Xu, Wenduo; Chen, Wei; He, Xingyuan; Huang, Yanqing; Wen, Hua

2014-01-01

Plant leaves, as the main photosynthetic organs and the high energy converters among primary producers in terrestrial ecosystems, have attracted significant research attention. Leaf lifespan is an adaptive characteristic formed by plants to obtain the maximum carbon in the long-term adaption process. It determines important functional and structural characteristics exhibited in the environmental adaptation of plants. However, the leaf lifespan and leaf characteristics of urban forests were not studied up to now. By using statistic, linear regression methods and correlation analysis, leaf phenological characters of main tree species in urban forest of Shenyang were observed for five years to obtain the leafing phenology (including leafing start time, end time, and duration), defoliating phenology (including defoliation start time, end time, and duration), and the leaf lifespan of the main tree species. Moreover, the relationships between temperature and leafing phenology, defoliating phenology, and leaf lifespan were analyzed. The timing of leafing differed greatly among species. The early leafing species would have relatively early end of leafing; the longer it took to the end of leafing would have a later time of completed leafing. The timing of defoliation among different species varied significantly, the early defoliation species would have relatively longer duration of defoliation. If the mean temperature rise for 1°C in spring, the time of leafing would experience 5 days earlier in spring. If the mean temperature decline for 1°C, the time of defoliation would experience 3 days delay in autumn. There is significant correlation between leaf longevity and the time of leafing and defoliation. According to correlation analysis and regression analysis, there is significant correlation between temperature and leafing and defoliation phenology. Early leafing species would have a longer life span and consequently have advantage on carbon accumulation compared with later defoliation species.

Adaptive critic designs for discrete-time zero-sum games with application to H(infinity) control.

PubMed

Al-Tamimi, Asma; Abu-Khalaf, Murad; Lewis, Frank L

2007-02-01

In this correspondence, adaptive critic approximate dynamic programming designs are derived to solve the discrete-time zero-sum game in which the state and action spaces are continuous. This results in a forward-in-time reinforcement learning algorithm that converges to the Nash equilibrium of the corresponding zero-sum game. The results in this correspondence can be thought of as a way to solve the Riccati equation of the well-known discrete-time H(infinity) optimal control problem forward in time. Two schemes are presented, namely: 1) a heuristic dynamic programming and 2) a dual-heuristic dynamic programming, to solve for the value function and the costate of the game, respectively. An H(infinity) autopilot design for an F-16 aircraft is presented to illustrate the results.

Plasticity in the Huber value contributes to homeostasis in leaf water relations of a mallee Eucalypt with variation to groundwater depth.

PubMed

Carter, Jennifer L; White, Donald A

2009-11-01

Information on how vegetation adapts to differences in water supply is critical for predicting vegetation survival, growth and water use, which, in turn, has important impacts on site hydrology. Many field studies assess adaptation to water stress by comparing between disparate sites, which makes it difficult to distinguish between physiological or morphological changes and long-term genetic adaptation. When planting trees into new environments, the phenotypic adaptations of a species to water stress will be of primary interest. This study examined the response to water availability of Eucalyptus kochii ssp. borealis (C. Gardner) D. Nicolle, commonly integrated with agriculture in south-western Australia for environmental and economic benefits. By choosing a site where the groundwater depth varied but where climate and soil type were the same, we were able to isolate tree response to water supply. Tree growth, leaf area and stand water use were much larger for trees over shallow groundwater than for trees over a deep water table below a silcrete hardpan. However, water use on a leaf area basis was similar in trees over deep and shallow groundwater, as were the minimum leaf water potential observed over different seasons and the turgor loss point. We conclude that homeostasis in leaf water use and water relations was maintained through a combination of stomatal control and adjustment of sapwood-to-leaf area ratios (Huber value). Differences in the Huber value with groundwater depth were associated with different sapwood-specific conductivity and water use on a sapwood area basis. Knowledge of the coordination between water supply, leaf area, sapwood area and leaf transpiration rate for different species will be important when predicting stand water use.

Pollen, wind and fire: how to investigate genetic effects of disturbance-induced change in forest trees.

PubMed

Bacles, Cecile F E

2014-01-01

Understanding the consequences of habitat disturbance on mating patterns although pollen and seed dispersal in forest trees has been a long-standing theme of forest and conservation genetics. Forest ecosystems face global environmental pressures from timber exploitation to genetic pollution and climate change, and it is therefore essential to comprehend how disturbances may alter the dispersal of genes and their establishment in tree populations in order to formulate relevant recommendations for sustainable resource management practices and realistic predictions of potential adaptation to climate change by means of range shift or expansion (Kremer et al. 2012). However, obtaining reliable evidence of disturbance-induced effects on gene dispersal processes from empirical evaluation of forest tree populations is difficult. Indeed, tree species share characteristics such as high longevity, long generation time and large reproductive population size, which may impede the experimenter's ability to assess parameters at the spatial and time scales at which any change may occur (Petit and Hampe 2006). It has been suggested that appropriate study designs should encompass comparison of populations before and after disturbance as well as account for demonstrated variation in conspecific density, that is, the spatial distribution of mates, and forest density, including all species and relating to alteration in landscape openness (Bacles & Jump 2011). However, more often than not, empirical studies aiming to assess the consequences of habitat disturbance on genetic processes in tree populations assume rather than quantify a change in tree densities in forests under disturbance and generally fail to account for population history, which may lead to inappropriate interpretation of a causal relationship between population genetic structure and habitat disturbance due to effects of unmonitored confounding variables (Gauzere et al. 2013). In this issue, Shohami and Nathan (2014) take advantage of the distinctive features of the fire-adapted wind-pollinated Aleppo pine Pinus halepensis (Fig. 1) to provide an elegant example of best practice. Thanks to long-term monitoring of the study site, a natural stand in Israel, Shohami and Nathan witnessed the direct impact of habitat disturbance, here taking the shape of fire, on conspecific and forest densities and compared pre- and postdisturbance mating patterns estimated from cones of different ages sampled on the same surviving maternal individuals (Fig. 2). This excellent study design is all the more strong that Shohami and Nathan took further analytical steps to account for confounding variables, such as historical population genetic structure and possible interannual variation in wind conditions, thus giving high credibility to their findings of unequivocal fire-induced alteration of mating patterns in P. halepensis. Most notably, the authors found, at the pollen pool level, a disruption of local genetic structure which, furthermore, they were able to attribute explicitly to enhanced pollen-mediated gene immigration into the low-density fire-disturbed stand. This cleverly designed research provides a model approach to be followed if we are to advance our understanding of disturbance-induced dispersal and genetic change in forest trees. © 2013 John Wiley & Sons Ltd.

Output Feedback Adaptive Control of Non-Minimum Phase Systems Using Optimal Control Modification

NASA Technical Reports Server (NTRS)

Nguyen, Nhan; Hashemi, Kelley E.; Yucelen, Tansel; Arabi, Ehsan

2018-01-01

This paper describes output feedback adaptive control approaches for non-minimum phase SISO systems with relative degree 1 and non-strictly positive real (SPR) MIMO systems with uniform relative degree 1 using the optimal control modification method. It is well-known that the standard model-reference adaptive control (MRAC) cannot be used to control non-SPR plants to track an ideal SPR reference model. Due to the ideal property of asymptotic tracking, MRAC attempts an unstable pole-zero cancellation which results in unbounded signals for non-minimum phase SISO systems. The optimal control modification can be used to prevent the unstable pole-zero cancellation which results in a stable adaptation of non-minimum phase SISO systems. However, the tracking performance using this approach could suffer if the unstable zero is located far away from the imaginary axis. The tracking performance can be recovered by using an observer-based output feedback adaptive control approach which uses a Luenberger observer design to estimate the state information of the plant. Instead of explicitly specifying an ideal SPR reference model, the reference model is established from the linear quadratic optimal control to account for the non-minimum phase behavior of the plant. With this non-minimum phase reference model, the observer-based output feedback adaptive control can maintain stability as well as tracking performance. However, in the presence of the mismatch between the SPR reference model and the non-minimum phase plant, the standard MRAC results in unbounded signals, whereas a stable adaptation can be achieved with the optimal control modification. An application of output feedback adaptive control for a flexible wing aircraft illustrates the approaches.

Topographic Control of Aboveground Carbon Pools Across an Environmental Gradient, Eastern Slope of the Rocky Mountains, Colorado.

NASA Astrophysics Data System (ADS)

Swetnam, T. L.; Brooks, P. D.; Gallo, E. L.; Barnard, H. R.; Harpold, A. A.

2015-12-01

Evaluating at high spatial-resolution the topographical and ecological structures of the critical zone (CZ) are now routine with aerial LiDAR. Here we evaluated the eco-hydrological differences of topographic metrics (the independent variables) versus individual tree and gridded aboveground carbon (AGC) pools (as dependent variables) at multiple length-scales across an elevation modified gradient of precipitation and temperature in the Boulder Creek CZ Observatory Watershed, Colorado USA. We describe the responses in AGC within the context of a three-zone eco-hydrological model, e.g. toe slope and valley bottoms (Zone 1), transitional hillslopes (Zone 2), and upper slopes to ridges (Zone 3). In a GIS we compared three separate zero-order basins: (1) the Betasso Preserve: 1,810-2,024 meters above mean sea level (m aμsl), area = 0.45 km2, n = 17,286 trees; (2) Upper and Lower Gordon Gulch: 2,446-2,737 m aμsl, area = 3.57 km2, n = 178,469 trees; and (3) Como Creek: 2,900m-3,560 m aμsl, area = 6.64 km2, n = 317,274 trees. In each of the three catchments Zone 1 held the greatest mean AGC (μ = 52.88-60.97 Mg C ha-1) and maximum AGC (99% confidence interval (CI, p = 0.01) = 152.95-184.95 Mg C ha-1) relative to Zone 2 (μ = 27.84-44.52 Mg C ha-1, 99% CI = 99.67-122.4 Mg C ha-1) and Zone 3 (μ = 12.63-30.33 Mg C ha-1, 99% CI = 62.16-92.65 Mg C ha-1). Topography with negative general curvatures (i.e. convergent shapes) had greater AGC (μ = 73.7-96.3 Mg C ha-1, 99% CI = 189.0-355.8 Mg C ha-1) than positive general curvatures (i.e. divergent shapes) (μ = 17.4-30.8 Mg C ha-1, 99% CI = 88.2-120.4 Mg C ha-1), but only when evaluated at longer length scales (<10 m). Larger AGC pools are postulated to be related to (1) increased soil depth which provides larger rooting zones and (2) access to groundwater along Zone 1, vs Zones 2 and 3 which have (a) shallower soils and (b) less or zero accessibility to groundwater.

Strategies for reforestation under uncertain future climates: guidelines for Alberta, Canada.

PubMed

Gray, Laura K; Hamann, Andreas

2011-01-01

Commercial forestry programs normally use locally collected seed for reforestation under the assumption that tree populations are optimally adapted to local environments. However, in western Canada this assumption is no longer valid because of climate trends that have occurred over the last several decades. The objective of this study is to show how we can arrive at reforestation recommendations with alternative species and genotypes that are viable under a majority of climate change scenarios. In a case study for commercially important tree species of Alberta, we use an ecosystem-based bioclimate envelope modeling approach for western North America to project habitat for locally adapted populations of tree species using multi-model climate projections for the 2020s, 2050s and 2080s. We find that genotypes of species that are adapted to drier climatic conditions will be the preferred planting stock over much of the boreal forest that is commercially managed. Interestingly, no alternative species that are currently not present in Alberta can be recommended with any confidence. Finally, we observe large uncertainties in projections of suitable habitat that make reforestation planning beyond the 2050s difficult for most species. More than 50,000 hectares of forests are commercially planted every year in Alberta. Choosing alternative planting stock, suitable for expected future climates, could therefore offer an effective climate change adaptation strategy at little additional cost. Habitat projections for locally adapted tree populations under observed climate change conform well to projections for the 2020s, which suggests that it is a safe strategy to change current reforestation practices and adapt to new climatic realities through assisted migration prescriptions.

Characterization of Forest Opacity Using Multi-Angular Emission and Backscatter Data

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; O'Neill, Peggy; Lang, Roger H.; Joseph, Alicia T.; Cosh, Michael H.; Jackson, Thomas J.

2010-01-01

This paper discusses the results from a series of field experiments using ground-based L-band microwave active/passive sensors. Three independent approaches are employed to the microwave data to determine vegetation opacity of coniferous trees. First, a zero-order radiative transfer model is fitted to multi-angular microwave emissivity data in a least-square sense to provide "effective" vegetation optical depth. Second, a ratio between radar backscatter measurements with the corner reflector under trees and in an open area is calculated to obtain "measured" tree propagation characteristics. Finally, the "theoretical" propagation constant is determined by forward scattering theorem using detailed measurements of size/angle distributions and dielectric constants of the tree constituents (trunk, branches, and needles). The results indicate that "effective" values underestimate attenuation values compared to both "theoretical" and "measured" values.

Transductive multi-view zero-shot learning.

PubMed

Fu, Yanwei; Hospedales, Timothy M; Xiang, Tao; Gong, Shaogang

2015-11-01

Most existing zero-shot learning approaches exploit transfer learning via an intermediate semantic representation shared between an annotated auxiliary dataset and a target dataset with different classes and no annotation. A projection from a low-level feature space to the semantic representation space is learned from the auxiliary dataset and applied without adaptation to the target dataset. In this paper we identify two inherent limitations with these approaches. First, due to having disjoint and potentially unrelated classes, the projection functions learned from the auxiliary dataset/domain are biased when applied directly to the target dataset/domain. We call this problem the projection domain shift problem and propose a novel framework, transductive multi-view embedding, to solve it. The second limitation is the prototype sparsity problem which refers to the fact that for each target class, only a single prototype is available for zero-shot learning given a semantic representation. To overcome this problem, a novel heterogeneous multi-view hypergraph label propagation method is formulated for zero-shot learning in the transductive embedding space. It effectively exploits the complementary information offered by different semantic representations and takes advantage of the manifold structures of multiple representation spaces in a coherent manner. We demonstrate through extensive experiments that the proposed approach (1) rectifies the projection shift between the auxiliary and target domains, (2) exploits the complementarity of multiple semantic representations, (3) significantly outperforms existing methods for both zero-shot and N-shot recognition on three image and video benchmark datasets, and (4) enables novel cross-view annotation tasks.

Adaptive sequential controller

DOEpatents

El-Sharkawi, Mohamed A.; Xing, Jian; Butler, Nicholas G.; Rodriguez, Alonso

1994-01-01

An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.

Cellulose factories: advancing bioenergy production from forest trees.

PubMed

Mizrachi, Eshchar; Mansfield, Shawn D; Myburg, Alexander A

2012-04-01

Fast-growing, short-rotation forest trees, such as Populus and Eucalyptus, produce large amounts of cellulose-rich biomass that could be utilized for bioenergy and biopolymer production. Major obstacles need to be overcome before the deployment of these genera as energy crops, including the effective removal of lignin and the subsequent liberation of carbohydrate constituents from wood cell walls. However, significant opportunities exist to both select for and engineer the structure and interaction of cell wall biopolymers, which could afford a means to improve processing and product development. The molecular underpinnings and regulation of cell wall carbohydrate biosynthesis are rapidly being elucidated, and are providing tools to strategically develop and guide the targeted modification required to adapt forest trees for the emerging bioeconomy. Much insight has already been gained from the perturbation of individual genes and pathways, but it is not known to what extent the natural variation in the sequence and expression of these same genes underlies the inherent variation in wood properties of field-grown trees. The integration of data from next-generation genomic technologies applied in natural and experimental populations will enable a systems genetics approach to study cell wall carbohydrate production in trees, and should advance the development of future woody bioenergy and biopolymer crops.

Photosynthetic temperature responses of tree species in Rwanda: evidence of pronounced negative effects of high temperature in montane rainforest climax species.

PubMed

Vårhammar, Angelica; Wallin, Göran; McLean, Christopher M; Dusenge, Mirindi Eric; Medlyn, Belinda E; Hasper, Thomas B; Nsabimana, Donat; Uddling, Johan

2015-05-01

The sensitivity of photosynthetic metabolism to temperature has been identified as a key uncertainty for projecting the magnitude of the terrestrial feedback on future climate change. While temperature responses of photosynthetic capacities have been comparatively well investigated in temperate species, the responses of tropical tree species remain unexplored. We compared the responses of seedlings of native cold-adapted tropical montane rainforest tree species with those of exotic warm-adapted plantation species, all growing in an intermediate temperature common garden in Rwanda. Leaf gas exchange responses to carbon dioxide (CO2 ) at different temperatures (20-40°C) were used to assess the temperature responses of biochemical photosynthetic capacities. Analyses revealed a lower optimum temperature for photosynthetic electron transport rates than for Rubisco carboxylation rates, along with lower electron transport optima in the native cold-adapted than in the exotic warm-adapted species. The photosynthetic optimum temperatures were generally exceeded by daytime peak leaf temperatures, in particular in the native montane rainforest climax species. This study thus provides evidence of pronounced negative effects of high temperature in tropical trees and indicates high susceptibility of montane rainforest climax species to future global warming. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Geospatial Technologies and i-Tree Echo Inventory for Predicting Climate Change on Urban Environment

NASA Astrophysics Data System (ADS)

Sriharan, S.; Robinson, L.; Ghariban, N.; Comar, M.; Pope, B.; Frey, G.

2015-12-01

Urban forests can be useful both in mitigating climate change and in helping cities adapt to higher temperatures and other impacts of climate change. Understanding and managing the impacts of climate change on the urban forest trees and natural communities will help us maintain their environmental, cultural, and economic benefits. Tree Inventory can provide important information on tree species, height, crown width, overall condition, health and maintenance needs. This presentation will demonstrate that a trees database system is necessary for developing a sustainable urban tree program. Virginia State University (VSU) campus benefits from large number and diversity of trees that are helping us by cleaning the air, retaining water, and providing shade on the buildings to reduce energy cost. The objectives of this study were to develop campus inventory of the trees, identify the tree species, map the locations of the trees with user-friendly tools such as i-Tree Eco and geospatial technologies by assessing the cost/benefit of employing student labor for training and ground validation of the results, and help campus landscape managers implement adaptive responses to climate change impacts. Data was collected on the location, species, and size of trees by using i-Tree urban forestry analysis software. This data was transferred to i-Tree inventory system for demonstrating types of trees, diameter of the trees, height of the trees, and vintage of the trees. The study site was mapped by collecting waypoints with GPS (Global Positioning System) at the trees and uploading these waypoints in ArcMap. The results of this study showed that: (i) students make good field crews, (ii) if more trees were placed in the proper area, the heating and cooling costs will reduce, and (iii) trees database system is necessary for planning, designing, planting, and maintenance, and removal of campus trees Research sponsored by the NIFA Grant, "Urban Forestry Management" (2012-38821-20153).

Folding Automaton for Trees

NASA Astrophysics Data System (ADS)

Subashini, N.; Thiagarajan, K.

2018-04-01

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

Modeling of air pollutant removal by dry deposition to urban trees using a WRF/CMAQ/i-Tree Eco coupled system

Treesearch

Maria Theresa I. Cabaraban; Charles N. Kroll; Satoshi Hirabayashi; David J. Nowak

2013-01-01

A distributed adaptation of i-Tree Eco was used to simulate dry deposition in an urban area. This investigation focused on the effects of varying temperature, LAI, and NO2 concentration inputs on estimated NO2 dry deposition to trees in Baltimore, MD. A coupled modeling system is described, wherein WRF provided temperature...

An effective fractal-tree closure model for simulating blood flow in large arterial networks.

PubMed

Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em

2015-06-01

The aim of the present work is to address the closure problem for hemodynamic simulations by developing a flexible and effective model that accurately distributes flow in the downstream vasculature and can stably provide a physiological pressure outflow boundary condition. To achieve this goal, we model blood flow in the sub-pixel vasculature by using a non-linear 1D model in self-similar networks of compliant arteries that mimic the structure and hierarchy of vessels in the meso-vascular regime (radii [Formula: see text]). We introduce a variable vessel length-to-radius ratio for small arteries and arterioles, while also addressing non-Newtonian blood rheology and arterial wall viscoelasticity effects in small arteries and arterioles. This methodology aims to overcome substantial cut-off radius sensitivities, typically arising in structured tree and linearized impedance models. The proposed model is not sensitive to outflow boundary conditions applied at the end points of the fractal network, and thus does not require calibration of resistance/capacitance parameters typically required for outflow conditions. The proposed model convergences to a periodic state in two cardiac cycles even when started from zero-flow initial conditions. The resulting fractal-trees typically consist of thousands to millions of arteries, posing the need for efficient parallel algorithms. To this end, we have scaled up a Discontinuous Galerkin solver that utilizes the MPI/OpenMP hybrid programming paradigm to thousands of computer cores, and can simulate blood flow in networks of millions of arterial segments at the rate of one cycle per 5 min. The proposed model has been extensively tested on a large and complex cranial network with 50 parent, patient-specific arteries and 21 outlets to which fractal trees where attached, resulting to a network of up to 4,392,484 vessels in total, and a detailed network of the arm with 276 parent arteries and 103 outlets (a total of 702,188 vessels after attaching the fractal trees), returning physiological flow and pressure wave predictions without requiring any parameter estimation or calibration procedures. We present a novel methodology to overcome substantial cut-off radius sensitivities.

An efective fractal-tree closure model for simulating blood flow in large arterial networks

PubMed Central

Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em.

2014-01-01

The aim of the present work is to address the closure problem for hemodynamic simulations by developing a exible and effective model that accurately distributes flow in the downstream vasculature and can stably provide a physiological pressure out flow boundary condition. To achieve this goal, we model blood flow in the sub-pixel vasculature by using a non-linear 1D model in self-similar networks of compliant arteries that mimic the structure and hierarchy of vessels in the meso-vascular regime (radii 500 μm – 10 μm). We introduce a variable vessel length-to-radius ratio for small arteries and arterioles, while also addressing non-Newtonian blood rheology and arterial wall viscoelasticity effects in small arteries and arterioles. This methodology aims to overcome substantial cut-off radius sensitivities, typically arising in structured tree and linearized impedance models. The proposed model is not sensitive to out flow boundary conditions applied at the end points of the fractal network, and thus does not require calibration of resistance/capacitance parameters typically required for out flow conditions. The proposed model convergences to a periodic state in two cardiac cycles even when started from zero-flow initial conditions. The resulting fractal-trees typically consist of thousands to millions of arteries, posing the need for efficient parallel algorithms. To this end, we have scaled up a Discontinuous Galerkin solver that utilizes the MPI/OpenMP hybrid programming paradigm to thousands of computer cores, and can simulate blood flow in networks of millions of arterial segments at the rate of one cycle per 5 minutes. The proposed model has been extensively tested on a large and complex cranial network with 50 parent, patient-specific arteries and 21 outlets to which fractal trees where attached, resulting to a network of up to 4,392,484 vessels in total, and a detailed network of the arm with 276 parent arteries and 103 outlets (a total of 702,188 vessels after attaching the fractal trees), returning physiological flow and pressure wave predictions without requiring any parameter estimation or calibration procedures. We present a novel methodology to overcome substantial cut-off radius sensitivities PMID:25510364

In vitro and in vivo killing of ocular Demodex by tea tree oil

PubMed Central

Gao, Y-Y; Di Pascuale, M A; Li, W; Baradaran-Rafii, A; Elizondo, A; Kuo, C-L; Raju, V K; Tseng, S C G

2005-01-01

Aims: To compare the in vitro killing effect of different agents on Demodex and to report the in vivo killing effect of tea tree oil (TTO) on ocular Demodex. Methods: Survival time of Demodex was measured under the microscope. Sampling and counting of Demodex was performed by a modified method. Results: Demodex folliculorum survived for more than 150 minutes in 10% povidone-iodine, 75% alcohol, 50% baby shampoo, and 4% pilocarpine. However, the survival time was significantly shortened to within 15 minutes in 100% alcohol, 100% TTO, 100% caraway oil, or 100% dill weed oil. TTO’s in vitro killing effect was dose dependent. Lid scrub with 50% TTO, but not with 50% baby shampoo, can further stimulate Demodex to move out to the skin. The Demodex count did not reach zero in any of the seven patients receiving daily lid scrub with baby shampoo for 40–350 days. In contrast, the Demodex count dropped to zero in seven of nine patients receiving TTO scrub in 4 weeks without recurrence. Conclusions: Demodex is resistant to a wide range of antiseptic solutions. Weekly lid scrub with 50% TTO and daily lid scrub with tea tree shampoo is effective in eradicating ocular Demodex. PMID:16234455

Tree-based solvers for adaptive mesh refinement code FLASH - I: gravity and optical depths

NASA Astrophysics Data System (ADS)

Wünsch, R.; Walch, S.; Dinnbier, F.; Whitworth, A.

2018-04-01

We describe an OctTree algorithm for the MPI parallel, adaptive mesh refinement code FLASH, which can be used to calculate the gas self-gravity, and also the angle-averaged local optical depth, for treating ambient diffuse radiation. The algorithm communicates to the different processors only those parts of the tree that are needed to perform the tree-walk locally. The advantage of this approach is a relatively low memory requirement, important in particular for the optical depth calculation, which needs to process information from many different directions. This feature also enables a general tree-based radiation transport algorithm that will be described in a subsequent paper, and delivers excellent scaling up to at least 1500 cores. Boundary conditions for gravity can be either isolated or periodic, and they can be specified in each direction independently, using a newly developed generalization of the Ewald method. The gravity calculation can be accelerated with the adaptive block update technique by partially re-using the solution from the previous time-step. Comparison with the FLASH internal multigrid gravity solver shows that tree-based methods provide a competitive alternative, particularly for problems with isolated or mixed boundary conditions. We evaluate several multipole acceptance criteria (MACs) and identify a relatively simple approximate partial error MAC which provides high accuracy at low computational cost. The optical depth estimates are found to agree very well with those of the RADMC-3D radiation transport code, with the tree-solver being much faster. Our algorithm is available in the standard release of the FLASH code in version 4.0 and later.

Evolution of the Genetic and Neural Architecture for Vertebrate Odor Perception

PubMed Central

Bear, Daniel M.; Lassance, Jean-Marc; Hoekstra, Hopi E.; Datta, Sandeep Robert

2016-01-01

Evolution sculpts the olfactory nervous system in response to the unique sensory challenges facing each species. In vertebrates, dramatic and diverse adaptations to the chemical environment are possible because of the hierarchical structure of the olfactory receptor (OR) gene superfamily: rapid growth or pruning across the OR gene tree accompany major changes in habitat and lifestyle; independent selection on OR subfamilies can permit local adaptation or conserved chemical communication; and genetic variation in single OR genes among thousands can alter odor percepts and behaviors driven by precise chemical cues. However, this genetic flexibility contrasts with the relatively fixed neural architecture of the vertebrate olfactory system, whose slower rate of divergence mandates that new olfactory receptors integrate into segregated and functionally-distinct neural pathways. This organization allows evolution to couple critical chemical signals with selectively advantageous responses, but also constrains relationships between olfactory receptors and behavior. The coevolution of the OR repertoire and the structure of the olfactory system therefore reveals general principles of how the brain solves specific sensory problems and how it adapts to new ones. PMID:27780046

Do ecohydrology and community dynamics feed back to banded-ecosystem structure and productivity?

NASA Astrophysics Data System (ADS)

Callegaro, Chiara; Ursino, Nadia

2016-04-01

Mixed communities including grass, shrubs and trees are often reported to populate self-organized vegetation patterns. Patterns of survey data suggest that species diversity and complementarity strengthen the dynamics of banded environments. Resource scarcity and local facilitation trigger self organization, whereas coexistence of multiple species in vegetated self-organizing patches, implying competition for water and nutrients and favorable reproduction sites, is made possible by differing adaptation strategies. Mixed community spatial self-organization has so far received relatively little attention, compared with local net facilitation of isolated species. We assumed that soil moisture availability is a proxy for the environmental niche of plant species according to Ursino and Callegaro (2016). Our modelling effort was focused on niche differentiation of coexisting species within a tiger bush type ecosystem. By minimal numerical modelling and stability analysis we try to answer a few open scientific questions: Is there an adaptation strategy that increases biodiversity and ecosystem functioning? Does specific adaptation to environmental niches influence the structure of self-organizing vegetation pattern? What specific niche distribution along the environmental gradient gives the highest global productivity?

Fire Impacts on Mixed Pine-oak Forests Assessed with High Spatial Resolution Imagery, Imaging Spectroscopy, and LiDAR

NASA Astrophysics Data System (ADS)

Meng, R.; Wu, J.; Zhao, F. R.; Kathy, S. L.; Dennison, P. E.; Cook, B.; Hanavan, R. P.; Serbin, S.

2016-12-01

As a primary disturbance agent, fire significantly influences forest ecosystems, including the modification or resetting of vegetation composition and structure, which can then significantly impact landscape-scale plant function and carbon stocks. Most ecological processes associated with fire effects (e.g. tree damage, mortality, and vegetation recovery) display fine-scale, species specific responses but can also vary spatially within the boundary of the perturbation. For example, both oak and pine species are fire-adapted, but fire can still induce changes in composition, structure, and dominance in a mixed pine-oak forest, mainly because of their varying degrees of fire adaption. Evidence of post-fire shifts in dominance between oak and pine species has been documented in mixed pine-oak forests, but these processes have been poorly investigated in a spatially explicit manner. In addition, traditional field-based means of quantifying the response of partially damaged trees across space and time is logistically challenging. Here we show how combining high resolution satellite imagery (i.e. Worldview-2,WV-2) and airborne imaging spectroscopy and LiDAR (i.e. NASA Goddard's Lidar, Hyperspectral and Thermal airborne imager, G-LiHT) can be effectively used to remotely quantify spatial and temporal patterns of vegetation recovery following a top-killing fire that occurred in 2012 within mixed pine-oak forests in the Long Island Central Pine Barrens Region, New York. We explore the following questions: 1) what are the impacts of fire on species composition, dominance, plant health, and vertical structure; 2) what are the recovery trajectories of forest biomass, structure, and spectral properties for three years following the fire; and 3) to what extent can fire impacts be captured and characterized by multi-sensor remote sensing techniques from active and passive optical remote sensing.

Interrelations between hydraulic and mechanical stress adaptations in woody plants

PubMed Central

Ennos, A Roland; Fournier, Meriem

2008-01-01

The fields of plant water relations and plant biomechanics have traditionally been studied separately even though often the same tissues are responsible for water transport and mechanical support. There is now increasing evidence that hydraulic and mechanical adaptations may influence one another. We studied the changes in the hydraulic and mechanical properties of the wood along lateral roots of two species of buttressed trees. In these roots, the mechanical contstraints quantified by strain measurements are known to decrease distally. Further, we investigated the effect of mechanical loading on the vessel anatomy in these and four other species of tropical trees. We found that as the strain decreased, the wood became progressively less stiff and strong but the conductivity increased exponentially. This was reflected in that adaptations towards re-enforcing mechanically loaded areas resulted in xylem with fewer and smaller vessels. In addition a controlled growth experiment on three tree species showed that drought adaptation may results in plants with stronger and stiffer tissue. Our results indicate that hydraulic and mechanical stress adaptations may be interrelated, and so support recent studied suggesting that physiological responses are complex balances rather than pure optimisations. PMID:19704486

Dynamic Event Tree advancements and control logic improvements

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

Alfonsi, Andrea; Rabiti, Cristian; Mandelli, Diego

The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN is currently equipped with three different sampling categories: Forward samplers (Monte Carlo, Latin Hyper Cube, Stratified, Grid Sampler, Factorials, etc.), Adaptive Samplers (Limit Surface search, Adaptive Polynomial Chaos, etc.) and Dynamic Event Tree (DET) samplers (Deterministic and Adaptive Dynamic Event Trees). The main subject of this document is to report the activities that have been donemore » in order to: start the migration of the RAVEN/RELAP-7 control logic system into MOOSE, and develop advanced dynamic sampling capabilities based on the Dynamic Event Tree approach. In order to provide to all MOOSE-based applications a control logic capability, in this Fiscal Year an initial migration activity has been initiated, moving the control logic system, designed for RELAP-7 by the RAVEN team, into the MOOSE framework. In this document, a brief explanation of what has been done is going to be reported. The second and most important subject of this report is about the development of a Dynamic Event Tree (DET) sampler named “Hybrid Dynamic Event Tree” (HDET) and its Adaptive variant “Adaptive Hybrid Dynamic Event Tree” (AHDET). As other authors have already reported, among the different types of uncertainties, it is possible to discern two principle types: aleatory and epistemic uncertainties. The classical Dynamic Event Tree is in charge of treating the first class (aleatory) uncertainties; the dependence of the probabilistic risk assessment and analysis on the epistemic uncertainties are treated by an initial Monte Carlo sampling (MCDET). From each Monte Carlo sample, a DET analysis is run (in total, N trees). The Monte Carlo employs a pre-sampling of the input space characterized by epistemic uncertainties. The consequent Dynamic Event Tree performs the exploration of the aleatory space. In the RAVEN code, a more general approach has been developed, not limiting the exploration of the epistemic space through a Monte Carlo method but using all the forward sampling strategies RAVEN currently employs. The user can combine a Latin Hyper Cube, Grid, Stratified and Monte Carlo sampling in order to explore the epistemic space, without any limitation. From this pre-sampling, the Dynamic Event Tree sampler starts its aleatory space exploration. As reported by the authors, the Dynamic Event Tree is a good fit to develop a goal-oriented sampling strategy. The DET is used to drive a Limit Surface search. The methodology that has been developed by the authors last year, performs a Limit Surface search in the aleatory space only. This report documents how this approach has been extended in order to consider the epistemic space interacting with the Hybrid Dynamic Event Tree methodology.« less

Nine Years of Irrigation Cause Vegetation and Fine Root Shifts in a Water-Limited Pine Forest

PubMed Central

Herzog, Claude; Steffen, Jan; Graf Pannatier, Elisabeth; Hajdas, Irka; Brunner, Ivano

2014-01-01

Scots pines (Pinus sylvestris L.) in the inner-Alpine dry valleys of Switzerland have suffered from increased mortality during the past decades, which has been caused by longer and more frequent dry periods. In addition, a proceeding replacement of Scots pines by pubescent oaks (Quercus pubescens Willd.) has been observed. In 2003, an irrigation experiment was performed to track changes by reducing drought pressure on the natural pine forest. After nine years of irrigation, we observed major adaptations in the vegetation and shifts in Scots pine fine root abundance and structure. Irrigation permitted new plant species to assemble and promote canopy closure with a subsequent loss of herb and moss coverage. Fine root dry weight increased under irrigation and fine roots had a tendency to elongate. Structural composition of fine roots remained unaffected by irrigation, expressing preserved proportions of cellulose, lignin and phenolic substances. A shift to a more negative δ13C signal in the fine root C indicates an increased photosynthetic activity in irrigated pine trees. Using radiocarbon (14C) measurement, a reduced mean age of the fine roots in irrigated plots was revealed. The reason for this is either an increase in newly produced fine roots, supported by the increase in fine root biomass, or a reduced lifespan of fine roots which corresponds to an enhanced turnover rate. Overall, the responses belowground to irrigation are less conspicuous than the more rapid adaptations aboveground. Lagged and conservative adaptations of tree roots with decadal lifespans are challenging to detect, hence demanding for long-term surveys. Investigations concerning fine root turnover rate and degradation processes under a changing climate are crucial for a complete understanding of C cycling. PMID:24802642

Research on the Forward and Reverse Calculation Based on the Adaptive Zero-Velocity Interval Adjustment for the Foot-Mounted Inertial Pedestrian-Positioning System

PubMed Central

Wang, Qiuying; Guo, Zheng; Sun, Zhiguo; Cui, Xufei; Liu, Kaiyue

2018-01-01

Pedestrian-positioning technology based on the foot-mounted micro inertial measurement unit (MIMU) plays an important role in the field of indoor navigation and has received extensive attention in recent years. However, the positioning accuracy of the inertial-based pedestrian-positioning method is rapidly reduced because of the relatively low measurement accuracy of the measurement sensor. The zero-velocity update (ZUPT) is an error correction method which was proposed to solve the cumulative error because, on a regular basis, the foot is stationary during the ordinary gait; this is intended to reduce the position error growth of the system. However, the traditional ZUPT has poor performance because the time of foot touchdown is short when the pedestrians move faster, which decreases the positioning accuracy. Considering these problems, a forward and reverse calculation method based on the adaptive zero-velocity interval adjustment for the foot-mounted MIMU location method is proposed in this paper. To solve the inaccuracy of the zero-velocity interval detector during fast pedestrian movement where the contact time of the foot on the ground is short, an adaptive zero-velocity interval detection algorithm based on fuzzy logic reasoning is presented in this paper. In addition, to improve the effectiveness of the ZUPT algorithm, forward and reverse multiple solutions are presented. Finally, with the basic principles and derivation process of this method, the MTi-G710 produced by the XSENS company is used to complete the test. The experimental results verify the correctness and applicability of the proposed method. PMID:29883399

Computational path planner for product assembly in complex environments

NASA Astrophysics Data System (ADS)

Shang, Wei; Liu, Jianhua; Ning, Ruxin; Liu, Mi

2013-03-01

Assembly path planning is a crucial problem in assembly related design and manufacturing processes. Sampling based motion planning algorithms are used for computational assembly path planning. However, the performance of such algorithms may degrade much in environments with complex product structure, narrow passages or other challenging scenarios. A computational path planner for automatic assembly path planning in complex 3D environments is presented. The global planning process is divided into three phases based on the environment and specific algorithms are proposed and utilized in each phase to solve the challenging issues. A novel ray test based stochastic collision detection method is proposed to evaluate the intersection between two polyhedral objects. This method avoids fake collisions in conventional methods and degrades the geometric constraint when a part has to be removed with surface contact with other parts. A refined history based rapidly-exploring random tree (RRT) algorithm which bias the growth of the tree based on its planning history is proposed and employed in the planning phase where the path is simple but the space is highly constrained. A novel adaptive RRT algorithm is developed for the path planning problem with challenging scenarios and uncertain environment. With extending values assigned on each tree node and extending schemes applied, the tree can adapts its growth to explore complex environments more efficiently. Experiments on the key algorithms are carried out and comparisons are made between the conventional path planning algorithms and the presented ones. The comparing results show that based on the proposed algorithms, the path planner can compute assembly path in challenging complex environments more efficiently and with higher success. This research provides the references to the study of computational assembly path planning under complex environments.

Tree structure and cavity microclimate: implications for bats and birds.

PubMed

Clement, Matthew J; Castleberry, Steven B

2013-05-01

It is widely assumed that tree cavity structure and microclimate affect cavity selection and use in cavity-dwelling bats and birds. Despite the interest in tree structure and microclimate, the relationship between the two has rarely been quantified. Currently available data often comes from artificial structures that may not accurately represent conditions in natural cavities. We collected data on tree cavity structure and microclimate from 45 trees in five cypress-gum swamps in the Coastal Plain of Georgia in the United States in 2008. We used hierarchical linear models to predict cavity microclimate from tree structure and ambient temperature and humidity, and used Aikaike's information criterion to select the most parsimonious models. We found large differences in microclimate among trees, but tree structure variables explained <28% of the variation, while ambient conditions explained >80% of variation common to all trees. We argue that the determinants of microclimate are complex and multidimensional, and therefore cavity microclimate cannot be deduced easily from simple tree structures. Furthermore, we found that daily fluctuations in ambient conditions strongly affect microclimate, indicating that greater weather fluctuations will cause greater differences among tree cavities.

Slowdowns in diversification rates from real phylogenies may not be real.

PubMed

Cusimano, Natalie; Renner, Susanne S

2010-07-01

Studies of diversification patterns often find a slowing in lineage accumulation toward the present. This seemingly pervasive pattern of rate downturns has been taken as evidence for adaptive radiations, density-dependent regulation, and metacommunity species interactions. The significance of rate downturns is evaluated with statistical tests (the gamma statistic and Monte Carlo constant rates (MCCR) test; birth-death likelihood models and Akaike Information Criterion [AIC] scores) that rely on null distributions, which assume that the included species are a random sample of the entire clade. Sampling in real phylogenies, however, often is nonrandom because systematists try to include early-diverging species or representatives of previous intrataxon classifications. We studied the effects of biased sampling, structured sampling, and random sampling by experimentally pruning simulated trees (60 and 150 species) as well as a completely sampled empirical tree (58 species) and then applying the gamma statistic/MCCR test and birth-death likelihood models/AIC scores to assess rate changes. For trees with random species sampling, the true model (i.e., the one fitting the complete phylogenies) could be inferred in most cases. Oversampling deep nodes, however, strongly biases inferences toward downturns, with simulations of structured and biased sampling suggesting that this occurs when sampling percentages drop below 80%. The magnitude of the effect and the sensitivity of diversification rate models is such that a useful rule of thumb may be not to infer rate downturns from real trees unless they have >80% species sampling.

The Refinement-Tree Partition for Parallel Solution of Partial Differential Equations

PubMed Central

Mitchell, William F.

1998-01-01

Dynamic load balancing is considered in the context of adaptive multilevel methods for partial differential equations on distributed memory multiprocessors. An approach that periodically repartitions the grid is taken. The important properties of a partitioning algorithm are presented and discussed in this context. A partitioning algorithm based on the refinement tree of the adaptive grid is presented and analyzed in terms of these properties. Theoretical and numerical results are given. PMID:28009355

The Refinement-Tree Partition for Parallel Solution of Partial Differential Equations.

PubMed

Mitchell, William F

1998-01-01

Dynamic load balancing is considered in the context of adaptive multilevel methods for partial differential equations on distributed memory multiprocessors. An approach that periodically repartitions the grid is taken. The important properties of a partitioning algorithm are presented and discussed in this context. A partitioning algorithm based on the refinement tree of the adaptive grid is presented and analyzed in terms of these properties. Theoretical and numerical results are given.

Predicting Douglas-fir's response to a warming climate

Treesearch

Andrea Watts; Sheel Bansal; Connie Harrington; Brad St. Clair

2015-01-01

Douglas-fir is an iconic tree in the Pacific Northwest. Although individual trees may appear to be identical, genetic differences within each tree have resulted from adaptation to the local environment. These genetic differences over time have resulted in differences among populations that are important to the species' survival and growth in changing climates....

Decision-Tree Models of Categorization Response Times, Choice Proportions, and Typicality Judgments

ERIC Educational Resources Information Center

Lafond, Daniel; Lacouture, Yves; Cohen, Andrew L.

2009-01-01

The authors present 3 decision-tree models of categorization adapted from T. Trabasso, H. Rollins, and E. Shaughnessy (1971) and use them to provide a quantitative account of categorization response times, choice proportions, and typicality judgments at the individual-participant level. In Experiment 1, the decision-tree models were fit to…

From forest to freezer: a comprehensive seed collection of the Kentucky coffeetree, Gymnocladus dioicus (L.) K

Treesearch

A.P. Schmitz; J.D. Carstens

2017-01-01

Kentucky coffeetree, Gymnocladus dioicus, is a picturesque shade tree adaptable to urban conditions and drought, with no serious insect or disease problems. These traits make G. dioicus a promising candidate among diverse tree genera to replace ash (Fraxinus) trees affected by the emerald ash borer (Agrilus...

Influence of repeated prescribed fire on tree growth and mortality in Pinus resinosa forests, northern Minnesota

USGS Publications Warehouse

Bottero, Alessandra; D'Amato, Anthony W.; Palik, Brian J.; Kern, Christel C.; Bradford, John B.; Scherer, Sawyer S.

2017-01-01

Prescribed fire is widely used for ecological restoration and fuel reduction in fire-dependent ecosystems, most of which are also prone to drought. Despite the importance of drought in fire-adapted forests, little is known about cumulative effects of repeated prescribed burning on tree growth and related response to drought. Using dendrochronological data in red pine (Pinus resinosa Ait.)-dominated forests in northern Minnesota, USA, we examined growth responses before and after understory prescribed fires between 1960 and 1970, to assess whether repeated burning influences growth responses of overstory trees and vulnerability of overstory tree growth to drought. We found no difference in tree-level growth vulnerability to drought, expressed as growth resistance, resilience, and recovery, between areas receiving prescribed fire treatments and untreated forests. Annual mortality rates during the period of active burning were also low (less than 2%) in all treatments. These findings indicate that prescribed fire can be effectively integrated into management plans and climate change adaptation strategies for red pine forest ecosystems without significant short- or long-term negative consequences for growth or mortality rates of overstory trees.

A Novel Zero Velocity Interval Detection Algorithm for Self-Contained Pedestrian Navigation System with Inertial Sensors

PubMed Central

Tian, Xiaochun; Chen, Jiabin; Han, Yongqiang; Shang, Jianyu; Li, Nan

2016-01-01

Zero velocity update (ZUPT) plays an important role in pedestrian navigation algorithms with the premise that the zero velocity interval (ZVI) should be detected accurately and effectively. A novel adaptive ZVI detection algorithm based on a smoothed pseudo Wigner–Ville distribution to remove multiple frequencies intelligently (SPWVD-RMFI) is proposed in this paper. The novel algorithm adopts the SPWVD-RMFI method to extract the pedestrian gait frequency and to calculate the optimal ZVI detection threshold in real time by establishing the function relationships between the thresholds and the gait frequency; then, the adaptive adjustment of thresholds with gait frequency is realized and improves the ZVI detection precision. To put it into practice, a ZVI detection experiment is carried out; the result shows that compared with the traditional fixed threshold ZVI detection method, the adaptive ZVI detection algorithm can effectively reduce the false and missed detection rate of ZVI; this indicates that the novel algorithm has high detection precision and good robustness. Furthermore, pedestrian trajectory positioning experiments at different walking speeds are carried out to evaluate the influence of the novel algorithm on positioning precision. The results show that the ZVI detected by the adaptive ZVI detection algorithm for pedestrian trajectory calculation can achieve better performance. PMID:27669266

Individual tree size inequality enhances aboveground biomass in homegarden agroforestry systems in the dry zone of Sri Lanka.

PubMed

Ali, Arshad; Mattsson, Eskil

2017-01-01

Individual tree size variation, which is generally quantified by variances in tree diameter at breast height (DBH) and height in isolation or conjunction, plays a central role in ecosystem functioning in both controlled and natural environments, including forests. However, none of the studies have been conducted in homegarden agroforestry systems. In this study, aboveground biomass, stand quality, cation exchange capacity (CEC), DBH variation, and species diversity were determined across 45 homegardens in the dry zone of Sri Lanka. We employed structural equation modeling (SEM) to test for the direct and indirect effects of stand quality and CEC, via tree size inequality and species diversity, on aboveground biomass. The SEM accounted for 26, 8, and 1% of the variation in aboveground biomass, species diversity and DBH variation, respectively. DBH variation had the strongest positive direct effect on aboveground biomass (β=0.49), followed by the non-significant direct effect of species diversity (β=0.17), stand quality (β=0.17) and CEC (β=-0.05). There were non-significant direct effects of CEC and stand quality on DBH variation and species diversity. Stand quality and CEC had also non-significant indirect effects, via DBH variation and species diversity, on aboveground biomass. Our study revealed that aboveground biomass substantially increased with individual tree size variation only, which supports the niche complementarity mechanism. However, aboveground biomass was not considerably increased with species diversity, stand quality and soil fertility, which might be attributable to the adaptation of certain productive species to the local site conditions. Stand structure shaped by few productive species or independent of species diversity is a main determinant for the variation in aboveground biomass in the studied homegardens. Maintaining stand structure through management practices could be an effective approach for enhancing aboveground biomass in these dry zone homegarden agroforestry systems. Copyright © 2016 Elsevier B.V. All rights reserved.

RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology

PubMed Central

Elmetwaly, Shereef; Schlick, Tamar

2014-01-01

Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in structural biology, structures of molecules can be described, including RNA structures. In our RNA-As-Graphs (RAG) framework, we represent RNA structures as tree graphs by translating unpaired regions into vertices and helices into edges. Here we explore the modularity of RNA structures by applying graph partitioning known in graph theory to divide an RNA graph into subgraphs. To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general. The graph partitioning algorithms utilize mathematical properties of the Laplacian eigenvector (µ2) corresponding to the second eigenvalues (λ2) associated with the topology matrix defining the graph: λ2 describes the overall topology, and the sum of µ2′s components is zero. The three types of algorithms, termed median, sign, and gap cuts, divide a graph by determining nodes of cut by median, zero, and largest gap of µ2′s components, respectively. We apply these algorithms to 45 graphs corresponding to all solved RNA structures up through 11 vertices (∼220 nucleotides). While we observe that the median cut divides a graph into two similar-sized subgraphs, the sign and gap cuts partition a graph into two topologically-distinct subgraphs. We find that the gap cut produces the best biologically-relevant partitioning for RNA because it divides RNAs at less stable connections while maintaining junctions intact. The iterative gap cuts suggest basic modules and assembly protocols to design large RNA structures. Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks. In our applications to RNA structures, subgraphs also suggest design strategies for novel RNA motifs. PMID:25188578

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat

PubMed Central

Guidugli, M C; Nazareno, A G; Feres, J M; Contel, E P B; Mestriner, M A; Alzate-Marin, A L

2016-01-01

Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population. PMID:26732014

Disturbance and productivity interactions mediate stability of forest composition and structure.

PubMed

O'Connor, Christopher D; Falk, Donald A; Lynch, Ann M; Swetnam, Thomas W; Wilcox, Craig P

2017-04-01

Fire is returning to many conifer-dominated forests where species composition and structure have been altered by fire exclusion. Ecological effects of these fires are influenced strongly by the degree of forest change during the fire-free period. Response of fire-adapted species assemblages to extended fire-free intervals is highly variable, even in communities with similar historical fire regimes. This variability in plant community response to fire exclusion is not well understood; however, ecological mechanisms such as individual species' adaptations to disturbance or competition and underlying site characteristics that facilitate or impede establishment and growth have been proposed as potential drivers of assemblage response. We used spatially explicit dendrochronological reconstruction of tree population dynamics and fire regimes to examine the influence of historical disturbance frequency (a proxy for adaptation to disturbance or competition), and potential site productivity (a proxy for underlying site characteristics) on the stability of forest composition and structure along a continuous ecological gradient of pine, dry mixed-conifer, mesic mixed-conifer, and spruce-fir forests following fire exclusion. While average structural density increased in all forests, species composition was relatively stable in the lowest productivity pine-dominated and highest productivity spruce-fir-dominated sites immediately following fire exclusion and for the next 100 years, suggesting site productivity as a primary control on species composition and structure in forests with very different historical fire regimes. Species composition was least stable on intermediate productivity sites dominated by mixed-conifer forests, shifting from primarily fire-adapted species to competition-adapted, fire-sensitive species within 20 years of fire exclusion. Rapid changes to species composition and stand densities have been interpreted by some as evidence of high-severity fire. We demonstrate that the very different ecological process of fire exclusion can produce similar changes by shifting selective pressures from disturbance-mediated to productivity-mediated controls. Restoring disturbance-adapted species composition and structure to intermediate productivity forests may help to buffer them against projected increasing temperatures, lengthening fire seasons, and more frequent and prolonged moisture stress. Fewer management options are available to promote adaptation in forest assemblages historically constrained by underlying site productivity. © 2016 by the Ecological Society of America.

On the zero-crossing of the three-gluon Green's function from lattice simulations

NASA Astrophysics Data System (ADS)

Athenodorou, Andreas; Boucaud, Philippe; de Soto, Feliciano; Rodríguez-Quintero, José; Zafeiropoulos, Savvas

2018-03-01

We report on some efforts recently made in order to gain a better understanding of some IR properties of the 3-point gluon Green's function by exploiting results from large-volume quenched lattice simulations. These lattice results have been obtained by using both tree-level Symanzik and the standard Wilson action, in the aim of assessing the possible impact of effects presumably resulting from a particular choice for the discretization of the action. The main resulting feature is the existence of a negative log-aritmic divergence at zero-momentum, which pulls the 3-gluon form factors down at low momenta and, consequently, yields a zero-crossing at a given deep IR momentum. The results can be correctly explained by analyzing the relevant Dyson-Schwinger equations and appropriate truncation schemes.

Strategies for Reforestation under Uncertain Future Climates: Guidelines for Alberta, Canada

PubMed Central

Gray, Laura K.; Hamann, Andreas

2011-01-01

Background Commercial forestry programs normally use locally collected seed for reforestation under the assumption that tree populations are optimally adapted to local environments. However, in western Canada this assumption is no longer valid because of climate trends that have occurred over the last several decades. The objective of this study is to show how we can arrive at reforestation recommendations with alternative species and genotypes that are viable under a majority of climate change scenarios. Methodology/Principal Findings In a case study for commercially important tree species of Alberta, we use an ecosystem-based bioclimate envelope modeling approach for western North America to project habitat for locally adapted populations of tree species using multi-model climate projections for the 2020s, 2050s and 2080s. We find that genotypes of species that are adapted to drier climatic conditions will be the preferred planting stock over much of the boreal forest that is commercially managed. Interestingly, no alternative species that are currently not present in Alberta can be recommended with any confidence. Finally, we observe large uncertainties in projections of suitable habitat that make reforestation planning beyond the 2050s difficult for most species. Conclusion/Significance More than 50,000 hectares of forests are commercially planted every year in Alberta. Choosing alternative planting stock, suitable for expected future climates, could therefore offer an effective climate change adaptation strategy at little additional cost. Habitat projections for locally adapted tree populations under observed climate change conform well to projections for the 2020s, which suggests that it is a safe strategy to change current reforestation practices and adapt to new climatic realities through assisted migration prescriptions. PMID:21853061

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.

PubMed

Herges, T; Wenzel, W

2005-01-14

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

NASA Astrophysics Data System (ADS)

Herges, T.; Wenzel, W.

2005-01-01

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

Local adaptation at the range peripheries of Sitka spruce.

PubMed

Mimura, M; Aitken, S N

2010-02-01

High-dispersal rates in heterogeneous environments and historical rapid range expansion can hamper local adaptation; however, we often see clinal variation in high-dispersal tree species. To understand the mechanisms of the species' distribution, we investigated local adaptation and adaptive plasticity in a range-wide context in Sitka spruce, a wind-pollinated tree species that has recently expanded its range after glaciations. Phenotypic traits were observed using growth chamber experiments that mimicked temperature and photoperiodic regimes from the limits of the species realized niche. Bud phenology exhibited parallel reaction norms among populations; however, putatively adaptive plasticity and strong divergent selection were seen in bud burst and bud set timing respectively. Natural selection appears to have favoured genotypes that maximize growth rate during available frost-free periods in each environment. We conclude that Sitka spruce has developed local adaptation and adaptive plasticity throughout its range in response to current climatic conditions despite generally high pollen flow and recent range expansion.

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.

PubMed

Beckers, Bram; Op De Beeck, Michiel; Weyens, Nele; Boerjan, Wout; Vangronsveld, Jaco

2017-02-23

The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches. We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats. We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus. Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.

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...

Quantitative metrics for assessing predicted climate change pressure on North American tree species

Treesearch

Kevin M. Potter; William W. Hargrove

2013-01-01

Changing climate may pose a threat to forest tree species, forcing three potential population-level responses: toleration/adaptation, movement to suitable environmental conditions, or local extirpation. Assessments that prioritize and classify tree species for management and conservation activities in the face of climate change will need to incorporate estimates of the...

Assisted migration: What it means to nursery managers and tree planters

Treesearch

Mary I. Williams; R. Kasten Dumroese

2014-01-01

Projections indicate that natural plant adaptation and migration may not keep pace with climate changes. This mismatch in rates will pose significant challenges for practitioners that select, grow, and outplant native tree species. Populations of native tree species planted today must be able to meet the climatic challenges they will face during this century. One...

Does biodiversity make a difference? Relationships between species richness, evolutionary diversity, and aboveground live tree biomass across US forests

Treesearch

Kevin M. Potter; Christopher W. Woodall

2014-01-01

Biodiversity conveys numerous functional benefits to forested ecosystems, including community stability and resilience. In the context of managing forests for climate change mitigation/adaptation, maximizing and/or maintaining aboveground biomass will require understanding the interactions between tree biodiversity, site productivity, and the stocking of live trees....

The use of witness trees as pyro-indicators for mapping past fire conditions

Treesearch

Melissa A. Thomas-Van Gundy; Gregory J. Nowacki

2013-01-01

Understanding and mapping presettlement fire regimes is vitally important for ecosystem restoration, helping ensure the proper placement of fire back into ecosystems that formerly burned. Witness trees can support this endeavor by serving as pyro-indicators of the past. We mapped fire-adapted traits across a landscape by categorizing trees into two classes, pyrophiles...

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...

Banking on the future: progress, challenges and opportunities for the genetic conservation of forest trees

Treesearch

Kevin M. Potter; Robert M. Jetton; Andrew Bower; Douglass F. Jacobs; Gary Man; Valerie D. Hipkins; Murphy Westwood

2017-01-01

Genetic diversity provides the essential basis for the adaptation and resilience of tree species to environmental stress and change. The genetic conservation of tree species is an urgent global necessity as forest conversion and fragmentation continue apace, damaging insects and pathogens are transported between continents, and climate change alters local habitat...

Safety and efficiency conflicts in hydraulic architecture: scaling from tissues to trees

Treesearch

John S. Sperry; Frederick C. Meinzer; Katherine A. McCulloh

2008-01-01

Tree hydraulic architecture exhibits patterns that propagate from tissue to tree scales. A challenge is to make sense of these patterns in terms of tradeoffs and adaptations. The universal trend for conduits per area to decrease with increasing conduit diameter below the theoretical packing limit may reflect the compromise between maximizing the area for conduction...

Fast Image Texture Classification Using Decision Trees

NASA Technical Reports Server (NTRS)

Thompson, David R.

2011-01-01

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

Neural network-based model reference adaptive control system.

PubMed

Patino, H D; Liu, D

2000-01-01

In this paper, an approach to model reference adaptive control based on neural networks is proposed and analyzed for a class of first-order continuous-time nonlinear dynamical systems. The controller structure can employ either a radial basis function network or a feedforward neural network to compensate adaptively the nonlinearities in the plant. A stable controller-parameter adjustment mechanism, which is determined using the Lyapunov theory, is constructed using a sigma-modification-type updating law. The evaluation of control error in terms of the neural network learning error is performed. That is, the control error converges asymptotically to a neighborhood of zero, whose size is evaluated and depends on the approximation error of the neural network. In the design and analysis of neural network-based control systems, it is important to take into account the neural network learning error and its influence on the control error of the plant. Simulation results showing the feasibility and performance of the proposed approach are given.

Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae).

PubMed

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G; González-Martínez, Santiago C

2015-03-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. Copyright © 2015 by the Genetics Society of America.

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)

PubMed Central

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H.; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G.; González-Martínez, Santiago C.

2015-01-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP–climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. PMID:25549630

Local biotic adaptation of trees and shrubs to plant neighbors

USGS Publications Warehouse

Grady, Kevin C.; Wood, Troy E.; Kolb, Thomas E.; Hersch-Green, Erika; Shuster, Stephen M.; Gehring, Catherine A.; Hart, Stephen C.; Allan, Gerard J.; Whitham, Thomas G.

2017-01-01

Natural selection as a result of plant–plant interactions can lead to local biotic adaptation. This may occur where species frequently interact and compete intensely for resources limiting growth, survival, and reproduction. Selection is demonstrated by comparing a genotype interacting with con- or hetero-specific sympatric neighbor genotypes with a shared site-level history (derived from the same source location), to the same genotype interacting with foreign neighbor genotypes (from different sources). Better genotype performance in sympatric than allopatric neighborhoods provides evidence of local biotic adaptation. This pattern might be explained by selection to avoid competition by shifting resource niches (differentiation) or by interactions benefitting one or more members (facilitation). We tested for local biotic adaptation among two riparian trees, Populus fremontii and Salix gooddingii, and the shrub Salix exigua by transplanting replicated genotypes from multiple source locations to a 17 000 tree common garden with sympatric and allopatric treatments along the Colorado River in California. Three major patterns were observed: 1) across species, 62 of 88 genotypes grew faster with sympatric neighbors than allopatric neighbors; 2) these growth rates, on an individual tree basis, were 44, 15 and 33% higher in sympatric than allopatric treatments for P. fremontii, S. exigua and S. gooddingii, respectively, and; 3) survivorship was higher in sympatric treatments for P. fremontiiand S. exigua. These results support the view that fitness of foundation species supporting diverse communities and dominating ecosystem processes is determined by adaptive interactions among multiple plant species with the outcome that performance depends on the genetic identity of plant neighbors. The occurrence of evolution in a plant-community context for trees and shrubs builds on ecological evolutionary research that has demonstrated co-evolution among herbaceous taxa, and evolution of native species during exotic plants invasion, and taken together, refutes the concept that plant communities are always random associations.

Role of tree size in moist tropical forest carbon cycling and water deficit responses.

PubMed

Meakem, Victoria; Tepley, Alan J; Gonzalez-Akre, Erika B; Herrmann, Valentine; Muller-Landau, Helene C; Wright, S Joseph; Hubbell, Stephen P; Condit, Richard; Anderson-Teixeira, Kristina J

2017-06-06

Drought disproportionately affects larger trees in tropical forests, but implications for forest composition and carbon (C) cycling in relation to dry season intensity remain poorly understood. In order to characterize how C cycling is shaped by tree size and drought adaptations and how these patterns relate to spatial and temporal variation in water deficit, we analyze data from three forest dynamics plots spanning a moisture gradient in Panama that have experienced El Niño droughts. At all sites, aboveground C cycle contributions peaked below 50-cm stem diameter, with stems ≥ 50 cm accounting for on average 59% of live aboveground biomass, 45% of woody productivity and 49% of woody mortality. The dominance of drought-avoidance strategies increased interactively with stem diameter and dry season intensity. Although size-related C cycle contributions did not vary systematically across the moisture gradient under nondrought conditions, woody mortality of larger trees was disproportionately elevated under El Niño drought stress. Thus, large (> 50 cm) stems, which strongly mediate but do not necessarily dominate C cycling, have drought adaptations that compensate for their more challenging hydraulic environment, particularly in drier climates. However, these adaptations do not fully buffer the effects of severe drought, and increased large tree mortality dominates ecosystem-level drought responses. © 2017 Smithsonian. Institute New Phytologist © 2017 New Phytologist Trust.

[Comprehensive evaluation and selection of urban eco-engineering virescent trees in Shenyang City].

PubMed

Lu, Min; Jiang, Fengqi; Li, Yingjie

2004-07-01

Urban virescence eco-engineering is the core of urban eco-environmental construction, which can promote urban sustainable development. In urban virescence eco-engineering, the comprehensive evaluation of ecological adapt-ability and ecological effect of urban plants is the scientific basis of rational application and selection of urban garden plants. The ecological effect and integrative functions of urban virescence eco-engineering depend upon the selection and layout of garden plants. Using the methods of garden expert consultation and evaluation, this paper established systematically integrative evaluation and application indices of virescence plants in Shenyang City, from the aspects of ecological adaptability, ecological effect, beautification effect, resistance to plant diseases and insect pests, anti-pollution and economic results. According to garden experts evaluation and location of Shenyang, 200 sorts of virescence trees were evaluated and classified on the basis of the comprehensive evaluation system of virescence trees, and using cold resistance, drought resistance, barren resistance, plant diseases and insect pests resistance, anti-pollution, ornamental quality and ecological effects as the indexes. The results showed that the number of first rank trees was 58, the second was 93, methods of third was 38, and the fourth was 11, ranked by integrative performance.

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

PubMed

Seidel, Dominik

2018-01-01

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

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

PubMed

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

2018-01-01

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

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

PubMed Central

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

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics. PMID:29515616

Interannual physiological and growth responses of glacial Juniperus to changes in atmospheric [CO2] since the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Gerhart, L. M.; Harris, J. M.; Ward, J. K.

2011-12-01

During the Last Glacial Maximum, atmospheric [CO2] was as low as 180 ppm and has currently risen to a modern value of 393 ppm as a result of fossil fuel combustion and deforestation. In order to understand how changing [CO2] influenced trees over the last 50,000 years, we analyzed carbon isotope ratios and width of individual tree rings from glacial Juniperus specimens preserved in the Rancho La Brea tar pits in southern California (aged 14-49 kyr BP). Modern trees were also analyzed to compare effects of changing precipitation, temperature and atmospheric [CO2] on physiology and growth. To assess physiological responses, we calculated ci/ca (intercellular [CO2]/atmospheric [CO2]) for each annual ring of each tree. This ratio incorporates numerous aspects of plant physiology, including stomatal conductance and photosynthetic capacity. In addition, we measured ring widths for each sample, and standardized these measurements into indices in order to compare across individuals. Mean ci/ca values remained constant throughout 50,000 years despite major environmental changes, indicating a long-term physiological set point for ci/ca in this group. Constant ci/ca ratios would be maintained through offsetting changes in stomatal conductance and photosynthetic capacity. Glacial Juniperus never experienced ci values below 90 ppm, suggesting a survival compensation point for Juniperus. In addition, glacial trees showed significantly reduced interannual variation in ci/ca, even though interannual climatic variability was as high during the LGM in this region as it is today. A lack of variability in ci/ca of glacial trees suggests that tree physiology was dominated by low [CO2], which shows low interannual variation. Modern trees showed high interannual variation in ci/ca, since water availability dominates current physiological responses and varies greatly from year to year. Interestingly, interannual variation in ring width index did not show significant differences between glacial and modern trees, suggesting these trees were adapted to maintain growth under low [CO2]. These adaptations may constrain the ability of modern trees to fully utilize increases in atmospheric [CO2]. These results have significant implications for our understanding of the adaptations of trees to changing [CO2] and indicate that the environmental factors that most strongly influence plant physiology may have changed over geologic time scales.

Study on the Adsorption Capacities for Airborne Particulates of Landscape Plants in Different Polluted Regions in Beijing (China)

PubMed Central

Zhang, Wei-Kang; Wang, Bing; Niu, Xiang

2015-01-01

Urban landscape plants are an important component of the urban ecosystem, playing a significant role in the adsorption of airborne particulates and air purification. In this study, six common landscape plants in Beijing were chosen as research subjects, and the adsorption capacities for each different plant leaf and the effects of the leaf structures for the adsorption capacities for particulates were determined. Preliminary results show that needle-leaved tree species adsorbed more airborne particulates than broad-leaved tree species for the same leaf area. Pinus tabuliformis exhibits the highest adsorption capacity, at 3.89 ± 0.026 μg·cm−2, almost two times as much as that of Populus tomentosa (2.00 ± 0.118 μg·cm−2). The adsorption capacities for PM10 of the same tree species leaves, in different polluted regions had significant differences, and the adsorption capacities for PM10 of the tree species leaf beside the Fifth Ring Road were higher than those of the tree species leaves in the Botanical Garden, although the adsorption capacities for PM2.5 of the same tree species in different polluted regions had no significant differences. By determining the soluble ion concentrations of the airborne particulates in two regions, it is suggested that the soluble ion concentrations of PM10 in the atmosphere in the Botanical Garden and beside the Fifth Ring Road have significant differences, while those of PM2.5 in the atmosphere had no significant differences. In different polluted regions there are significant adaptive changes to the leaf structures, and when compared with slightly polluted region, in the seriously polluted region the epidermis cells of the plant leaves shrinked, the surface textures of the leaves became rougher, and the stomas’ frequency and the pubescence length increased. Even though the plant leaves exposed to the seriously polluted region changed significantly, these plants can still grow normally and healthily. PMID:26287227

Effects of forest structure and composition on food availability for Varecia variegata at Ranomafana National Park, Madagascar

USGS Publications Warehouse

Balko, E.A.; Underwood, H.B.

2005-01-01

We present a summary of a long-term field study that examined the effects of forest disturbance on the availability of palatable fruit and its utilization by V. variegata. Forest structure and tree species composition were measured in three adjacent study areas, with different histories of disturbance, in Ranomafana National Park (RNP), Madagascar. V. variegata abundance was monitored by frequent encounters with resident groups and periodic censuses conducted along trails. Finally, the abundance of mature fruit in species used by V. variegata was scored monthly at representative trees at several locations. V. variegata abundance was most consistent in the least anthropogenically disturbed site, while no established lemur groups were observed in the heavily logged site for over a decade post-harvest. Lemur abundance was variable in the selectively logged site. The presence of select food trees, particularly specimens with voluminous crowns capable of producing abundant fruit crops, appears to be key to the establishment and expansion of V variegata groups. Our analysis of year-long fruit utilization revealed a high degree of preference for several species of trees. Two species exhibited mature fruit in a low percentage of stems but were available for a protracted period of time, while two additional species showed high intraspecific fruiting synchrony and were available for a shorter period of time. These contrasting phenologies, rather than the individual tree species, may be most important to V. variegata due to their coincident timing of fruit maturation with key lemur life-history events. Any disturbance-natural or anthropogenic-that disrupts the phenology cycles of food trees has the potential to impact lemur abundance and dispersion. Intense disturbances, such as heavy logging or severe cyclones, have long-lasting impacts on fruit production, while selective logging or moderate cyclonic windthrow cause more transient impacts. V. variegata is adapted to deal with an intrinsically erratic food supply by virtue of its reproductive biology and social behavior.

Parallel fast multipole boundary element method applied to computational homogenization

NASA Astrophysics Data System (ADS)

Ptaszny, Jacek

2018-01-01

In the present work, a fast multipole boundary element method (FMBEM) and a parallel computer code for 3D elasticity problem is developed and applied to the computational homogenization of a solid containing spherical voids. The system of equation is solved by using the GMRES iterative solver. The boundary of the body is dicretized by using the quadrilateral serendipity elements with an adaptive numerical integration. Operations related to a single GMRES iteration, performed by traversing the corresponding tree structure upwards and downwards, are parallelized by using the OpenMP standard. The assignment of tasks to threads is based on the assumption that the tree nodes at which the moment transformations are initialized can be partitioned into disjoint sets of equal or approximately equal size and assigned to the threads. The achieved speedup as a function of number of threads is examined.

Characterization of Adaptation by Morphology in a Planar Biological Network of Plasmodial Slime Mold

NASA Astrophysics Data System (ADS)

Ito, Masateru; Okamoto, Riki; Takamatsu, Atsuko

2011-07-01

Growth processes of a planar biological network of plasmodium of a true slime mold, Physarum polycephalum, were analyzed quantitatively. The plasmodium forms a transportation network through which protoplasm conveys nutrients, oxygen, and cellular organelles similarly to blood in a mammalian vascular network. To analyze the network structure, vertices were defined at tube bifurcation points. Then edges were defined for the tubes connecting both end vertices. Morphological analysis was attempted along with conventional topological analysis, revealing that the growth process of the plasmodial network structure depends on environmental conditions. In an attractive condition, the network is a polygonal lattice with more than six edges per vertex at the early stage and the hexagonal lattice at a later stage. Through all growing stages, the tube structure was not highly developed but an unstructured protoplasmic thin sheet was dominantly formed. The network size is small. In contrast, in the repulsive condition, the network is a mixture of polygonal lattice and tree-graph. More specifically, the polygonal lattice has more than six edges per vertex in the early stage, then a tree-graph structure is added to the lattice network at a later stage. The thick tube structure was highly developed. The network size, in the meaning of Euclidean distance but not topological one, grows considerably. Finally, the biological meaning of the environment-dependent network structure in the plasmodium is discussed.

The environmental zero-point problem in evolutionary reaction norm modeling.

PubMed

Ergon, Rolf

2018-04-01

There is a potential problem in present quantitative genetics evolutionary modeling based on reaction norms. Such models are state-space models, where the multivariate breeder's equation in some form is used as the state equation that propagates the population state forward in time. These models use the implicit assumption of a constant reference environment, in many cases set to zero. This zero-point is often the environment a population is adapted to, that is, where the expected geometric mean fitness is maximized. Such environmental reference values follow from the state of the population system, and they are thus population properties. The environment the population is adapted to, is, in other words, an internal population property, independent of the external environment. It is only when the external environment coincides with the internal reference environment, or vice versa, that the population is adapted to the current environment. This is formally a result of state-space modeling theory, which is an important theoretical basis for evolutionary modeling. The potential zero-point problem is present in all types of reaction norm models, parametrized as well as function-valued, and the problem does not disappear when the reference environment is set to zero. As the environmental reference values are population characteristics, they ought to be modeled as such. Whether such characteristics are evolvable is an open question, but considering the complexity of evolutionary processes, such evolvability cannot be excluded without good arguments. As a straightforward solution, I propose to model the reference values as evolvable mean traits in their own right, in addition to other reaction norm traits. However, solutions based on an evolvable G matrix are also possible.

Climate Patterns and Trends of Tree-Mortality in the Southwestern United States

NASA Astrophysics Data System (ADS)

Yi, C.; Mu, G.; Hendrey, G. R.; Vicente-Serrano, S.

2016-12-01

Evidence suggests a world-wide increase in tree mortality associated with climate change in regions subjected to prolonged drought. This is particularly evident in the Southwestern USA (SWUSA) where trees are dying at an accelerating and alarming rate where we investigated climate patterns and trends over the past century in combination with abundant tree-ring data, and thresholds of tree-mortality. In this drought-prone region we found a strong correlation between annual tree-ring width and the corresponding annual average temperature and amount of precipitation. A standardized precipitation-evapotranspiration index (SPEI) was a robust predictor of annual tree growth. At a SPEI of -1.6, tree-ring width was found to be zero. We hypothesize that this is a tipping point for tree-ring mortality. This is confirmed in that approximately 225 million trees died in SWUSA in 2002 when SPEI fell below this tipping point. An analysis of future trends in SPEI based on four GHG concentration scenarios of the IPCC predicts that in coming decades, the conifer forest in SWUSA is expected to be lost entirely due to the prolonged drought there, as the SPEI is predicted to pass the tipping point. It can be anticipated that as the area impacted by prolonged drought increases with SPEI falling below -1.6 tree mortality will become a regional or semi-continental phenomenon. Acknowledgement:This research was supported by PSC-CUNY award (PSC-CUNY-ENHC-68849-0046) and the CUNY Collaborative Incentive Research Grant (CUNY-CIRG-80209-08 22).

Drought-induced defoliation and long periods of near-zero gas exchange play a key role in accentuating metabolic decline of Scots pine.

PubMed

Poyatos, Rafael; Aguadé, David; Galiano, Lucía; Mencuccini, Maurizio; Martínez-Vilalta, Jordi

2013-10-01

Drought-induced defoliation has recently been associated with the depletion of carbon reserves and increased mortality risk in Scots pine (Pinus sylvestris). We hypothesize that defoliated individuals are more sensitive to drought, implying that potentially higher gas exchange (per unit of leaf area) during wet periods may not compensate for their reduced photosynthetic area. We measured sap flow, needle water potentials and whole-tree hydraulic conductance to analyse the drought responses of co-occurring defoliated and nondefoliated Scots pines in northeast Spain during typical (2010) and extreme (2011) drought conditions. Defoliated Scots pines showed higher sap flow per unit leaf area during spring, but were more sensitive to summer drought, relative to nondefoliated pines. This pattern was associated with a steeper decline in soil-to-leaf hydraulic conductance with drought and an enhanced sensitivity of canopy conductance to soil water availability. Near-homeostasis in midday water potentials was observed across years and defoliation classes, with minimum values of -2.5 MPa. Enhanced sensitivity to drought and prolonged periods of near-zero gas exchange were consistent with low levels of carbohydrate reserves in defoliated trees. Our results support the critical links between defoliation, water and carbon availability, and their key roles in determining tree survival and recovery under drought. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Three-dimensional feature extraction and geometric mappings for improved parameter estimation in forested terrain using airborne LiDAR data

NASA Astrophysics Data System (ADS)

Lee, Heezin

Scanning laser ranging technology is well suited for measuring point-to-point distances because of its ability to generate small beam divergences. As a result, many of the laser pulses emitted from airborne light detection and ranging (LiDAR) systems are able to reach the ground underneath tree canopies through small (10 cm scale) gaps in the foliage. Using high pulse rate lasers and fast optical scanners, airborne LiDAR systems can provide both high spatial resolution and canopy penetration, and these data have become more widely available in recent years for use in environmental and forestry applications. The small-footprint, discrete-return Airborne Laser Swath Mapping (ALSM) system at the University of Florida (UF) is used to directly measure ground surface elevations and the three-dimensional (3D) distribution of the vegetative material above the soil surface. Field of view geometric mappings are explored to find optical gaps inside forests. First, a method is developed to detect walking trails in natural forests that are obscured from above by the canopy. Several features are derived from the ALSM data and used to constrain the search space and infer the location of trails. Second, a robust and simple procedure for estimating intercepted photosynthetically active radiation (IPAR), which is an important measure of forest timber productivity and of daylight visibility in forested terrain, is presented. Simple scope functions that isolate the relevant LiDAR reflections between observer locations and the sun are defined and shown to give good agreement between the LiDAR-derived estimates and values of IPAR measured in situ. A conical scope function with an angular divergence from the centerline of +/-7° provided the best agreement with the in situ measurements. This scope function yielded remarkably consistent IPAR estimates for different pine species and growing conditions. The developed idea could be extended, through potential future work, to characterize the spatial distribution of attenuation of GPS (L-band) microwave signals and of detectability from the sky for military personnel operating in forested terrain. Measuring individual trees can provide valuable information about forests, and airborne LiDAR sensors have been recently used to identify individual trees and measure structural tree parameters. Past results, however, have been mixed because of reliance on interpolated (image) versions of the LiDAR measurements and search methods that do not adapt to variations in canopies. In this work, an adaptive clustering method is developed using 3D airborne LiDAR data acquired over two distinctly different managed pine forests in North-Central Florida, USA. A critical issue in isolating individual trees is determining the appropriate size of the moving window (search radius) when locating seed points. The proposed approach works directly on the 3D "cloud" of LiDAR points and adapts to irregular canopy sizes. The region growing step yields collectively exhaustive sets in an initial segmentation of tree canopies. An agglomerative clustering step is then used to merge clusters that represent parts of whole canopies using the locally varying height distribution. The overall tree detection accuracy achieved is 95.1% with no significant bias. The tree detection enables subsequent estimation of tree height and vertical crown length to an accuracy of better than 0.8 m and 1.5 m, respectively. Lastly, a compact representation of the different geometric characteristics of the segmented LiDAR points is introduced using spin images as a new tool that can potentially help tree detection in complex natural forests.

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...

Photoperiod- and temperature-mediated control of growth cessation and dormancy in trees: a molecular perspective.

PubMed

Maurya, Jay P; Bhalerao, Rishikesh P

2017-09-01

How plants adapt their developmental patterns to regular seasonal changes is an important question in biology. The annual growth cycle in perennial long-lived trees is yet another example of how plants can adapt to seasonal changes. The two main signals that plants rely on to respond to seasonal changes are photoperiod and temperature, and these signals have critical roles in the temporal regulation of the annual growth cycle of trees. This review presents the latest findings to provide insight into the molecular mechanisms that underlie how photoperiodic and temperature signals regulate seasonal growth in trees. The results point to a high level of conservation in the signalling pathways that mediate photoperiodic control of seasonal growth in trees and flowering in annual plants such as arabidopsis. Furthermore, the data indicate that symplastic communication may mediate certain aspects of seasonal growth. Although considerable insight into the control of phenology in model plants such as poplar and spruce has been obtained, the future challenge is extending these studies to other, non-model trees. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Tree-ring formation as an indicator of forest capacity to adapt to the main threats of environmental changes in Lithuania.

PubMed

Augustaitis, Algirdas; Augustaitienė, Ingrida; Baugarten, Manuela; Bičenkienė, Steigvilė; Girgždienė, Raselė; Kulbokas, Gintaras; Linkevičius, Edgaras; Marozas, Vitas; Mikalajūnas, Marius; Mordas, Genrik; Mozgeris, Gintautas; Petrauskas, Edmundas; Pivoras, Ainis; Šidlauskas, Giedrius; Ulevičius, Vidmantas; Vitas, Adomas; Matyssek, Rainer

2018-02-15

Global changes occurring under different environmental conditions have changed stand competition, as well as nutrient and light availability, which has resulted in changes in productivity. Therefore, in the present study, the characteristics of tree-ring width formation of the prevailing Lithuanian tree species, Norway spruce, Scots pine and silver and downy birch, and key factors resulting in their differences during the last 36-year period were investigated at forest sites located on poor mineral oligotrophic and on nutrient-rich organic mesoeutrophic soils. The aim of the study was as follows: first, to separately detect the maximum possible seasonal effect of three groups of variables - meteorology, acidifying pollutants and surface ozone on the stem basal area increment (BAI) of the evaluated tree species; second, to assess the significance of each group of variables affecting the BAI of these tree species integrally with the remaining groups of variables. Norway spruce was found to be well adapted to recent environmental changes, which makes it one of the most favourable tree species for silviculture in the northeastern part of Europe. The rapid increases recorded in growth intensity since 1980 were attributed to the increase in air temperature, precipitation amount, nitrogen deposition during the vegetative stage and reductions in SO 2 concentrations and S deposition. Scots pine demonstrated the highest level of resilience and capacity to adapt to recent global changes because its reaction to both negative and favourable environmental factors was best expressed. Silver and downy birch tree reactions to the effects of air concentrations of acidifying compounds, their deposition and surface ozone concentrations were the least expressed; however, a significant decline in growth intensity indicated that these tree species experienced a reduced resistance to recent changes in environmental conditions in the mature and over-mature age groups. Copyright © 2017 Elsevier B.V. All rights reserved.

On the zero-crossing of the three-gluon Green's function from lattice simulations

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

Athenodorou, Andreas; Boucaud, Philippe; de Soto, Feliciano

We report on some efforts recently made in order to gain a better understanding of some IR properties of the 3-point gluon Green’s function by exploiting results from large-volume quenched lattice simulations. These lattice results have been obtained by using both tree-level Symanzik and the standard Wilson action, in the aim of assessing the possible impact of effects presumably resulting from a particular choice for the discretization of the action. The main resulting feature is the existence of a negative log-aritmic divergence at zero-momentum, which pulls the 3-gluon form factors down at low momenta and, consequently, yields a zero-crossing atmore » a given deep IR momentum. The results can be correctly explained by analyzing the relevant Dyson-Schwinger equations and appropriate truncation schemes.« less

Tree Colors: Color Schemes for Tree-Structured Data.

PubMed

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

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

Robust Adaptive Dynamic Programming of Two-Player Zero-Sum Games for Continuous-Time Linear Systems.

PubMed

Fu, Yue; Fu, Jun; Chai, Tianyou

2015-12-01

In this brief, an online robust adaptive dynamic programming algorithm is proposed for two-player zero-sum games of continuous-time unknown linear systems with matched uncertainties, which are functions of system outputs and states of a completely unknown exosystem. The online algorithm is developed using the policy iteration (PI) scheme with only one iteration loop. A new analytical method is proposed for convergence proof of the PI scheme. The sufficient conditions are given to guarantee globally asymptotic stability and suboptimal property of the closed-loop system. Simulation studies are conducted to illustrate the effectiveness of the proposed method.

A robust bi-orthogonal/dynamically-orthogonal method using the covariance pseudo-inverse with application to stochastic flow problems

NASA Astrophysics Data System (ADS)

Babaee, Hessam; Choi, Minseok; Sapsis, Themistoklis P.; Karniadakis, George Em

2017-09-01

We develop a new robust methodology for the stochastic Navier-Stokes equations based on the dynamically-orthogonal (DO) and bi-orthogonal (BO) methods [1-3]. Both approaches are variants of a generalized Karhunen-Loève (KL) expansion in which both the stochastic coefficients and the spatial basis evolve according to system dynamics, hence, capturing the low-dimensional structure of the solution. The DO and BO formulations are mathematically equivalent [3], but they exhibit computationally complimentary properties. Specifically, the BO formulation may fail due to crossing of the eigenvalues of the covariance matrix, while both BO and DO become unstable when there is a high condition number of the covariance matrix or zero eigenvalues. To this end, we combine the two methods into a robust hybrid framework and in addition we employ a pseudo-inverse technique to invert the covariance matrix. The robustness of the proposed method stems from addressing the following issues in the DO/BO formulation: (i) eigenvalue crossing: we resolve the issue of eigenvalue crossing in the BO formulation by switching to the DO near eigenvalue crossing using the equivalence theorem and switching back to BO when the distance between eigenvalues is larger than a threshold value; (ii) ill-conditioned covariance matrix: we utilize a pseudo-inverse strategy to invert the covariance matrix; (iii) adaptivity: we utilize an adaptive strategy to add/remove modes to resolve the covariance matrix up to a threshold value. In particular, we introduce a soft-threshold criterion to allow the system to adapt to the newly added/removed mode and therefore avoid repetitive and unnecessary mode addition/removal. When the total variance approaches zero, we show that the DO/BO formulation becomes equivalent to the evolution equation of the Optimally Time-Dependent modes [4]. We demonstrate the capability of the proposed methodology with several numerical examples, namely (i) stochastic Burgers equation: we analyze the performance of the method in the presence of eigenvalue crossing and zero eigenvalues; (ii) stochastic Kovasznay flow: we examine the method in the presence of a singular covariance matrix; and (iii) we examine the adaptivity of the method for an incompressible flow over a cylinder where for large stochastic forcing thirteen DO/BO modes are active.

Adaptive Broadcasting Mechanism for Bandwidth Allocation in Mobile Services

PubMed Central

Horng, Gwo-Jiun; Wang, Chi-Hsuan; Chou, Chih-Lun

2014-01-01

This paper proposes a tree-based adaptive broadcasting (TAB) algorithm for data dissemination to improve data access efficiency. The proposed TAB algorithm first constructs a broadcast tree to determine the broadcast frequency of each data and splits the broadcast tree into some broadcast wood to generate the broadcast program. In addition, this paper develops an analytical model to derive the mean access latency of the generated broadcast program. In light of the derived results, both the index channel's bandwidth and the data channel's bandwidth can be optimally allocated to maximize bandwidth utilization. This paper presents experiments to help evaluate the effectiveness of the proposed strategy. From the experimental results, it can be seen that the proposed mechanism is feasible in practice. PMID:25057509

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

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

Offdiagonal complexity: A computationally quick complexity measure for graphs and networks

NASA Astrophysics Data System (ADS)

Claussen, Jens Christian

2007-02-01

A vast variety of biological, social, and economical networks shows topologies drastically differing from random graphs; yet the quantitative characterization remains unsatisfactory from a conceptual point of view. Motivated from the discussion of small scale-free networks, a biased link distribution entropy is defined, which takes an extremum for a power-law distribution. This approach is extended to the node-node link cross-distribution, whose nondiagonal elements characterize the graph structure beyond link distribution, cluster coefficient and average path length. From here a simple (and computationally cheap) complexity measure can be defined. This offdiagonal complexity (OdC) is proposed as a novel measure to characterize the complexity of an undirected graph, or network. While both for regular lattices and fully connected networks OdC is zero, it takes a moderately low value for a random graph and shows high values for apparently complex structures as scale-free networks and hierarchical trees. The OdC approach is applied to the Helicobacter pylori protein interaction network and randomly rewired surrogates.

Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

NASA Astrophysics Data System (ADS)

Destefano, Anthony; Heerikhuisen, Jacob

2015-04-01

Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

Learning to classify in large committee machines

NASA Astrophysics Data System (ADS)

O'kane, Dominic; Winther, Ole

1994-10-01

The ability of a two-layer neural network to learn a specific non-linearly-separable classification task, the proximity problem, is investigated using a statistical mechanics approach. Both the tree and fully connected architectures are investigated in the limit where the number K of hidden units is large, but still much smaller than the number N of inputs. Both have continuous weights. Within the replica symmetric ansatz, we find that for zero temperature training, the tree architecture exhibits a strong overtraining effect. For nonzero temperature the asymptotic error is lowered, but it is still higher than the corresponding value for the simple perceptron. The fully connected architecture is considered for two regimes. First, for a finite number of examples we find a symmetry among the hidden units as each performs equally well. The asymptotic generalization error is finite, and minimal for T-->∞ where it goes to the same value as for the simple perceptron. For a large number of examples we find a continuous transition to a phase with broken hidden-unit symmetry, which has an asymptotic generalization error equal to zero.

Absolute phase estimation: adaptive local denoising and global unwrapping.

PubMed

Bioucas-Dias, Jose; Katkovnik, Vladimir; Astola, Jaakko; Egiazarian, Karen

2008-10-10

The paper attacks absolute phase estimation with a two-step approach: the first step applies an adaptive local denoising scheme to the modulo-2 pi noisy phase; the second step applies a robust phase unwrapping algorithm to the denoised modulo-2 pi phase obtained in the first step. The adaptive local modulo-2 pi phase denoising is a new algorithm based on local polynomial approximations. The zero-order and the first-order approximations of the phase are calculated in sliding windows of varying size. The zero-order approximation is used for pointwise adaptive window size selection, whereas the first-order approximation is used to filter the phase in the obtained windows. For phase unwrapping, we apply the recently introduced robust (in the sense of discontinuity preserving) PUMA unwrapping algorithm [IEEE Trans. Image Process.16, 698 (2007)] to the denoised wrapped phase. Simulations give evidence that the proposed algorithm yields state-of-the-art performance, enabling strong noise attenuation while preserving image details. (c) 2008 Optical Society of America

[Fitness of sexual reproduction of Toona ciliata var. pubescens natural populations and their sexual reproduction and regeneration].

PubMed

Huang, Hong Lan; Zhang, Lu; Jia, Li Ming; Liang, Yue-Long; Cai, Jun Huo

2018-04-01

To examine the reproduction fitness coefficients and individual-level fitness of Toona ciliata var. pubescens, their sexual reproduction and natural regeneration were investigated during 2006-2016, with four natural populations in Jiulianshan National Reserve as test objects. The results showed that there were only 2-10 trees for the natural populations of T. ciliata var. pubescens with a small initial number of fruiting plants (3-9 trees), which were from the initial fruiting plants or their first/second generation. The sexual reproduction of these isolated populations were significantly different, and their seed production capacities tended to decline over time. With the maturing of communities, soil seed banks and seed germinations were extremely poor, and the number of trees that could be growing to mature stage was nearly zero. The optimum maturity age of T. ciliata var. pubescens was about 40 a, and the fitness coefficients (2.0-2.8) rapidly increased in early development stage, but then was sharply reduced (0.3-0.5), and then gradually dropped to almost 0. There were significant differences in the fitness at individual level (0-14 tree·cm -2 ) among different populations, but their values were low (close to zero). Based on the existing reproduction rate, the actual values of sexual reproduction and regeneration fitness were much lower than the predicted ones. Due to the low level of genetic fitness, the sexual reproductive ability of different populations all showed decreasing trends. The natural sexual regeneration ability tended to decline, while the fitness of T. ciliata var. pubescens further decreased. All those factors suggested higher investment risks. Therefore, the systems of sexual reproduction became unbalanced and deteriorating. We proposed that more studies, including breeding mating, pollination, seed setting, and genetic diversity evaluation, are needed. Moreover, we should provide suitable forest environment through cleaning up litter in the fruiting stage and applying appropriate thinning during the transition period from seedling to young tree growth.

Coseismic fault slip associated with the 1992 M(sub w) 6.1 Joshua Tree, California, earthquake: Implications for the Joshua Tree-Landers earthquake sequence

NASA Technical Reports Server (NTRS)

Bennett, Richard A.; Reilinger, Robert E.; Rodi, William; Li, Yingping; Toksoz, M. Nafi; Hudnut, Ken

1995-01-01

Coseismic surface deformation associated with the M(sub w) 6.1, April 23, 1992, Joshua Tree earthquake is well represented by estimates of geodetic monument displacements at 20 locations independently derived from Global Positioning System and trilateration measurements. The rms signal to noise ratio for these inferred displacements is 1.8 with near-fault displacement estimates exceeding 40 mm. In order to determine the long-wavelength distribution of slip over the plane of rupture, a Tikhonov regularization operator is applied to these estimates which minimizes stress variability subject to purely right-lateral slip and zero surface slip constraints. The resulting slip distribution yields a geodetic moment estimate of 1.7 x 10(exp 18) N m with corresponding maximum slip around 0.8 m and compares well with independent and complementary information including seismic moment and source time function estimates and main shock and aftershock locations. From empirical Green's functions analyses, a rupture duration of 5 s is obtained which implies a rupture radius of 6-8 km. Most of the inferred slip lies to the north of the hypocenter, consistent with northward rupture propagation. Stress drop estimates are in the range of 2-4 MPa. In addition, predicted Coulomb stress increases correlate remarkably well with the distribution of aftershock hypocenters; most of the aftershocks occur in areas for which the mainshock rupture produced stress increases larger than about 0.1 MPa. In contrast, predicted stress changes are near zero at the hypocenter of the M(sub w) 7.3, June 28, 1992, Landers earthquake which nucleated about 20 km beyond the northernmost edge of the Joshua Tree rupture. Based on aftershock migrations and the predicted static stress field, we speculate that redistribution of Joshua Tree-induced stress perturbations played a role in the spatio-temporal development of the earth sequence culminating in the Landers event.

Forest structure and carbon dynamics in Amazonian tropical rain forests.

PubMed

Vieira, Simone; de Camargo, Plinio Barbosa; Selhorst, Diogo; da Silva, Roseana; Hutyra, Lucy; Chambers, Jeffrey Q; Brown, I Foster; Higuchi, Niro; dos Santos, Joaquim; Wofsy, Steven C; Trumbore, Susan E; Martinelli, Luiz Antonio

2004-08-01

Living trees constitute one of the major stocks of carbon in tropical forests. A better understanding of variations in the dynamics and structure of tropical forests is necessary for predicting the potential for these ecosystems to lose or store carbon, and for understanding how they recover from disturbance. Amazonian tropical forests occur over a vast area that encompasses differences in topography, climate, and geologic substrate. We observed large differences in forest structure, biomass, and tree growth rates in permanent plots situated in the eastern (near Santarém, Pará), central (near Manaus, Amazonas) and southwestern (near Rio Branco, Acre) Amazon, which differed in dry season length, as well as other factors. Forests at the two sites experiencing longer dry seasons, near Rio Branco and Santarém, had lower stem frequencies (460 and 466 ha(-1) respectively), less biodiversity (Shannon-Wiener diversity index), and smaller aboveground C stocks (140.6 and 122.1 Mg C ha(-1)) than the Manaus site (626 trees ha(-1), 180.1 Mg C ha(-1)), which had less seasonal variation in rainfall. The forests experiencing longer dry seasons also stored a greater proportion of the total biomass in trees with >50 cm diameter (41-45 vs 30% in Manaus). Rates of annual addition of C to living trees calculated from monthly dendrometer band measurements were 1.9 (Manaus), 2.8 (Santarém), and 2.6 (Rio Branco) Mg C ha(-1) year(-1). At all sites, trees in the 10-30 cm diameter class accounted for the highest proportion of annual growth (38, 55 and 56% in Manaus, Rio Branco and Santarém, respectively). Growth showed marked seasonality, with largest stem diameter increment in the wet season and smallest in the dry season, though this may be confounded by seasonal variation in wood water content. Year-to-year variations in C allocated to stem growth ranged from nearly zero in Rio Branco, to 0.8 Mg C ha(-1) year(-1) in Manaus (40% of annual mean) and 0.9 Mg C ha(-1) year(-1) (33% of annual mean) in Santarém, though this variability showed no significant relation with precipitation among years. Initial estimates of the C balance of live wood including recruitment and mortality as well as growth suggests that live wood biomass is at near steady-state in Manaus, but accumulating at about 1.5 Mg C ha(-1) at the other two sites. The causes of C imbalance in living wood pools in Santarém and Rio Branco sites are unknown, but may be related to previous disturbance at these sites. Based on size distribution and growth rate differences in the three sites, we predict that trees in the Manaus forest have greater mean age (approximately 240 years) than those of the other two forests (approximately 140 years).

Dying piece by piece: carbohydrate dynamics in aspen (Populus tremuloides) seedlings under severe carbon stress.

PubMed

Wiley, Erin; Hoch, Günter; Landhäusser, Simon M

2017-11-02

Carbon starvation as a mechanism of tree mortality is poorly understood. We exposed seedlings of aspen (Populus tremuloides) to complete darkness at 20 or 28 °C to identify minimum non-structural carbohydrate (NSC) concentrations at which trees die and to see if these levels vary between organs or with environmental conditions. We also first grew seedlings under different shade levels to determine if size affects survival time under darkness due to changes in initial NSC concentration and pool size and/or respiration rates. Darkness treatments caused a gradual dieback of tissues. Even after half the stem had died, substantial starch reserves were still present in the roots (1.3-3% dry weight), indicating limitations to carbohydrate remobilization and/or transport during starvation in the absence of water stress. Survival time decreased with increased temperature and with increasing initial shade level, which was associated with smaller biomass, higher respiration rates, and initially smaller NSC pool size. Dead tissues generally contained no starch, but sugar concentrations were substantially above zero and differed between organs (~2% in stems up to ~7.5% in leaves) and, at times, between temperature treatments and initial, pre-darkness shade treatments. Minimum root NSC concentrations were difficult to determine because dead roots quickly began to decompose, but we identify 5-6% sugar as a potential threshold for living roots. This variability may complicate efforts to identify critical NSC thresholds below which trees starve. © Society for Experimental Biology 2017.

Evolutionary Quantitative Genomics of Populus trichocarpa

PubMed Central

McKown, Athena D.; La Mantia, Jonathan; Guy, Robert D.; Ingvarsson, Pär K.; Hamelin, Richard; Mansfield, Shawn D.; Ehlting, Jürgen; Douglas, Carl J.; El-Kassaby, Yousry A.

2015-01-01

Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing Q ST -F ST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense Q ST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant Q ST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We also provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species’ potential adaptive capacity to future climatic scenarios. PMID:26599762

Multiple description distributed image coding with side information for mobile wireless transmission

NASA Astrophysics Data System (ADS)

Wu, Min; Song, Daewon; Chen, Chang Wen

2005-03-01

Multiple description coding (MDC) is a source coding technique that involves coding the source information into multiple descriptions, and then transmitting them over different channels in packet network or error-prone wireless environment to achieve graceful degradation if parts of descriptions are lost at the receiver. In this paper, we proposed a multiple description distributed wavelet zero tree image coding system for mobile wireless transmission. We provide two innovations to achieve an excellent error resilient capability. First, when MDC is applied to wavelet subband based image coding, it is possible to introduce correlation between the descriptions in each subband. We consider using such a correlation as well as potentially error corrupted description as side information in the decoding to formulate the MDC decoding as a Wyner Ziv decoding problem. If only part of descriptions is lost, however, their correlation information is still available, the proposed Wyner Ziv decoder can recover the description by using the correlation information and the error corrupted description as side information. Secondly, in each description, single bitstream wavelet zero tree coding is very vulnerable to the channel errors. The first bit error may cause the decoder to discard all subsequent bits whether or not the subsequent bits are correctly received. Therefore, we integrate the multiple description scalar quantization (MDSQ) with the multiple wavelet tree image coding method to reduce error propagation. We first group wavelet coefficients into multiple trees according to parent-child relationship and then code them separately by SPIHT algorithm to form multiple bitstreams. Such decomposition is able to reduce error propagation and therefore improve the error correcting capability of Wyner Ziv decoder. Experimental results show that the proposed scheme not only exhibits an excellent error resilient performance but also demonstrates graceful degradation over the packet loss rate.

The nodal count {0,1,2,3,…} implies the graph is a tree

PubMed Central

Band, Ram

2014-01-01

Sturm's oscillation theorem states that the nth eigenfunction of a Sturm–Liouville operator on the interval has n−1 zeros (nodes) (Sturm 1836 J. Math. Pures Appl. 1, 106–186; 373–444). This result was generalized for all metric tree graphs (Pokornyĭ et al. 1996 Mat. Zametki 60, 468–470 (doi:10.1007/BF02320380); Schapotschnikow 2006 Waves Random Complex Media 16, 167–178 (doi:10.1080/1745530600702535)) and an analogous theorem was proved for discrete tree graphs (Berkolaiko 2007 Commun. Math. Phys. 278, 803–819 (doi:10.1007/S00220-007-0391-3); Dhar & Ramaswamy 1985 Phys. Rev. Lett. 54, 1346–1349 (doi:10.1103/PhysRevLett.54.1346); Fiedler 1975 Czechoslovak Math. J. 25, 607–618). We prove the converse theorems for both discrete and metric graphs. Namely if for all n, the nth eigenfunction of the graph has n−1 zeros, then the graph is a tree. Our proofs use a recently obtained connection between the graph's nodal count and the magnetic stability of its eigenvalues (Berkolaiko 2013 Anal. PDE 6, 1213–1233 (doi:10.2140/apde.2013.6.1213); Berkolaiko & Weyand 2014 Phil. Trans. R. Soc. A 372, 20120522 (doi:10.1098/rsta.2012.0522); Colin de Verdière 2013 Anal. PDE 6, 1235–1242 (doi:10.2140/apde.2013.6.1235)). In the course of the proof, we show that it is not possible for all (or even almost all, in the metric case) the eigenvalues to exhibit a diamagnetic behaviour. In addition, we develop a notion of ‘discretized’ versions of a metric graph and prove that their nodal counts are related to those of the metric graph. PMID:24344337

A scale-based connected coherence tree algorithm for image segmentation.

PubMed

Ding, Jundi; Ma, Runing; Chen, Songcan

2008-02-01

This paper presents a connected coherence tree algorithm (CCTA) for image segmentation with no prior knowledge. It aims to find regions of semantic coherence based on the proposed epsilon-neighbor coherence segmentation criterion. More specifically, with an adaptive spatial scale and an appropriate intensity-difference scale, CCTA often achieves several sets of coherent neighboring pixels which maximize the probability of being a single image content (including kinds of complex backgrounds). In practice, each set of coherent neighboring pixels corresponds to a coherence class (CC). The fact that each CC just contains a single equivalence class (EC) ensures the separability of an arbitrary image theoretically. In addition, the resultant CCs are represented by tree-based data structures, named connected coherence tree (CCT)s. In this sense, CCTA is a graph-based image analysis algorithm, which expresses three advantages: 1) its fundamental idea, epsilon-neighbor coherence segmentation criterion, is easy to interpret and comprehend; 2) it is efficient due to a linear computational complexity in the number of image pixels; 3) both subjective comparisons and objective evaluation have shown that it is effective for the tasks of semantic object segmentation and figure-ground separation in a wide variety of images. Those images either contain tiny, long and thin objects or are severely degraded by noise, uneven lighting, occlusion, poor illumination, and shadow.

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

PubMed Central

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-01

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology. PMID:18199838

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks.

PubMed

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-22

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology.

Compensatory mechanisms mitigate the effect of warming and drought on wood formation.

PubMed

Balducci, Lorena; Cuny, Henri E; Rathgeber, Cyrille B K; Deslauriers, Annie; Giovannelli, Alessio; Rossi, Sergio

2016-06-01

Because of global warming, high-latitude ecosystems are expected to experience increases in temperature and drought events. Wood formation will have to adjust to these new climatic constraints to maintain tree mechanical stability and long-distance water transport. The aim of this study is to understand the dynamic processes involved in wood formation under warming and drought. Xylogenesis, gas exchange, water relations and wood anatomy of black spruce [Picea mariana (Mill.) B.S.P.] saplings were monitored during a greenhouse experiment where temperature was increased during daytime or night-time (+6 °C) combined with a drought period. The kinetics of tracheid development expressed as rate and duration of the xylogenesis sub-processes were quantified using generalized additive models. Drought and warming had a strong influence on cell production, but little effect on wood anatomy. The increase in cell production rate under warmer temperatures, and especially during the night-time warming at the end of the growing season, resulted in wider tree-rings. However, the strong compensation between rates and durations of cell differentiation processes mitigates warming and drought effects on tree-ring structure. Our results allowed quantification of how wood formation kinetics is regulated when water and heat stress increase, allowing trees to adapt to future environmental conditions. © 2015 John Wiley & Sons Ltd.

Allocation to leaf area and sapwood area affects water relations of co-occurring savanna and forest trees

Treesearch

Sybil G. Gotsch; Erika L. Geiger; Augusto C. Franco; Guillermo Goldstein; Frederick C. Meinzer; William A. Hoffmann

2010-01-01

Water availability is a principal factor limiting the distribution of closed-canopy forest in the seasonal tropics, suggesting that forest tree species may not be well adapted to cope with seasonal drought. We studied 11 congeneric species pairs, each containing one forest and one savanna species, to test the hypothesis that forest trees have a lower capacity to...

Portable Language-Independent Adaptive Translation from OCR. Phase 1

DTIC Science & Technology

2009-04-01

including brute-force k-Nearest Neighbors ( kNN ), fast approximate kNN using hashed k-d trees, classification and regression trees, and locality...achieved by refinements in ground-truthing protocols. Recent algorithmic improvements to our approximate kNN classifier using hashed k-D trees allows...recent years discriminative training has been shown to outperform phonetic HMMs estimated using ML for speech recognition. Standard ML estimation

Trees and logs important to wildlife in the interior Columbia River basin.

Treesearch

Evelyn L. Bull; Catherine G. Parks; Torolf R. Torgersen

1997-01-01

This publication provides qualitative and quantitative information on five distinct structures: living trees with decayed parts, trees with hollow chambers, trees with brooms, dead trees, and logs. Information is provided on the value of these structures to wildlife, the decay or infection processes involved in the formation of these structures, and the principles to...

Mesoscopic structure formation in condensed matter due to vacuum fluctuations

NASA Astrophysics Data System (ADS)

Sen, Siddhartha; Gupta, Kumar S.; Coey, J. M. D.

2015-10-01

An observable influence of zero-point fluctuations of the vacuum electromagnetic field on bound electrons is well known in the hydrogen atom, where it produces the Lamb shift. Here, we adapt an approach used to explain the Lamb shift in terms of a slight expansion of the orbits due to interaction with the zero-point field and apply it to assemblies of N electrons that are modeled as independent atomically bound two-level systems. The effect is to stabilize a collective ground-state energy, which leads to a prediction of novel effects at room temperature for quasi-two-dimensional systems over a range of parameters in the model, namely, N , the two-level excitation energy ℏ ω and the ionization energy ℏ ω +ɛ . Some mesoscopic systems where these effects may be observable include water sheaths on protein or DNA, surfaces of gaseous nanobubbles, and the magnetic response of inhomogeneous, electronically dilute oxides. No such effects are envisaged for uniform three-dimensional systems.

Leaf Phenological Characters of Main Tree Species in Urban Forest of Shenyang

PubMed Central

Xu, Sheng; Xu, Wenduo; Chen, Wei; He, Xingyuan; Huang, Yanqing; Wen, Hua

2014-01-01

Background Plant leaves, as the main photosynthetic organs and the high energy converters among primary producers in terrestrial ecosystems, have attracted significant research attention. Leaf lifespan is an adaptive characteristic formed by plants to obtain the maximum carbon in the long-term adaption process. It determines important functional and structural characteristics exhibited in the environmental adaptation of plants. However, the leaf lifespan and leaf characteristics of urban forests were not studied up to now. Methods By using statistic, linear regression methods and correlation analysis, leaf phenological characters of main tree species in urban forest of Shenyang were observed for five years to obtain the leafing phenology (including leafing start time, end time, and duration), defoliating phenology (including defoliation start time, end time, and duration), and the leaf lifespan of the main tree species. Moreover, the relationships between temperature and leafing phenology, defoliating phenology, and leaf lifespan were analyzed. Findings The timing of leafing differed greatly among species. The early leafing species would have relatively early end of leafing; the longer it took to the end of leafing would have a later time of completed leafing. The timing of defoliation among different species varied significantly, the early defoliation species would have relatively longer duration of defoliation. If the mean temperature rise for 1°C in spring, the time of leafing would experience 5 days earlier in spring. If the mean temperature decline for 1°C, the time of defoliation would experience 3 days delay in autumn. Interpretation There is significant correlation between leaf longevity and the time of leafing and defoliation. According to correlation analysis and regression analysis, there is significant correlation between temperature and leafing and defoliation phenology. Early leafing species would have a longer life span and consequently have advantage on carbon accumulation compared with later defoliation species. PMID:24963625

Model Selection for the Multiple Model Adaptive Algorithm for In-Flight Simulation.

DTIC Science & Technology

1987-12-01

of the two models, while the other model was given a probability of approximately zero. If the probabilties were exactly one and zero for the...Figures 6-103 through 6-107. From Figure 6-103, it can be seen that the probabilty of the model associated with the 10,000 ft, 0.35 Mach flight con

A finite-difference method for the variable coefficient Poisson equation on hierarchical Cartesian meshes

NASA Astrophysics Data System (ADS)

Raeli, Alice; Bergmann, Michel; Iollo, Angelo

2018-02-01

We consider problems governed by a linear elliptic equation with varying coefficients across internal interfaces. The solution and its normal derivative can undergo significant variations through these internal boundaries. We present a compact finite-difference scheme on a tree-based adaptive grid that can be efficiently solved using a natively parallel data structure. The main idea is to optimize the truncation error of the discretization scheme as a function of the local grid configuration to achieve second-order accuracy. Numerical illustrations are presented in two and three-dimensional configurations.

African Savanna-Forest Boundary Dynamics: A 20-Year Study

PubMed Central

Cuni-Sanchez, Aida; White, Lee J. T.; Calders, Kim; Jeffery, Kathryn J.; Abernethy, Katharine; Burt, Andrew; Disney, Mathias; Gilpin, Martin; Gomez-Dans, Jose L.; Lewis, Simon L.

2016-01-01

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types. PMID:27336632

African Savanna-Forest Boundary Dynamics: A 20-Year Study.

PubMed

Cuni-Sanchez, Aida; White, Lee J T; Calders, Kim; Jeffery, Kathryn J; Abernethy, Katharine; Burt, Andrew; Disney, Mathias; Gilpin, Martin; Gomez-Dans, Jose L; Lewis, Simon L

2016-01-01

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types.

Are Scots pine forest edges particularly prone to drought-induced mortality?

NASA Astrophysics Data System (ADS)

Buras, Allan; Schunk, Christian; Zeiträg, Claudia; Herrmann, Corinna; Kaiser, Laura; Lemme, Hannes; Straub, Christoph; Taeger, Steffen; Gößwein, Sebastian; Klemmt, Hans-Joachim; Menzel, Annette

2018-02-01

Climate change is expected to exacerbate the frequency of drought-induced tree mortality world-wide. To better predict the associated change of species composition and forest dynamics on various scales and develop adequate adaptation strategies, more information on the mechanisms driving the often observed patchiness of tree die-back is needed. Although forest-edge effects may play an important role within the given context, only few corresponding studies exist. Here, we investigate the regional die-back of Scots pine in Franconia, Germany, after a hot and dry summer in 2015, thereby emphasizing possible differences in mortality between forest edge and interior. By means of dendroecological investigations and close-range remote sensing, we assess long-term growth performance and current tree vitality along five different forest-edge distance gradients. Our results clearly indicate a differing growth performance between edge and interior trees, associated with a higher vulnerability to drought, increased mortality rates, and lower tree vitality at the forest edge. Prior long-lasting growth decline of dead trees compared to live trees suggests depletion of carbon reserves in course of a long-term drought persisting since the 1990s to be the cause of regional Scots pine die-back. These findings highlight the forest edge as a potential focal point of forest management adaptation strategies in the context of drought-induced mortality.

[Supernumerary chromosomes in the karyotype of the Siberian spruce, P. obovata].

PubMed

Muratova, E N; Vladimirova, O S

2001-01-01

Results of karyological study of ornamental forms of Picea obovata Ledeb. are presented. Typical chromosome number (2n) is 24, but some trees have one or two additional chromosomes (2n = 24 + 1B; 2n = 24 + 2B). Heritability of additional chromosomes, pollen fertility, morphological features of cones, and seed quality in trees with and without additional chromosomes were studied. System of B-chromosomes is of importance for population and species adaptation and possibly plays a role in adaptation of P. obovata under introduction.

Delivery Path Length and Holding Tree Minimization Method of Securities Delivery among the Registration Agencies Connected as Non-Tree

NASA Astrophysics Data System (ADS)

Shimamura, Atsushi; Moritsu, Toshiyuki; Someya, Harushi

To dematerialize the securities such as stocks or cooporate bonds, the securities were registered to account in the registration agencies which were connected as tree. This tree structure had the advantage in the management of the securities those were issued large amount and number of brands of securities were limited. But when the securities such as account receivables or advance notes are dematerialized, number of brands of the securities increases extremely. In this case, the management of securities with tree structure becomes very difficult because of the concentration of information to root of the tree. To resolve this problem, using the graph structure is assumed instead of the tree structure. When the securities are kept with tree structure, the delivery path of securities is unique, but when securities are kept with graph structure, path of delivery is not unique. In this report, we describe the requirement of the delivery path of securities, and we describe selecting method of the path.

Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models

DOE PAGES

Carlberg, Kevin T.

2014-11-05

Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less

Lee-Wick black holes

NASA Astrophysics Data System (ADS)

Bambi, Cosimo; Modesto, Leonardo; Wang, Yixu

2017-01-01

We derive and study an approximate static vacuum solution generated by a point-like source in a higher derivative gravitational theory with a pair of complex conjugate ghosts. The gravitational theory is local and characterized by a high derivative operator compatible with Lee-Wick unitarity. In particular, the tree-level two-point function only shows a pair of complex conjugate poles besides the massless spin two graviton. We show that singularity-free black holes exist when the mass of the source M exceeds a critical value Mcrit. For M >Mcrit the spacetime structure is characterized by an outer event horizon and an inner Cauchy horizon, while for M =Mcrit we have an extremal black hole with vanishing Hawking temperature. The evaporation process leads to a remnant that approaches the zero-temperature extremal black hole state in an infinite amount of time.

Development of an automated ultrasonic testing system

NASA Astrophysics Data System (ADS)

Shuxiang, Jiao; Wong, Brian Stephen

2005-04-01

Non-Destructive Testing is necessary in areas where defects in structures emerge over time due to wear and tear and structural integrity is necessary to maintain its usability. However, manual testing results in many limitations: high training cost, long training procedure, and worse, the inconsistent test results. A prime objective of this project is to develop an automatic Non-Destructive testing system for a shaft of the wheel axle of a railway carriage. Various methods, such as the neural network, pattern recognition methods and knowledge-based system are used for the artificial intelligence problem. In this paper, a statistical pattern recognition approach, Classification Tree is applied. Before feature selection, a thorough study on the ultrasonic signals produced was carried out. Based on the analysis of the ultrasonic signals, three signal processing methods were developed to enhance the ultrasonic signals: Cross-Correlation, Zero-Phase filter and Averaging. The target of this step is to reduce the noise and make the signal character more distinguishable. Four features: 1. The Auto Regressive Model Coefficients. 2. Standard Deviation. 3. Pearson Correlation 4. Dispersion Uniformity Degree are selected. And then a Classification Tree is created and applied to recognize the peak positions and amplitudes. Searching local maximum is carried out before feature computing. This procedure reduces much computation time in the real-time testing. Based on this algorithm, a software package called SOFRA was developed to recognize the peaks, calibrate automatically and test a simulated shaft automatically. The automatic calibration procedure and the automatic shaft testing procedure are developed.

Silvics of Missouri bottomland tree species

Treesearch

John Kabrick; Daniel Dey

2001-01-01

This issue of Notes For Forest Managers provides a concise summary of important silvical characteristics of Missouri's bottomland trees. It focuses on species adaptations to or tolerances of, environmental and site conditions. It is a compilation of information from seven different references cited in the text.

30 CFR 715.20 - Revegetation.

Code of Federal Regulations, 2012 CFR

2012-07-01

... meet applicable State and Federal seed or introduced species statutes, and shall not include poisonous... for the type of plant materials selected to meet specific site conditions and climate. Any disturbed... postmining land use, the permittee shall plant trees adapted for local site conditions and climate. Trees...

30 CFR 715.20 - Revegetation.

Code of Federal Regulations, 2014 CFR

2014-07-01

... meet applicable State and Federal seed or introduced species statutes, and shall not include poisonous... for the type of plant materials selected to meet specific site conditions and climate. Any disturbed... postmining land use, the permittee shall plant trees adapted for local site conditions and climate. Trees...

30 CFR 715.20 - Revegetation.

Code of Federal Regulations, 2013 CFR

2013-07-01

... meet applicable State and Federal seed or introduced species statutes, and shall not include poisonous... for the type of plant materials selected to meet specific site conditions and climate. Any disturbed... postmining land use, the permittee shall plant trees adapted for local site conditions and climate. Trees...

Use of zerotree coding in a high-speed pyramid image multiresolution decomposition

NASA Astrophysics Data System (ADS)

Vega-Pineda, Javier; Cabrera, Sergio D.; Lucero, Aldo

1995-03-01

A Zerotree (ZT) coding scheme is applied as a post-processing stage to avoid transmitting zero data in the High-Speed Pyramid (HSP) image compression algorithm. This algorithm has features that increase the capability of the ZT coding to give very high compression rates. In this paper the impact of the ZT coding scheme is analyzed and quantified. The HSP algorithm creates a discrete-time multiresolution analysis based on a hierarchical decomposition technique that is a subsampling pyramid. The filters used to create the image residues and expansions can be related to wavelet representations. According to the pixel coordinates and the level in the pyramid, N2 different wavelet basis functions of various sizes and rotations are linearly combined. The HSP algorithm is computationally efficient because of the simplicity of the required operations, and as a consequence, it can be very easily implemented with VLSI hardware. This is the HSP's principal advantage over other compression schemes. The ZT coding technique transforms the different quantized image residual levels created by the HSP algorithm into a bit stream. The use of ZT's compresses even further the already compressed image taking advantage of parent-child relationships (trees) between the pixels of the residue images at different levels of the pyramid. Zerotree coding uses the links between zeros along the hierarchical structure of the pyramid, to avoid transmission of those that form branches of all zeros. Compression performance and algorithm complexity of the combined HSP-ZT method are compared with those of the JPEG standard technique.

Predicting climate change extirpation risk for central and southern Appalachian forest tree species

Treesearch

Kevin M. Potter; William W. Hargrove; Frank H. Koch

2010-01-01

Climate change will likely pose a severe threat to the viability of certain forest tree species, which will be forced either to adapt to new conditions or to shift to more favorable environments if they are to survive. Several forest tree species of the central and southern Appalachians may be at particular risk, since they occur in limited high-elevation ranges and/or...

Varying selection differential throughout the climatic range of Norway spruce in Central Europe.

PubMed

Kapeller, Stefan; Dieckmann, Ulf; Schueler, Silvio

2017-01-01

Predicting species distribution changes in global warming requires an understanding of how climatic constraints shape the genetic variation of adaptive traits and force local adaptations. To understand the genetic capacity of Norway spruce populations in Central Europe, we analyzed the variation in tree heights at the juvenile stage in common garden experiments established from the species' warm-dry to cold-moist distribution limits. We report the following findings: First, 47% of the total tree height variation at trial sites is attributable to the tree populations irrespective of site climate. Second, tree height variation within populations is higher at cold-moist trial sites than at warm-dry sites and higher within populations originating from cold-moist habitats than from warm-dry habitats. Third, for tree ages of 7-15 years, the variation within populations increases at cold-moist trial sites, whereas it remains constant at warm-dry sites. Fourth, tree height distributions are right-skewed at cold-moist trial sites, whereas they are nonskewed, but platykurtic at warm-dry sites. Our results suggest that in cold environments, climatic conditions impose stronger selection and probably restrict the distribution of spruce, whereas at the warm distribution limit, the species' realized niche might rather be controlled by external drivers, for example, forest insects.

Aerobic biological treatment of low-strength synthetic wastewater in membrane-coupled bioreactors: the structure and function of bacterial enrichment cultures as the net growth rate approaches zero.

PubMed

Chen, Ruoyu; LaPara, Timothy M

2006-01-01

The goal of the current research was to determine if the stringent nutrient limitation imposed by membrane-coupled bioreactors (MBRs) could be used to force mixed bacterial communities to exhibit a zero net growth rate over an extended time period. Mechanistically, this zero net growth rate could be achieved when the amount of energy available for growth is balanced by the maintenance requirements of the bacterial community. Bench-scale MBRs were fed synthetic feed medium containing gelatin as the major organic substrate. Biomass concentrations initially increased rapidly, but subsequently declined until an asymptote was reached. Leucine aminopeptidase activities concomitantly increased by at least 10-fold, suggesting that bacterial catabolic activity remained high even while growth rates became negligible. In contrast, alpha-glucosidase and heptanoate esterase activities decreased, indicating that the bacterial community specifically adapted to the carbon source in the feed medium. Bacterial community analysis by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments (PCR-DGGE) suggested that the bacterial community structure completely changed from the beginning to the end of each MBR. Excision and nucleotide sequence analysis of prominent PCR-DGGE bands suggested that many of the dominant populations were similar to novel bacterial strains that were previously uncultivated or recently cultivated during studies specifically targeting these novel populations. This research demonstrates that MBRs have substantial practical applications for biological wastewater treatment; in addition, MBRs are a useful tool to study the ecology of slow-growing bacteria.

Structures, phase transitions, and magnetic properties of C o3Si from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhao, Xin; Yu, Shu; Wu, Shunqing; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Ho, Kai-Ming

2017-07-01

C o3Si was recently reported to exhibit remarkable magnetic properties in the nanoparticle form [B. Balasubramanian et al., Appl. Phys. Lett. 108, 152406 (2016)], 10.1063/1.4945987, yet better understanding of this material should be promoted. Here we report a study on the crystal structures of C o3Si using an adaptive genetic algorithm and discuss its electronic and magnetic properties from first-principles calculations. Several competing phases of C o3Si have been revealed from our calculations. We show that the hexagonal C o3Si structure reported in experiments has lower energy in the nonmagnetic state than in the ferromagnetic state at zero temperature. The ferromagnetic state of the hexagonal structure is dynamically unstable with imaginary phonon modes and transforms into a new orthorhombic structure, which is confirmed by our structure searches to have the lowest energy for both C o3Si and C o3Ge . Magnetic properties of the experimental hexagonal structure and the lowest-energy structures obtained from our structure searches are investigated in detail.

Characteristics of zero-absenteeism in hospital care.

PubMed

Schreuder, J A H; Roelen, C A M; van der Klink, J J L; Groothoff, J W

2013-06-01

Literature on sickness presenteeism is emerging, but still little is known about employees who are never absent from work due to injuries or illness. Insight into the determinants and characteristics of such zero-absentees may provide clues for preventing sickness absence. To investigate the characteristics of zero-absentees, defined as employees without sickness absence over a period of 5 years. A mixed-method qualitative study comprising semi-structured interviews and focus groups for which Azjen and Fishbein's theory of planned behaviour was used as a framework. Zero-absentees working in hospital care were invited for semi-structured interviews until saturation was reached. The results of semi-structured interviews were validated in two focus groups. Of 1053 hospital employees, 47 were zero-absentees of whom 31 (66%) agreed to participate in the study. After 16 semi-structured interviews, no new insights or information were gathered from the interviews. The remaining 15 employees were invited to two (n = 8 and n = 7) focus groups. Personal attitudes and self-efficacy were more important in zero-absenteeism than social pressures of managers, colleagues or patients. Zero-absentees were found to be intrinsically motivated to try attending work when ill. In the present study population of hospital employees, we found indications that zero-absenteeism and sickness presenteeism might be different types of work attendance. Managers should realize that zero-absentees are driven by intrinsic motivation rather than social pressures to attend work.

Potential for on-orbit manufacture of large space structures using the pultrusion process

NASA Technical Reports Server (NTRS)

Wilson, Maywood L.; Macconochie, Ian O.; Johnson, Gary S.

1987-01-01

On-orbit manufacture of lightweight, high-strength, advanced-composite structures using the pultrusion process is proposed. This process is adaptable to a zero-gravity environment by using preimpregnated graphite-fiber reinforcement systems. The reinforcement material is preimpregnated with a high-performance thermoplastic resin at a ground station, is coiled on spools for compact storage, and is transported into Earth orbit. A pultrusion machine is installed in the Shuttle cargo bay from which very long lengths of the desired structure is fabricated on-orbit. Potential structural profiles include rods, angles, channels, hat sections, tubes, honeycomb-cored panels, and T, H, and I beams. A potential pultrudable thermoplastic/graphite composite material is presented as a model for determining the effect on Earth-to-orbit package density of an on-orbit manufacture, the package density is increased by 132 percent, and payload volume requirement is decreased by 56.3 percent. The fabrication method has the potential for on-orbit manufacture of structural members for space platforms, large space antennas, and long tethers.

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

PubMed Central

Ethayathulla, Abdul S.; Tse, Pui-Wah; Monti, Paola; Nguyen, Sonha; Inga, Alberto; Fronza, Gilberto; Viadiu, Hector

2012-01-01

The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation. PMID:22474346

Climate Warming Threatens Semi-arid Forests in Inner Asia

NASA Astrophysics Data System (ADS)

WU, X.; Liu, H.; Qi, Z.; Li, X.

2014-12-01

A line of evidences reveal an increasing tree growth decline and tree mortality mainly attributable to climate warming and the warming-mediated changes in drought and other processes (such as fire and insect dynamics) in many parts of world tropical, temperate and boreal forests. However, the growth responses to climate change of the widely distributed semi-arid forests are unclear. Here, we synthetically investigate the tree growth patterns during past decades and its interannual response to climate variations in Inner Asia combining the ground truth field survey and samplings, remote sensing observations and climate data. We identified a pervasive tree growth decline since mid-1990s in semi-arid forests in Inner Asia. The widely observed tree growth decline is dominantly attributable to warming-induced water stress during pre- and early growing season. Tree growth of semi-arid forests in Inner Asia is particularly susceptible to spring warming and has been suffering a prolonged growth limitation in recent decades due to spring warming-mediated water conditions. Additionally, we identified a much slower growth rate in younger trees and a lack of tree regeneration in these semi-arid forests. The widely observed forest growth reduction and lack of tree regeneration over semi-arid forests in Inner Asia could predictably exert great effects on forest structure, regionally/globally biophysical and biochemical processes and the feedbacks between biosphere and atmosphere. Notably, further increases in forest stress and tree mortality could be reasonably expected, especially in context of the increase frequency and severity of high temperature and heat waves and changes in forest disturbances, potentially driving the eventual regional loss of current semi-arid forests. Given the potential risks of climate induced forest dieback, increased management attention to adaptation options for enhancing forest resistance and resilience to projected climate stress can be expected. However, the functionally realistic mechanisms beneath the pervasively climate-induced forest decline/dieback still remain unclear. Network-based long-term surveys and experiment studies are urgently needed for further understandings regarding the responses of forest/tree growth to climate warming/variations.

Global tree network for computing structures enabling global processing operations

DOEpatents

Blumrich; Matthias A.; Chen, Dong; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Steinmacher-Burow, Burkhard D.; Takken, Todd E.; Vranas, Pavlos M.

2010-01-19

A system and method for enabling high-speed, low-latency global tree network communications among processing nodes interconnected according to a tree network structure. The global tree network enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the tree via links to facilitate performance of low-latency global processing operations at nodes of the virtual tree and sub-tree structures. The global operations performed include one or more of: broadcast operations downstream from a root node to leaf nodes of a virtual tree, reduction operations upstream from leaf nodes to the root node in the virtual tree, and point-to-point message passing from any node to the root node. The global tree network is configurable to provide global barrier and interrupt functionality in asynchronous or synchronized manner, and, is physically and logically partitionable.

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

PubMed

Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; Dos Santos, Flavio Antonio Maës

2015-05-01

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

From process to proxy: Ecological challenges and opportunities of tree-ring based environmental reconstructions

NASA Astrophysics Data System (ADS)

Wilmking, Martin; Buras, Allan; Heinrich, Ingo; Scharnweber, Tobias; Simard, Sonia; Smiljanic, Marko; van der Maaten, Ernst; van der Maaten-Theunissen, Marieke

2014-05-01

Trees are sessile, long-living organisms and as such constantly need to adapt to changing environmental conditions. Accordingly, they often show high phenotypic plasticity (the ability to change phenotypic traits, such as allocation of resources) in response to environmental change. This high phenotypic plasticity is generally considered as one of the main ingredients for a sessile organism to survive and reach high ages. Precisely because of the ability of trees to reach old age and their in-ability to simply run away when conditions get worse, growth information recorded in tree rings has long been used as a major environmental proxy, covering time scales from decades to millennia. Past environmental conditions (e.g. climate) are recorded in i.e. annual tree-ring width, early- and latewood width, wood density, isotopic concentrations, cell anatomy or wood chemistry. One prerequisite for a reconstruction is that the relationship between the environmental variable influencing tree growth and the tree-growth variable itself is stable through time. This, however, might contrast the ecological theory of high plasticity and the trees ability to adapt to change. To untangle possible mechanisms leading to stable or unstable relationships between tree growth and environmental variables, it is helpful to have exact site information and several proxy variables of each tree-ring series available. Although we gain insight into the environmental history of a sampling site when sampling today, this is extremely difficult when using archeological wood. In this latter case, we face the additional challenge of unknown origin, provenance and (or) site conditions, making it even more important to use multiple proxy time-series from the same sample. Here, we review typical examples, where the relationship between tree growth and environmental variables seems 1) stable and 2) instable through time, and relate these two cases to ecological theory. Based on ecological theory, we then give recommendations to improve the reliability of environmental reconstructions using tree rings.

Context-aware adaptive spelling in motor imagery BCI.

PubMed

Perdikis, S; Leeb, R; Millán, J D R

2016-06-01

This work presents a first motor imagery-based, adaptive brain-computer interface (BCI) speller, which is able to exploit application-derived context for improved, simultaneous classifier adaptation and spelling. Online spelling experiments with ten able-bodied users evaluate the ability of our scheme, first, to alleviate non-stationarity of brain signals for restoring the subject's performances, second, to guide naive users into BCI control avoiding initial offline BCI calibration and, third, to outperform regular unsupervised adaptation. Our co-adaptive framework combines the BrainTree speller with smooth-batch linear discriminant analysis adaptation. The latter enjoys contextual assistance through BrainTree's language model to improve online expectation-maximization maximum-likelihood estimation. Our results verify the possibility to restore single-sample classification and BCI command accuracy, as well as spelling speed for expert users. Most importantly, context-aware adaptation performs significantly better than its unsupervised equivalent and similar to the supervised one. Although no significant differences are found with respect to the state-of-the-art PMean approach, the proposed algorithm is shown to be advantageous for 30% of the users. We demonstrate the possibility to circumvent supervised BCI recalibration, saving time without compromising the adaptation quality. On the other hand, we show that this type of classifier adaptation is not as efficient for BCI training purposes.

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.

Northern Forest DroughtNet: Initial results from a multi-year throughfall manipulation experiment in New Hampshire

NASA Astrophysics Data System (ADS)

McIntire, C.; Vadeboncoeur, M. A.; Coble, A.; Jennings, K.; Asbjornsen, H.

2016-12-01

Climate change is likely to affect the Northern Forest region through the increased frequency and severity of drought events. However, our understanding of how the Northern Forest, which is adapted to humid temperate conditions, will respond to moderate to extreme droughts is limited. Given the important role that these forests play in protecting ecosystem services and in supplying forest products, enhancing our knowledge about impacts of drought is critical to ensuring effective forest management and adaptation to climate change. The Northern Forest DroughtNet project aims to simulate a four-year severe drought by removing 55% of the incoming throughfall; thus representing the 99th percentile of annual precipitation based on historic precipitation data in Durham, NH. This is accomplished using two replicated 900 m2 throughfall removal structures consisting of a network of gutters that capture and divert incoming precipitation away from the established treatment area. Data presented here will address the ecosystem response to the drought treatment over the course of the first year of the experiment as well as validate the effectiveness and artifacts of the throughfall removal structure. Response variables of interest include soil moisture content, above and below ground biomass production, litterfall, decomposition rates, leaf water potential, foliar gas exchange, and whole tree transpiration rates. Preliminary findings provide insight into the effectiveness of using throughfall manipulation experiments in a temperate forest ecosystem to simulate an extreme drought event, as well as initial tree physiological and growth responses in relation to soil moisture availability and the implications for future climate change impacts.

180,000 years of climate change in Europe: avifaunal responses and vegetation implications.

PubMed

Holm, Sandra Ravnsbæk; Svenning, Jens-Christian

2014-01-01

Providing an underutilized source of information for paleoenvironmental reconstructions, birds are rarely used to infer paleoenvironments despite their well-known ecology and extensive Quaternary fossil record. Here, we use the avian fossil record to investigate how Western Palearctic bird assemblages and species ranges have changed across the latter part of the Pleistocene, with focus on the links to climate and the implications for vegetation structure. As a key issue we address the full-glacial presence of trees in Europe north of the Mediterranean region, a widely debated issue with evidence for and against emerging from several research fields and data sources. We compiled and analyzed a database of bird fossil occurrences from archaeological sites throughout the Western Palearctic and spanning the Saalian-Eemian-Weichselian stages, i.e. 190,000-10,000 years BP. In general, cold and dry-adapted species dominated these late Middle Pleistocene and Late Pleistocene fossil assemblages, with clear shifts of northern species southwards during glacials, as well as northwards and westwards shifts of open-vegetation species from the south and east, respectively and downwards shifts of alpine species. A direct link to climate was clear in Northwestern Europe. However, in general, bird assemblages more strongly reflected vegetation changes, underscoring their usefulness for inferring the vegetation structure of past landscapes. Forest-adapted birds were found in continuous high proportions throughout the study period, providing support for the presence of trees north of the Alps, even during full-glacial stages. Furthermore, the results suggest forest-dominated but partially open Eemian landscapes in the Western Palearctic, including the Northwestern European subregion.

Body wiping behaviors associated with cutaneous lipids in hylid tree frogs of Florida.

PubMed

Barbeau, Tamatha R; Lillywhite, Harvey B

2005-06-01

Body wiping behavior, integumentary secretions and rates of evaporative water loss (EWL) were examined in six species of Florida tree frogs (Anura: Hylidae). Additionally, morphology of the integument and dermal glands were compared among these and one other Florida tree frog (Hyla andersonii), an arid-adapted tree frog (Phyllomedusa hypochondrialis), and a highly aquatic frog (Rana utricularia). An extra-epidermal layer of lipid and mucus, presumably secreted from dermal granular glands, was detected on the skin of all Florida hylid frogs examined. Distinct body wiping behaviors were observed in the hylid frogs, but these were less complex than those described previously in phyllomedusine frogs, which occupy arid habitats, secrete lipids onto their skin, and are regarded as relatively 'waterproof'. Florida hylids occupy seasonally arid habitats and appear to have reduced rates of EWL. The suite of traits we observed in these frogs have been previously documented in a rhacophorid tree frog from seasonally arid regions of India and likely represent an evolutionary convergent response to periodic dehydration stress. The presence of lipids that are spread by simple wiping behaviors to form an extra-epidermal water barrier may represent an early stage of the more advanced adaptations described in more waterproof arboreal frogs.

Prognoses of diameter and height of trees of eucalyptus using artificial intelligence.

PubMed

Vieira, Giovanni Correia; de Mendonça, Adriano Ribeiro; da Silva, Gilson Fernandes; Zanetti, Sidney Sára; da Silva, Mayra Marques; Dos Santos, Alexandre Rosa

2018-04-01

Models of individual trees are composed of sub-models that generally estimate competition, mortality, and growth in height and diameter of each tree. They are usually adopted when we want more detailed information to estimate forest multiproduct. In these models, estimates of growth in diameter at 1.30m above the ground (DBH) and total height (H) are obtained by regression analysis. Recently, artificial intelligence techniques (AIT) have been used with satisfactory performance in forest measurement. Therefore, the objective of this study was to evaluate the performance of two AIT, artificial neural networks and adaptive neuro-fuzzy inference system, to estimate the growth in DBH and H of eucalyptus trees. We used data of continuous forest inventories of eucalyptus, with annual measurements of DBH, H, and the dominant height of trees of 398 plots, plus two qualitative variables: genetic material and site index. It was observed that the two AIT showed accuracy in growth estimation of DBH and H. Therefore, the two techniques discussed can be used for the prognosis of DBH and H in even-aged eucalyptus stands. The techniques used could also be adapted to other areas and forest species. Copyright © 2017 Elsevier B.V. All rights reserved.

Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

PubMed

Deacon, Nicholas John; Cavender-Bares, Jeannine

2015-01-01

Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by examining a common, tropical tree over multiple habitats and provide information for managers of a successional forest in a protected area.

A Functional and Structural Mongolian Scots Pine (Pinus sylvestris var. mongolica) Model Integrating Architecture, Biomass and Effects of Precipitation

PubMed Central

Wang, Feng; Letort, Véronique; Lu, Qi; Bai, Xuefeng; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2012-01-01

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal tree species in the network of Three-North Shelterbelt for windbreak and sand stabilisation in China. The functions of shelterbelts are highly correlated with the architecture and eco-physiological processes of individual tree. Thus, model-assisted analysis of canopy architecture and function dynamic in Mongolian Scots pine is of value for better understanding its role and behaviour within shelterbelt ecosystems in these arid and semiarid regions. We present here a single-tree functional and structural model, derived from the GreenLab model, which is adapted for young Mongolian Scots pines by incorporation of plant biomass production, allocation, allometric rules and soil water dynamics. The model is calibrated and validated based on experimental measurements taken on Mongolian Scots pines in 2007 and 2006 under local meteorological conditions. Measurements include plant biomass, topology and geometry, as well as soil attributes and standard meteorological data. After calibration, the model allows reconstruction of three-dimensional (3D) canopy architecture and biomass dynamics for trees from one- to six-year-old at the same site using meteorological data for the six years from 2001 to 2006. Sensitivity analysis indicates that rainfall variation has more influence on biomass increment than on architecture, and the internode and needle compartments and the aboveground biomass respond linearly to increases in precipitation. Sensitivity analysis also shows that the balance between internode and needle growth varies only slightly within the range of precipitations considered here. The model is expected to be used to investigate the growth of Mongolian Scots pines in other regions with different soils and climates. PMID:22927982

Above ground biomass and tree species richness estimation with airborne lidar in tropical Ghana forests

NASA Astrophysics Data System (ADS)

Vaglio Laurin, Gaia; Puletti, Nicola; Chen, Qi; Corona, Piermaria; Papale, Dario; Valentini, Riccardo

2016-10-01

Estimates of forest aboveground biomass are fundamental for carbon monitoring and accounting; delivering information at very high spatial resolution is especially valuable for local management, conservation and selective logging purposes. In tropical areas, hosting large biomass and biodiversity resources which are often threatened by unsustainable anthropogenic pressures, frequent forest resources monitoring is needed. Lidar is a powerful tool to estimate aboveground biomass at fine resolution; however its application in tropical forests has been limited, with high variability in the accuracy of results. Lidar pulses scan the forest vertical profile, and can provide structure information which is also linked to biodiversity. In the last decade the remote sensing of biodiversity has received great attention, but few studies focused on the use of lidar for assessing tree species richness in tropical forests. This research aims at estimating aboveground biomass and tree species richness using discrete return airborne lidar in Ghana forests. We tested an advanced statistical technique, Multivariate Adaptive Regression Splines (MARS), which does not require assumptions on data distribution or on the relationships between variables, being suitable for studying ecological variables. We compared the MARS regression results with those obtained by multilinear regression and found that both algorithms were effective, but MARS provided higher accuracy either for biomass (R2 = 0.72) and species richness (R2 = 0.64). We also noted strong correlation between biodiversity and biomass field values. Even if the forest areas under analysis are limited in extent and represent peculiar ecosystems, the preliminary indications produced by our study suggest that instrument such as lidar, specifically useful for pinpointing forest structure, can also be exploited as a support for tree species richness assessment.

Identification and characterization of NF-YB family genes in tung tree.

PubMed

Yang, Susu; Wang, Yangdong; Yin, Hengfu; Guo, Haobo; Gao, Ming; Zhu, Huiping; Chen, Yicun

2015-12-01

The NF-YB transcription factor gene family encodes a subunit of the CCAAT box-binding factor (CBF), a highly conserved trimeric activator that strongly binds to the CCAAT box promoter element. Studies on model plants have shown that NF-YB proteins participate in important developmental and physiological processes, but little is known about NF-YB proteins in trees. Here, we identified seven NF-YB transcription factor-encoding genes in Vernicia fordii, an important oilseed tree in China. A phylogenetic analysis separated the genes into two groups; non-LEC1 type (VfNF-YB1, 5, 7, 9, 11, 13) and LEC1-type (VfNF-YB 14). A gene structure analysis showed that VfNF-YB 5 has three introns and the other genes have no introns. The seven VfNF-YB sequences contain highly conserved domains, a disordered region at the N terminus, and two long helix structures at the C terminus. Phylogenetic analyses showed that VfNF-YB family genes are highly homologous to GmNF-YB genes, and many of them are closely related to functionally characterized NF-YBs. In expression analyses of various tissues (root, stem, leaf, and kernel) and the root during pathogen infection, VfNF-YB1, 5, and 11 were dominantly expressed in kernels, and VfNF-YB7 and 9 were expressed only in the root. Different VfNF-YB family genes showed different responses to pathogen infection, suggesting that they play different roles in the pathogen response. Together, these findings represent the first extensive evaluation of the NF-YB family in tung tree and provide a foundation for dissecting the functions of VfNF-YB genes in seed development, stress adaption, fatty acid synthesis, and pathogen response.

Effects of tree height on branch hydraulics, leaf structure and gas exchange in California redwoods.

PubMed

Ambrose, Anthony R; Sillett, Stephen C; Dawson, Todd E

2009-07-01

We examined changes in branch hydraulic, leaf structure and gas exchange properties in coast redwood (Sequoia sempervirens) and giant sequoia (Sequoiadendron giganteum) trees of different sizes. Leaf-specific hydraulic conductivity (k(L)) increased with height in S. sempervirens but not in S. giganteum, while xylem cavitation resistance increased with height in both species. Despite hydraulic adjustments, leaf mass per unit area (LMA) and leaf carbon isotope ratios (delta(13)C) increased, and maximum mass-based stomatal conductance (g(mass)) and photosynthesis (A(mass)) decreased with height in both species. As a result, both A(mass) and g(mass) were negatively correlated with branch hydraulic properties in S. sempervirens and uncorrelated in S. giganteum. In addition, A(mass) and g(mass) were negatively correlated with LMA in both species, which we attributed to the effects of decreasing leaf internal CO(2) conductance (g(i)). Species-level differences in wood density, LMA and area-based gas exchange capacity constrained other structural and physiological properties, with S. sempervirens exhibiting increased branch water transport efficiency and S. giganteum exhibiting increased leaf-level water-use efficiency with increasing height. Our results reveal different adaptive strategies for the two redwoods that help them compensate for constraints associated with growing taller, and reflect contrasting environmental conditions each species faces in its native habitat.

[Adsorption Capacity of the Air Particulate Matter in Urban Landscape Plants in Different Polluted Regions of Beijing].

PubMed

Zhang, Wei-kang; Wang, Bing; Niu, Xiang

2015-07-01

Urban landscape plants, as one of the important factors of the urban ecosystem, play an important role in stagnating airborne particulates and purifying urban atmospheric environment. In this article, six kinds of common garden plants were studied, and aerosol generator (QRJZFSQ-I) was used to measure the ability of their leaves to stagnate atmospheric particulates (TSP and PM2.5) in different polluted regions. Meanwhile, environmental scanning electron microscope was used to observe changes in the leaf structure of the tested tree species. The results showed: (1)Among the tested tree species, the ability of coniferous species to stagnate atmospheric particulates was higher than that of broad-leaved species per unit leaf area. Pinus tabuliformis stagnated the highest volume of (3. 89± 0. 026) µg . m-2, followed by Pinus bungeana of (2. 82 ± 0. 392) µg . cm-2, and Populus tomentosa stagnated the minimum of (2. 00 ± 0. 118) µg . cm-2; (2) Through observing the leaf microstructure morphology, coniferous species were found to have tightly packed stomas, stoma density and surface roughness higher than those of broad-leaved species, and they could also secrete oil; (3) In different polluted regions, the leaves of the same tree species showed significant difference in stagnating TSP. Per unit leaf area, the tree species leaves situated around the 5th Ring Road had higher ability to absorb TSP than the tree species leaves at Botanical Garden, while their abilities to absorb PM2.5 showed no significant difference; (4) In different polluted regions, significantly adaptive changes were found in leaf structure. Comparing to the region with light pollution, the outer epidermal cells of the plant leaves in region with heavy pollution shrank, and the roughness of the leaf skin textures as well as the stomatal frequency and villous length increased. In spite of the significant changes in plant leaves exposed to the heavy pollution, these plants could still maintain normal and healthy growth.

Tree-Structured Infinite Sparse Factor Model

PubMed Central

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

2013-01-01

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

Fine structure and functional comments of mouthparts in Platypus cylindrus (Col., Curculionidae: Platypodinae).

PubMed

Belhoucine, Latifa; Bouhraoua, Rachid T; Prats, Eva; Pulade-Villar, Juli

2013-02-01

Oak pinhole borer, Platypus cylindrus is seen in recent years as one of the biggest enemies directly involved in the observed decline of cork oak in Mediterranean forests with all the economic implications. As an ambrosia beetle, it has developed its effective drilling mouthpart enough to make tunnels in hardwood of the tree. The fine structural aspects of the mouthpart using the field emission scanning electron microscopy are analyzed about 23 adults collected in galleries of infested cork oak trees (Quercus suber) in a littoral forest of northwest Algeria. These adults are preserved in alcohol 70%, cleaned and coated with gold. The mouthparts of this beetle consist commonly of a labrum, a pair of mandibles, a pair of maxillae and the labium but with adapted structure to excavate galleries in the hardwood. In this role is also involved the first pair of legs. The function that present the different structures related to the construction of the tunnels is discussed. Both of maxillary and labial palpi direct the food to the mouth and hold it while the mandibles chew the food. The distal ends of these palpi are flattened and have shovel-like setae. Females have larger maxillary palpi than males and this is related to the particular biology of each sex. Copyright © 2012 Elsevier Ltd. All rights reserved.

Distribution-free Inference of Zero-inated Binomial Data for Longitudinal Studies.

PubMed

He, H; Wang, W J; Hu, J; Gallop, R; Crits-Christoph, P; Xia, Y L

2015-10-01

Count reponses with structural zeros are very common in medical and psychosocial research, especially in alcohol and HIV research, and the zero-inflated poisson (ZIP) and zero-inflated negative binomial (ZINB) models are widely used for modeling such outcomes. However, as alcohol drinking outcomes such as days of drinkings are counts within a given period, their distributions are bounded above by an upper limit (total days in the period) and thus inherently follow a binomial or zero-inflated binomial (ZIB) distribution, rather than a Poisson or zero-inflated Poisson (ZIP) distribution, in the presence of structural zeros. In this paper, we develop a new semiparametric approach for modeling zero-inflated binomial (ZIB)-like count responses for cross-sectional as well as longitudinal data. We illustrate this approach with both simulated and real study data.

Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat.

PubMed

Hess, Moritz; Wildhagen, Henning; Junker, Laura Verena; Ensminger, Ingo

2016-08-26

Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction. The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.

The interaction between freezing tolerance and phenology in temperate deciduous trees

PubMed Central

Vitasse, Yann; Lenz, Armando; Körner, Christian

2014-01-01

Temperate climates are defined by distinct temperature seasonality with large and often unpredictable weather during any of the four seasons. To thrive in such climates, trees have to withstand a cold winter and the stochastic occurrence of freeze events during any time of the year. The physiological mechanisms trees adopt to escape, avoid, and tolerate freezing temperatures include a cold acclimation in autumn, a dormancy period during winter (leafless in deciduous trees), and the maintenance of a certain freezing tolerance during dehardening in early spring. The change from one phase to the next is mediated by complex interactions between temperature and photoperiod. This review aims at providing an overview of the interplay between phenology of leaves and species-specific freezing resistance. First, we address the long-term evolutionary responses that enabled temperate trees to tolerate certain low temperature extremes. We provide evidence that short term acclimation of freezing resistance plays a crucial role both in dormant and active buds, including re-acclimation to cold conditions following warm spells. This ability declines to almost zero during leaf emergence. Second, we show that the risk that native temperate trees encounter freeze injuries is low and is confined to spring and underline that this risk might be altered by climate warming depending on species-specific phenological responses to environmental cues. PMID:25346748

Diversity Dynamics in Nymphalidae Butterflies: Effect of Phylogenetic Uncertainty on Diversification Rate Shift Estimates

PubMed Central

Peña, Carlos; Espeland, Marianne

2015-01-01

The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution. PMID:25830910

Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.

PubMed

Peña, Carlos; Espeland, Marianne

2015-01-01

The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.

Forest-management modelling

Treesearch

Mark J. Twery; Aaron R. Weiskittel

2013-01-01

Forests are complex and dynamic ecosystems comprising individual trees that can vary in both size and species. In comparison to other organisms, trees are relatively long lived (40-2000 years), quite plastic in terms of their morphology and ecological niche, and adapted to a wide variety of habitats, which can make predicting their behaviour exceedingly difficult....

A Botanical Treasure Hunt: A Fun and Educational Tree Identification Exercise.

ERIC Educational Resources Information Center

Fox, Marty; Gaynor, John J.; Cribben, Larry

1998-01-01

Shares an approach to tree identification that can be adapted to use with all levels from middle school through college. Stresses student involvement and cooperation in a botanical scavenger hunt. Describes the development of the treasure map and how to use the guide sheet. (DDR)

Eucalyptus as a landscape tree

Treesearch

W. Douglas Hamilton

1983-01-01

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

How low can you go? Assessing minimum concentrations of NSC in carbon limited tree saplings

NASA Astrophysics Data System (ADS)

Hoch, Guenter; Hartmann, Henrik; Schwendener, Andrea

2016-04-01

Tissue concentrations of non-structural carbohydrates (NSC) are frequently used to determine the carbon balance of plants. Over the last years, an increasing number of studies have inferred carbon starvation in trees under environmental stress like drought from low tissue NSC concentrations. However, such inferences are limited by the fact that minimum concentrations of NSC required for survival are not known. So far, it was hypothesized that even under lethal carbon starvation, starch and low molecular sugar concentrations cannot be completely depleted and that minimum NSC concentrations at death vary across tissues and species. Here we present results of an experiment that aimed to determine minimum NSC concentrations in different tissues of saplings of two broad-leaved tree species (Acer pseudoplatanus and Quercus petratea) exposed to lethal carbon starvation via continuous darkening. In addition, we investigated recovery rates of NSC concentrations in saplings that had been darkened for different periods of time and were then re-exposed to light. Both species survived continuous darkening for about 12 weeks (confirmed by testing the ability to re-sprout after darkness). In all investigated tissues, starch concentrations declined close to zero within three to six weeks of darkness. Low molecular sugars also decreased strongly within the first weeks of darkness, but seemed to stabilize at low concentrations of 0.5 to 2 % dry matter (depending on tissue and species) almost until death. NSC concentrations recovered surprisingly fast in saplings that were re-exposed to light. After 3 weeks of continuous darkness, tissue NSC concentrations recovered within 6 weeks to levels of unshaded control saplings in all tissues and in both species. To our knowledge, this study represents the first experimental attempt to quantify minimum tissue NSC concentrations at lethal carbon starvation. Most importantly, our results suggest that carbon-starved tree saplings are able to survive several weeks without starch reserves and with extremely low sugar concentrations in all organs. Although it remains to be tested whether our findings are also valid for mature trees, these results show that NSC pools in trees are very sensitive to carbon limitation and that lethal carbon starvation is preceded by a significant (almost complete) depletion of starch and sugars in all tree organs.

Estimating Forest Vertical Structure from Multialtitude, Fixed-Baseline Radar Interferometric and Polarimetric Data

NASA Technical Reports Server (NTRS)

Treuhaft, Robert N.; Law, Beverly E.; Siqueira, Paul R.

2000-01-01

Parameters describing the vertical structure of forests, for example tree height, height-to-base-of-live-crown, underlying topography, and leaf area density, bear on land-surface, biogeochemical, and climate modeling efforts. Single, fixed-baseline interferometric synthetic aperture radar (INSAR) normalized cross-correlations constitute two observations from which to estimate forest vertical structure parameters: Cross-correlation amplitude and phase. Multialtitude INSAR observations increase the effective number of baselines potentially enabling the estimation of a larger set of vertical-structure parameters. Polarimetry and polarimetric interferometry can further extend the observation set. This paper describes the first acquisition of multialtitude INSAR for the purpose of estimating the parameters describing a vegetated land surface. These data were collected over ponderosa pine in central Oregon near longitude and latitude -121 37 25 and 44 29 56. The JPL interferometric TOPSAR system was flown at the standard 8-km altitude, and also at 4-km and 2-km altitudes, in a race track. A reference line including the above coordinates was maintained at 35 deg for both the north-east heading and the return southwest heading, at all altitudes. In addition to the three altitudes for interferometry, one line was flown with full zero-baseline polarimetry at the 8-km altitude. A preliminary analysis of part of the data collected suggests that they are consistent with one of two physical models describing the vegetation: 1) a single-layer, randomly oriented forest volume with a very strong ground return or 2) a multilayered randomly oriented volume; a homogeneous, single-layer model with no ground return cannot account for the multialtitude correlation amplitudes. Below the inconsistency of the data with a single-layer model is followed by analysis scenarios which include either the ground or a layered structure. The ground returns suggested by this preliminary analysis seem too strong to be plausible, but parameters describing a two-layer compare reasonably well to a field-measured probability distribution of tree heights in the area.

Annual global tree cover estimated by fusing optical and SAR satellite observations

NASA Astrophysics Data System (ADS)

Feng, M.; Sexton, J. O.; Channan, S.; Townshend, J. R.

2017-12-01

Tree cover defined structurally as the proportional, vertically projected area of vegetation (including leaves, stems, branches, etc.) of woody plants above a given height affects terrestrial energy and water exchanges, photosynthesis and transpiration, net primary production, and carbon and nutrient fluxes. Tree cover provides a measurable attribute upon which forest cover may be defined. Changes in tree cover over time can be used to monitor and retrieve site-specific histories of forest disturbance, succession, and degradation. Measurements of Earth's tree cover have been produced at regional, national, and global extents. However, most representations are static, and those for which multiple time periods have been produced are neither intended nor adequate for consistent, long-term monitoring. Moreover, although a substantial proportion of change has been shown to occur at resolutions below 250 m, existing long-term, Landsat-resolution datasets are either produced as static layers or with annual, five- or ten-year temporal resolution. We have developed an algorithms to retrieve seamless and consistent, sub-hectare resolution estimates of tree-canopy from optical and radar satellite data sources (e.g., Landsat, Sentinel-2, and ALOS-PALSAR). Our approach to estimation enables assimilation of multiple data sources and produces estimates of both cover and its uncertainty at the scale of pixels. It has generated the world's first Landsat-based percent tree cover dataset in 2013. Our previous algorithms are being adapted to produce prototype percent-tree and water-cover layers globally in 2000, 2005, and 2010—as well as annually over North and South America from 2010 to 2015—from passive-optical (Landsat and Sentinel-2) and SAR measurements. Generating a global, annual dataset is beyond the scope of this support; however, North and South America represent all of the world's major biomes and so offer the complete global range of environmental sources of error and uncertainty.

Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding.

PubMed

Holliday, Jason A; Aitken, Sally N; Cooke, Janice E K; Fady, Bruno; González-Martínez, Santiago C; Heuertz, Myriam; Jaramillo-Correa, Juan-Pablo; Lexer, Christian; Staton, Margaret; Whetten, Ross W; Plomion, Christophe

2017-02-01

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology. © 2016 John Wiley & Sons Ltd.

New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning.

PubMed

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

2018-04-06

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

Worldsheet scattering in AdS3/CFT2

NASA Astrophysics Data System (ADS)

Sundin, Per; Wulff, Linus

2013-07-01

We confront the recently proposed exact S-matrices for AdS 3/ CFT 2 with direct worldsheet calculations. Utilizing the BMN and Near Flat Space (NFS) expansions for strings on AdS 3 × S 3 × S 3 × S 1 and AdS 3 × S 3 × T 4 we compute both tree-level and one-loop scattering amplitudes. Up to some minor issues we find nice agreement in the tree-level sector. At the one-loop level however we find that certain non-zero tree-level processes, which are not visible in the exact solution, contribute, via the optical theorem, and give an apparent mismatch for certain amplitudes. Furthermore we find that a proposed one-loop modification of the dressing phase correctly reproduces the worldsheet calculation while the standard Hernandez-Lopez phase does not. We also compute several massless to massless processes.

Wood properties of immature ponderosa pine after thinning

Treesearch

Donald C. Markstrom; Harry E. Troxell; C. E. Boldt

1983-01-01

Trees from growing stock levels of 20, 60, and 100 in sapling and pole stands were sampled at three vertical positions -zero, 25, and 50 percent of total height above the 1-foot stump. Wood grown during the 10-year period after initial thinning was compared for growth and wood properties. Wide differences in radial growth, induced by thinning treatments, were not...

Extended Full Computation-Tree Logic with Sequence Modal Operator: Representing Hierarchical Tree Structures

NASA Astrophysics Data System (ADS)

Kamide, Norihiro; Kaneiwa, Ken

An extended full computation-tree logic, CTLS*, is introduced as a Kripke semantics with a sequence modal operator. This logic can appropriately represent hierarchical tree structures where sequence modal operators in CTLS* are applied to tree structures. An embedding theorem of CTLS* into CTL* is proved. The validity, satisfiability and model-checking problems of CTLS* are shown to be decidable. An illustrative example of biological taxonomy is presented using CTLS* formulas.

A structured approach to Exposure Based Waiving of human health endpoints under REACH developed in the OSIRIS project.

PubMed

Marquart, Hans; Meijster, Tim; Van de Bovenkamp, Marja; Ter Burg, Wouter; Spaan, Suzanne; Van Engelen, Jacqueline

2012-03-01

Exposure Based Waiving (EBW) is one of the options in REACH when there is insufficient hazard data on a specific endpoint. Rules for adaptation of test requirements are specified and a general option for EBW is given via Appendix XI of REACH, allowing waiving of repeated dose toxicity studies, reproductive toxicity studies and carcinogenicity studies under a number of conditions if exposure is very low. A decision tree is described that was developed in the European project OSIRIS (Optimised Strategies for Risk Assessment of Industrial Chemicals through Integration of Non-Test and Test Information) to help decide in what cases EBW can be justified. The decision tree uses specific criteria as well as more general questions. For the latter, guidance on interpretation and resulting conclusions is provided. Criteria and guidance are partly based on an expert elicitation process. Among the specific criteria a number of proposed Thresholds of Toxicological Concern are used. The decision tree, expanded with specific parts on absorption, distribution, metabolism and excretion that are not described in this paper, is implemented in the OSIRIS webtool on integrated testing strategies. Copyright © 2011 Elsevier Inc. All rights reserved.

"Growing trees backwards": Description of a stand reconstruction model (P-53)

Treesearch

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

2008-01-01

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

"Growing trees backwards": Description of a stand reconstruction model

Treesearch

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

2008-01-01

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

Bayesian Ensemble Trees (BET) for Clustering and Prediction in Heterogeneous Data

PubMed Central

Duan, Leo L.; Clancy, John P.; Szczesniak, Rhonda D.

2016-01-01

We propose a novel “tree-averaging” model that utilizes the ensemble of classification and regression trees (CART). Each constituent tree is estimated with a subset of similar data. We treat this grouping of subsets as Bayesian Ensemble Trees (BET) and model them as a Dirichlet process. We show that BET determines the optimal number of trees by adapting to the data heterogeneity. Compared with the other ensemble methods, BET requires much fewer trees and shows equivalent prediction accuracy using weighted averaging. Moreover, each tree in BET provides variable selection criterion and interpretation for each subset. We developed an efficient estimating procedure with improved estimation strategies in both CART and mixture models. We demonstrate these advantages of BET with simulations and illustrate the approach with a real-world data example involving regression of lung function measurements obtained from patients with cystic fibrosis. Supplemental materials are available online. PMID:27524872

Supervised Learning of Two-Layer Perceptron under the Existence of External Noise — Learning Curve of Boolean Functions of Two Variables in Tree-Like Architecture —

NASA Astrophysics Data System (ADS)

Uezu, Tatsuya; Kiyokawa, Shuji

2016-06-01

We investigate the supervised batch learning of Boolean functions expressed by a two-layer perceptron with a tree-like structure. We adopt continuous weights (spherical model) and the Gibbs algorithm. We study the Parity and And machines and two types of noise, input and output noise, together with the noiseless case. We assume that only the teacher suffers from noise. By using the replica method, we derive the saddle point equations for order parameters under the replica symmetric (RS) ansatz. We study the critical value αC of the loading rate α above which the learning phase exists for cases with and without noise. We find that αC is nonzero for the Parity machine, while it is zero for the And machine. We derive the exponents barβ of order parameters expressed as (α - α C)bar{β} when α is near to αC. Furthermore, in the Parity machine, when noise exists, we find a spin glass solution, in which the overlap between the teacher and student vectors is zero but that between student vectors is nonzero. We perform Markov chain Monte Carlo simulations by simulated annealing and also by exchange Monte Carlo simulations in both machines. In the Parity machine, we study the de Almeida-Thouless stability, and by comparing theoretical and numerical results, we find that there exist parameter regions where the RS solution is unstable, and that the spin glass solution is metastable or unstable. We also study asymptotic learning behavior for large α and derive the exponents hat{β } of order parameters expressed as α - hat{β } when α is large in both machines. By simulated annealing simulations, we confirm these results and conclude that learning takes place for the input noise case with any noise amplitude and for the output noise case when the probability that the teacher's output is reversed is less than one-half.

Co-ordination of growth, gas exchange and hydraulics define the carbon safety margin in tree species with contrasting drought strategies.

PubMed

Mitchell, P J; O'Grady, A P; Tissue, D T; Worledge, D; Pinkard, E A

2014-05-01

Gas exchange, growth, water transport and carbon (C) metabolism diminish during drought according to their respective sensitivities to declining water status. The timing of this sequence of declining physiological functions may determine how water and C relations compromise plant survival. In this paper, we test the hypothesis that the degree of asynchrony between declining C supply (photosynthesis) and C demand (growth and respiration) determines the rate and magnitude of changes in whole-plant non-structural carbohydrates (NSC) during drought. Two complementary experiments using two tree species (Eucalyptus globulus Labill. and Pinus radiata D. Don) with contrasting drought response strategies were performed to (i) assess changes in radial stem growth, transpiration, leaf water potential and gas exchange in response to chronic drought, and (ii) evaluate the concomitant impacts of these drought responses on the temporal patterns of NSC during terminal drought. The three distinct phases of water stress were delineated by thresholds of growth cessation and stomatal closure that defined the 'carbon safety margin' (i.e., the difference between leaf water potential when growth is zero and leaf water potential when net photosynthesis is zero). A wider C safety margin in E. globulus was defined by an earlier cessation of growth relative to photosynthesis that reduced the demand for NSC while maintaining C acquisition. By contrast, the narrower C safety margin in P. radiata was characterized by a synchronous decline in growth and photosynthesis, whereby growth continued under a declining supply of NSC from photosynthesis. The narrower C safety margin in P. radiata was associated with declines in starch concentrations after ∼ 90 days of chronic drought and significant depletion of starch in all organs at mortality. The observed divergence in the sensitivity of drought responses is indicative of a potential trade-off between maintaining hydraulic safety and adequate C availability. © The Author 2014. Published by Oxford University Press. All rights reserved.

FMM-Yukawa: An adaptive fast multipole method for screened Coulomb interactions

NASA Astrophysics Data System (ADS)

Huang, Jingfang; Jia, Jun; Zhang, Bo

2009-11-01

A Fortran program package is introduced for the rapid evaluation of the screened Coulomb interactions of N particles in three dimensions. The method utilizes an adaptive oct-tree structure, and is based on the new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related packages are also available at http://www.fastmultipole.org/. This paper is a brief review of the program and its performance. Catalogue identifier: AEEQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 12 385 No. of bytes in distributed program, including test data, etc.: 79 222 Distribution format: tar.gz Programming language: Fortran77 and Fortran90 Computer: Any Operating system: Any RAM: Depends on the number of particles, their distribution, and the adaptive tree structure Classification: 4.8, 4.12 Nature of problem: To evaluate the screened Coulomb potential and force field of N charged particles, and to evaluate a convolution type integral where the Green's function is the fundamental solution of the modified Helmholtz equation. Solution method: An adaptive oct-tree is generated, and a new version of fast multipole method is applied in which the "multipole-to-local" translation operator is diagonalized. Restrictions: Only three and six significant digits accuracy options are provided in this version. Unusual features: Most of the codes are written in Fortran77. Functions for memory allocation from Fortran90 and above are used in one subroutine. Additional comments: For supplementary information see http://www.fastmultipole.org/ Running time: The running time varies depending on the number of particles (denoted by N) in the system and their distribution. The running time scales linearly as a function of N for nearly uniform particle distributions. For three digits accuracy, the solver breaks even with direct summation method at about N = 750. References: [1] L. Greengard, J. Huang, A new version of the fast multipole method for screened Coulomb interactions in three dimensions, J. Comput. Phys. 180 (2002) 642-658.

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

PubMed

O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-02-25

We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the phylogenetic tree topology of the homologous group. The classical QR factorization with pivoting, developed as a fast numerical solution to eigenvalue and linear least-squares problems of the form Ax=b, was designed to re-order the columns of A by increasing linear dependence. Removing the most linear dependent columns from A leads to the formation of a minimal basis set which well spans the phase space of the problem at hand. By recasting the problem of redundancy in multiple structural alignments into this framework, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to produce a minimal basis set of protein structures which best spans the evolutionary (phase) space. The non-redundant and representative profiles obtained from this procedure, termed evolutionary profiles, are shown in initial results to outperform well-tested profiles in homology detection searches over a large sequence database. A measure of structural similarity between homologous proteins, Q(H), is presented. By properly accounting for the effect and presence of gaps, a phylogenetic tree computed using this metric is shown to be congruent with the maximum-likelihood sequence-based phylogeny. The results indicate that evolutionary information is indeed recoverable from the comparative analysis of protein structure alone. Applications of the QR ordering and this structural similarity metric to analyze the evolution of structure among key, universally distributed proteins involved in translation, and to the selection of representatives from an ensemble of NMR structures are also discussed.

Secondary Growth and Carbohydrate Storage Patterns Differ between Sexes in Juniperus thurifera

PubMed Central

DeSoto, Lucía; Olano, José M.; Rozas, Vicente

2016-01-01

Differences in reproductive costs between male and female plants have been shown to foster sex-related variability in growth and C-storage patterns. The extent to which differential secondary growth in dioecious trees is associated with changes in stem carbohydrate storage patterns, however, has not been fully assessed. We explored the long-term radial growth and the seasonal variation of non-structural carbohydrate (NSC) content in sapwood of 40 males and 40 females Juniperus thurifera trees at two sites. NSC content was analyzed bimonthly for 1 year, and tree-ring width was measured for the 1931–2010 period. Sex-related differences in secondary growth and carbohydrate storage were site-dependent. Under less restrictive environmental conditions females grew more and stored more non-soluble sugars than males. Our results reinforce that sex-related differences in growth and resource storage may be a consequence of local adaptation to environmental conditions. Seasonal variation in soluble sugars concentration was opposite to cambial activity, with minima seen during periods of maximal secondary growth, and did not differ between the sexes or sites. Trees with higher stem NSC levels at critical periods showed higher radial growth, suggesting a common mechanism irrespective of site or sex. Sex-related patterns of secondary growth were linked to differences in non-soluble sugars content indicating sex-specific strategies of long-term performance. PMID:27303418

Non-unique key B-Tree implementation

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

Ries, D.R.

1980-12-23

The B-Trees are an indexed method to allow fast retrieval and order preserving updates to a FRAMIS relation based on a designated set of keys in the relation. A B-Tree access method is being implemented to provide indexed and sequential (in index order) access to FRAMIS relations. The implementation modifies the basic B-Tree structure to correctly allow multiple key values and still maintain the balanced page fill property of B-Trees. The data structures of the B-Tree are presented first, including the FRAMIS solution to the duplicate key value problem. Then the access level routines and utilities are presented. These routinesmore » include the original B-Tree creation; searching the B-Tree; and inserting, deleting, and replacing tuples on the B-Tree. In conclusion, the uses of the B-Tree access structures at the semantic level to enhance the FRAMIS performance are discussed. 10 figures.« less

Continuing Climate Warming Will Result in Failure of Post-Harvest Natural Regeneration across the Landscape in Interior Alaska

NASA Astrophysics Data System (ADS)

Morimoto, M.; Juday, G. P.; Huettmann, F.

2016-12-01

Following forest disturbance, the stand initiation stage decisively influences future forest structure. Understanding post-harvest regeneration, especially under climate change, is essential to predicting future carbon stores in this extensive forest biome. We apply IPCC B1, A1B, and A2 climate scenarios to generate plausible future forest conditions under different management. We recorded presence of white spruce, birch, and aspen in 726 plots on 30 state forest white spruce harvest units. We built spatially explicit models and scenarios of species presence/absence using TreeNet (Stochastic Gradient Boosting). Post-harvest tree regeneration predictions in calibration data closely matched the validation set, indicating tree regeneration scenarios are reliable. Early stage post-harvest regeneration is similar to post-fire regeneration and matches the pattern of long-term natural vegetation distribution, confirming that site environmental factors are more important than management practices. Post-harvest natural regeneration of tree species increases under moderate warming scenarios, but fails under strong warming scenarios in landscape positions with high temperatures and low precipitation. Under all warming scenarios, the most successful regenerating species following white spruce harvest is white spruce. Birch experiences about 30% regeneration failure under A2 scenario by 2050. White spruce and aspen are projected to regenerate more successfully when site preparation is applied. Although white spruce has been the major managed species, birch may require more intensive management. Sites likely to experience regeneration failure of current tree species apparently will experience biome shift, although adaptive migration of existing or new species might be an option. Our scenario modeling tool allows resource managers to forecast tree regeneration on productive managed sites that have made a disproportionate contribution to carbon flux in a critical region.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.

PubMed

Walker, Joseph F; Yang, Ya; Feng, Tao; Timoneda, Alfonso; Mikenas, Jessica; Hutchison, Vera; Edwards, Caroline; Wang, Ning; Ahluwalia, Sonia; Olivieri, Julia; Walker-Hale, Nathanael; Majure, Lucas C; Puente, Raúl; Kadereit, Gudrun; Lauterbach, Maximilian; Eggli, Urs; Flores-Olvera, Hilda; Ochoterena, Helga; Brockington, Samuel F; Moore, Michael J; Smith, Stephen A

2018-03-01

The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Relative Suffix Trees.

PubMed

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-05-01

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.

Relative Suffix Trees

PubMed Central

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-01-01

Abstract Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees. PMID:29795706

Adaptive Numerical Algorithms in Space Weather Modeling

NASA Technical Reports Server (NTRS)

Toth, Gabor; vanderHolst, Bart; Sokolov, Igor V.; DeZeeuw, Darren; Gombosi, Tamas I.; Fang, Fang; Manchester, Ward B.; Meng, Xing; Nakib, Dalal; Powell, Kenneth G.;

TOPICAL REVIEW: Experimental study of organic zero-gap conductor α-(BEDT-TTF)2I3

NASA Astrophysics Data System (ADS)

Tajima, Naoya; Kajita, Koji

2009-04-01

A zero-gap state with a Dirac cone type energy dispersion was discovered in the organic conductor α-(BEDT-TTF)2I3 under high hydrostatic pressures. This is the first two-dimensional (2D) zero-gap state discovered in bulk crystals with a layered structure. In contrast to the case of graphene, the Dirac cone in this system is highly anisotropic. The present system, therefore, provides a new type of massless Dirac fermion system with anisotropic Fermi velocity. This system exhibits remarkable transport phenomena characteristic to electrons on the Dirac cone type energy structure. The carrier density, written as n~T2, is a characteristic feature of the 2D zero-gap structure. On the other hand, the resistivity per layer (sheet resistance RS) is given as RS=h/e2 and is independent of temperature. The effect of a magnetic field on samples in the zero-gap system was examined. The difference between zero-gap conductors and conventional conductors is the appearance of a Landau level called the zero mode at the contact points when a magnetic field is applied normal to the conductive layer. Zero-mode Landau carriers give rise to strong negative out-of-plane magnetoresistance.

Genetically informed ecological niche models improve climate change predictions.

PubMed

Ikeda, Dana H; Max, Tamara L; Allan, Gerard J; Lau, Matthew K; Shuster, Stephen M; Whitham, Thomas G

2017-01-01

We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species' ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species' niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12-fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change. © 2016 John Wiley & Sons Ltd.

Tree Planting at the Bent Creek Experimental Forest

Treesearch

John C. Barber

1953-01-01

Foresters everywhere are becoming increasingly conscious of the potentialities of tree selection and breeding. In the quest for suitable breeding material, many of the plantations of the past are assuming importance, for each plantation of introduced species may provide information on its adaptability to a certain area and the desirable and undesirable traits which...

Effect of global climate change on rare trees and shrubs

Treesearch

Margaret S. Devall

2008-01-01

In the past, climate has fluctuated with periodsof cooler, warmer, drier or wetter weather thanat present. Plants have been able to adapt,but widespread, rapid warming could be disastrousfor rare trees and shrubs – i.e. thosenative species that are among an area’s most

The efficacy of using inventory data to develop optimal diameter increment models

Treesearch

Don C. Bragg

2002-01-01

Most optimal tree diameter growth models have arisen through either the conceptualization of physiological processes or the adaptation of empirical increment models. However, surprisingly little effort has been invested in the melding of these approaches even though it is possible to develop theoretically sound, computationally efficient optimal tree growth models...

Genomic science provides new insights into the biology of forest trees

Treesearch

Andrew Groover

2015-01-01

Forest biology is undergoing a fundamental change fostered by the application of genomic science to longstanding questions surrounding the evolution, adaptive traits, development, and environmental interactions of tree species. Genomic science has made major technical leaps in recent years, most notably with the advent of 'next generation sequencing' but...

Provenance research: investigation of genetic diversity associated with geography

Treesearch

Robert Z. Callaham

1963-01-01

Provenance in forestry refers to the population of trees growing at n particular place of origin. Provenance research defines the genetic and environmental components of phenotypic variation associated with geographic source. Information on provenance is important in assuring sources of seed to give well-adapted, productive trees and in directing breeding of...

Adaptive economic and ecological forest management under risk

Treesearch

Joseph Buongiorno; Mo Zhou

2015-01-01

Background: Forest managers must deal with inherently stochastic ecological and economic processes. The future growth of trees is uncertain, and so is their value. The randomness of low-impact, high frequency or rare catastrophic shocks in forest growth has significant implications in shaping the mix of tree species and the forest landscape...

Enumeration of spanning trees in planar unclustered networks

NASA Astrophysics Data System (ADS)

Xiao, Yuzhi; Zhao, Haixing; Hu, Guona; Ma, Xiujuan

2014-07-01

Among a variety of subgraphs, spanning trees are one of the most important and fundamental categories. They are relevant to diverse aspects of networks, including reliability, transport, self-organized criticality, loop-erased random walks and so on. In this paper, we introduce a family of modular, self-similar planar networks with zero clustering. Relevant properties of this family are comparable to those networks associated with technological systems having low clustering, like power grids, some electronic circuits, the Internet and some biological systems. So, it is very significant to research on spanning trees of planar networks. However, for a large network, evaluating the relevant determinant is intractable. In this paper, we propose a fairly generic linear algorithm for counting the number of spanning trees of a planar network. Using the algorithm, we derive analytically the exact numbers of spanning trees in planar networks. Our result shows that the computational complexity is O(t) , which is better than that of the matrix tree theorem with O(m2t2) , where t is the number of steps and m is the girth of the planar network. We also obtain the entropy for the spanning trees of a given planar network. We find that the entropy of spanning trees in the studied network is small, which is in sharp contrast to the previous result for planar networks with the same average degree. We also determine an upper bound and a lower bound for the numbers of spanning trees in the family of planar networks by the algorithm. As another application of the algorithm, we give a formula for the number of spanning trees in an outerplanar network with small-world features.

Hunter-gatherer adaptations and environmental change in the southern Great Basin: The evidence from Pahute and Rainier mesas

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

Pippin, L.C.

This paper reviews the evidence for fluctuations in past environments in the southern Great Basin and examines how these changes may have affected the strategies followed by past hunter and gatherers in their utilization of the resources available on a highland in this region. The evidence used to reconstruct past environments for the region include botanical remains from packrat middens, pollen spectra from lake and spring deposits, faunal remains recovered from archaeological and geologic contexts, tree-ring indices from trees located in sensitive (tree-line) environments, and eolian, alluvial and fluvial sediments deposited in a variety of contexts. Interpretations of past huntermore » and gatherer adaptive strategies are based on a sample of 1,311 archaeological sites recorded during preconstruction surveys on Pahute and Rainier mesas in advance of the US Department of Energy`s nuclear weapons testing program. Projectile point chronologies and available tree-ring, radiocarbon, thermoluminescence and obsidian hydration dates were used to assign these archaeological sites to specific periods of use.« less

Iterative adaption of the bidimensional wall of the French T2 wind tunnel around a C5 axisymmetrical model: Infinite variation of the Mach number at zero incidence and a test at increased incidence

NASA Technical Reports Server (NTRS)

Archambaud, J. P.; Dor, J. B.; Payry, M. J.; Lamarche, L.

1986-01-01

The top and bottom two-dimensional walls of the T2 wind tunnel are adapted through an iterative process. The adaptation calculation takes into account the flow three-dimensionally. This method makes it possible to start with any shape of walls. The tests were performed with a C5 axisymmetric model at ambient temperature. Comparisons are made with the results of a true three-dimensional adaptation.

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data.

PubMed

Chen, Li; Reeve, James; Zhang, Lujun; Huang, Shengbing; Wang, Xuefeng; Chen, Jun

2018-01-01

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero-inflation remain largely undeveloped. Here we propose geometric mean of pairwise ratios-a simple but effective normalization method-for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.

Application of Infrared and Raman Spectroscopy for the Identification of Disease Resistant Trees.

PubMed

Conrad, Anna O; Bonello, Pierluigi

2015-01-01

New approaches for identifying disease resistant trees are needed as the incidence of diseases caused by non-native and invasive pathogens increases. These approaches must be rapid, reliable, cost-effective, and should have the potential to be adapted for high-throughput screening or phenotyping. Within the context of trees and tree diseases, we summarize vibrational spectroscopic and chemometric methods that have been used to distinguish between groups of trees which vary in disease susceptibility or other important characteristics based on chemical fingerprint data. We also provide specific examples from the literature of where these approaches have been used successfully. Finally, we discuss future application of these approaches for wide-scale screening and phenotyping efforts aimed at identifying disease resistant trees and managing forest diseases.

Uncertainty of large-area estimates of indicators of forest structural gamma diversity: A study based on national forest inventory data

Treesearch

Susanne Winter; Andreas Böck; Ronald E. McRoberts

2012-01-01

Tree diameter and height are commonly measured forest structural variables, and indicators based on them are candidates for assessing forest diversity. We conducted our study on the uncertainty of estimates for mostly large geographic scales for four indicators of forest structural gamma diversity: mean tree diameter, mean tree height, and standard deviations of tree...

The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

PubMed

Yang, Yizi; Luo, Damin

2013-01-01

Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient.

PubMed

Firmat, C; Delzon, S; Louvet, J-M; Parmentier, J; Kremer, A

2017-12-01

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long-lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common-garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change-induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short-term population survival in a changing climate. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

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

PubMed

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

2015-02-01

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

Managing hardwood-softwood mixtures for future forests in eastern North America: assessing suitability to projected climate change

Treesearch

John M. Kabrick; Kenneth L. Clark; Anthony W. D' Amato; Daniel C. Dey; Laura S. Kenefic; Christel C. Kern; Benjamin O. Knapp; David A. MacLean; Patricia Raymond; Justin D. Waskiewicz

2017-01-01

Despite growing interest in management strategies for climate change adaptation, there are few methods for assessing the ability of stands to endure or adapt to projected future climates. We developed a means for assigning climate "Compatibility" and "Adaptability" scores to stands for assessing the suitability of tree species for projected climate...

Eliminating the zero spectrum in Fourier transform profilometry using empirical mode decomposition.

PubMed

Li, Sikun; Su, Xianyu; Chen, Wenjing; Xiang, Liqun

2009-05-01

Empirical mode decomposition is introduced into Fourier transform profilometry to extract the zero spectrum included in the deformed fringe pattern without the need for capturing two fringe patterns with pi phase difference. The fringe pattern is subsequently demodulated using a standard Fourier transform profilometry algorithm. With this method, the deformed fringe pattern is adaptively decomposed into a finite number of intrinsic mode functions that vary from high frequency to low frequency by means of an algorithm referred to as a sifting process. Then the zero spectrum is separated from the high-frequency components effectively. Experiments validate the feasibility of this method.

Gender-specific patterns of aboveground allocation, canopy conductance and water use in a dominant riparian tree species: Acer negundo.

PubMed

Hultine, K R; Bush, S E; West, A G; Burtch, K G; Pataki, D E; Ehleringer, J R

2008-09-01

Acer negundo Sarg. (box elder) is a dioecious tree species that dominates riparian systems at mid elevations throughout the southwest and Intermountain West of the United States. Previous studies have shown that female A. negundo trees occur at higher frequencies along stream margins, whereas males occur at higher frequencies in drier microsites. To better understand the adaptive significance of sex ratio biases and their impact on the ecohydrology of riparian ecosystems, we examined whole-plant water relations and hydraulic properties of mature male and female A. negundo trees occurring within 1 m of a perennial stream channel. We hypothesized that (1) females would have significantly greater canopy water fluxes than males (particularly during periods of seed production: May-June), and (2) xylem in females is more hydraulically efficient but more vulnerable to cavitation than xylem in males. Mean sap flux density (J(s)) during the early growing season (May and June) was 43% higher in female trees than in male trees (n = 6 and 7 trees respectively, P < 0.0001). Mean J(s) in July and August remained 17% higher in females than in males (P = 0.0009). Mean canopy stomatal conductance per unit leaf area (g(s,leaf)) in May and June was on average 140% higher in females than in males (P < 0.0001). Mean g(s,leaf) in July and August remained 69% higher in female trees than in male trees (P < 0.0001). Canopy stomatal conductance scaled to basal area was 90 and 31% higher in females relative to males during May-June and July-August, respectively (P < 0.0001 during both periods). Conversely, there were no apparent differences in either branch hydraulic conductance or branch xylem cavitation vulnerability between genders. These results improve our capacity to describe the adaptive forces that shape the spatial distribution of male and female trees in dioecious species, and their consequences for ecohydrological processes in riparian ecosystems.

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

Patterns in hydraulic architecture from roots to branches in six tropical tree species from cacao agroforestry and their relation to wood density and stem growth.

PubMed

Kotowska, Martyna M; Hertel, Dietrich; Rajab, Yasmin Abou; Barus, Henry; Schuldt, Bernhard

2015-01-01

For decades it has been assumed that the largest vessels are generally found in roots and that vessel size and corresponding sapwood area-specific hydraulic conductivity are acropetally decreasing toward the distal twigs. However, recent studies from the perhumid tropics revealed a hump-shaped vessel size distribution. Worldwide tropical perhumid forests are extensively replaced by agroforestry systems often using introduced species of various biogeographical and climatic origins. Nonetheless, it is unknown so far what kind of hydraulic architectural patterns are developed in those agroforestry tree species and which impact this exerts regarding important tree functional traits, such as stem growth, hydraulic efficiency and wood density (WD). We investigated wood anatomical and hydraulic properties of the root, stem and branch wood in Theobroma cacao and five common shade tree species in agroforestry systems on Sulawesi (Indonesia); three of these were strictly perhumid tree species, and the other three tree species are tolerating seasonal drought. The overall goal of our study was to relate these properties to stem growth and other tree functional traits such as foliar nitrogen content and sapwood to leaf area ratio. Our results confirmed a hump-shaped vessel size distribution in nearly all species. Drought-adapted species showed divergent patterns of hydraulic conductivity, vessel density, and relative vessel lumen area between root, stem and branch wood compared to wet forest species. Confirming findings from natural old-growth forests in the same region, WD showed no relationship to specific conductivity. Overall, aboveground growth performance was better predicted by specific hydraulic conductivity than by foliar traits and WD. Our study results suggest that future research on conceptual trade-offs of tree hydraulic architecture should consider biogeographical patterns underlining the importance of anatomical adaptation mechanisms to environment.

Adaptive control: Myths and realities

NASA Technical Reports Server (NTRS)

Athans, M.; Valavani, L.

1984-01-01

It was found that all currently existing globally stable adaptive algorithms have three basic properties in common: positive realness of the error equation, square-integrability of the parameter adjustment law and, need for sufficient excitation for asymptotic parameter convergence. Of the three, the first property is of primary importance since it satisfies a sufficient condition for stabillity of the overall system, which is a baseline design objective. The second property has been instrumental in the proof of asymptotic error convergence to zero, while the third addresses the issue of parameter convergence. Positive-real error dynamics can be generated only if the relative degree (excess of poles over zeroes) of the process to be controlled is known exactly; this, in turn, implies perfect modeling. This and other assumptions, such as absence of nonminimum phase plant zeros on which the mathematical arguments are based, do not necessarily reflect properties of real systems. As a result, it is natural to inquire what happens to the designs under less than ideal assumptions. The issues arising from violation of the exact modeling assumption which is extremely restrictive in practice and impacts the most important system property, stability, are discussed.

Adaptively Refined Euler and Navier-Stokes Solutions with a Cartesian-Cell Based Scheme

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1995-01-01

A Cartesian-cell based scheme with adaptive mesh refinement for solving the Euler and Navier-Stokes equations in two dimensions has been developed and tested. Grids about geometrically complicated bodies were generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells were created using polygon-clipping algorithms. The grid was stored in a binary-tree data structure which provided a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations were solved on the resulting grids using an upwind, finite-volume formulation. The inviscid fluxes were found in an upwinded manner using a linear reconstruction of the cell primitives, providing the input states to an approximate Riemann solver. The viscous fluxes were formed using a Green-Gauss type of reconstruction upon a co-volume surrounding the cell interface. Data at the vertices of this co-volume were found in a linearly K-exact manner, which ensured linear K-exactness of the gradients. Adaptively-refined solutions for the inviscid flow about a four-element airfoil (test case 3) were compared to theory. Laminar, adaptively-refined solutions were compared to accepted computational, experimental and theoretical results.

An adaptive mesh-moving and refinement procedure for one-dimensional conservation laws

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Flaherty, Joseph E.; Arney, David C.

1993-01-01

We examine the performance of an adaptive mesh-moving and /or local mesh refinement procedure for the finite difference solution of one-dimensional hyperbolic systems of conservation laws. Adaptive motion of a base mesh is designed to isolate spatially distinct phenomena, and recursive local refinement of the time step and cells of the stationary or moving base mesh is performed in regions where a refinement indicator exceeds a prescribed tolerance. These adaptive procedures are incorporated into a computer code that includes a MacCormack finite difference scheme wih Davis' artificial viscosity model and a discretization error estimate based on Richardson's extrapolation. Experiments are conducted on three problems in order to qualify the advantages of adaptive techniques relative to uniform mesh computations and the relative benefits of mesh moving and refinement. Key results indicate that local mesh refinement, with and without mesh moving, can provide reliable solutions at much lower computational cost than possible on uniform meshes; that mesh motion can be used to improve the results of uniform mesh solutions for a modest computational effort; that the cost of managing the tree data structure associated with refinement is small; and that a combination of mesh motion and refinement reliably produces solutions for the least cost per unit accuracy.

Searching for early-warning signals of impending dieback and death in Mediterranean oaks

NASA Astrophysics Data System (ADS)

Colangelo, Michele; Ripullone, Francesco; Julio Camarero, Jesus; De Micco, Veronica; Gazol, Antonio; Gentilesca, Tiziana; Borghetti, Marco

2017-04-01

In recent decades, forest dieback episodes have been recorded worldwide affecting different tree species. In particular, several cases of widespread dieback and increased mortality rates have been described for Mediterranean oak (Quercus spp.) species. These dieback cases are revealing the high vulnerability of Mediterranean oaks, manifested as a loss in tree vigour (leaf shedding, canopy and shoot dieback), growth decline and sometimes tree death, as a consequence of temperatures rising at unprecedented rates and drying trends. However, in the wake of the so-called 'oak decline phenomenon', the attention on these species has generally been limited, perhaps because they are often regarded as well-adapted to the dry conditions typical of Mediterranean areas. Indeed, according to recent studies, the reduced size, the ability to sprout and the anisohydric behavior of Mediterranean oak species (reduced control of water loss and high stomatal conductance rates) would make them better adapted to withstand heat and drought stress then taller and non-sprouting isohydric species (e.g. conifer, with strict control of water loss by closing stomata). Here, we investigated the vulnerability of Mediterranean oaks by comparing neighboring living and recently dead trees in species with low (Q. pubescens), intermediate (Q. cerris, Q. frainetto) and high (Q. robur) sensitivity to water shortage. We analysed changes in tree vigour using tree-ring width and functional wood anatomical traits as proxies to search for early-warning signals of dieback, in connection with the main proposed dieback mechanisms (hydraulic failure and/or carbon starvation). We also modeled the probability of tree death as a function of tree size (diameter, height) by quantifying recent changes in growth and wood anatomy along tree-ring series. Contrary to the general concept that trees tend to experience increasing cavitation risk with increasing height, our studies show that smaller oaks are more prone to die than taller conspecifics. Further, irrespective of differences in drought sensitivity, dead trees showed lower radial-growth rates than surviving trees from 10 to 20 years prior to tree death. Contrastingly, differences in wood anatomical traits (vessel lumen size, vessel density) between dead and living trees were not always significant, being species-dependent. Our findings indicate that: (i) tree height is a proxy of the probability of drought-induced death, and (ii) recent growth trends constitute valuable early-warning signals of impending dieback and death in Mediterranean oak species.

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1994-01-01

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: a gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment, and other accepted computational results for a series of low and moderate Reynolds number flows.

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1995-01-01

A Cartesian, cell-based approach for adaptively-refined solutions of the Euler and Navier-Stokes equations in two dimensions is developed and tested. Grids about geometrically complicated bodies are generated automatically, by recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, N-sided 'cut' cells are created using polygon-clipping algorithms. The grid is stored in a binary-tree data structure which provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite-volume formulation. The convective terms are upwinded: A gradient-limited, linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The more robust of a series of viscous flux functions is used to provide the viscous fluxes at the cell interfaces. Adaptively-refined solutions of the Navier-Stokes equations using the Cartesian, cell-based approach are obtained and compared to theory, experiment and other accepted computational results for a series of low and moderate Reynolds number flows.

Solution-Adaptive Cartesian Cell Approach for Viscous and Inviscid Flows

NASA Technical Reports Server (NTRS)

Coirier, William J.; Powell, Kenneth G.

1996-01-01

A Cartesian cell-based approach for adaptively refined solutions of the Euler and Navier-Stokes equations in two dimensions is presented. Grids about geometrically complicated bodies are generated automatically, by the recursive subdivision of a single Cartesian cell encompassing the entire flow domain. Where the resulting cells intersect bodies, polygonal cut cells are created using modified polygon-clipping algorithms. The grid is stored in a binary tree data structure that provides a natural means of obtaining cell-to-cell connectivity and of carrying out solution-adaptive mesh refinement. The Euler and Navier-Stokes equations are solved on the resulting grids using a finite volume formulation. The convective terms are upwinded: A linear reconstruction of the primitive variables is performed, providing input states to an approximate Riemann solver for computing the fluxes between neighboring cells. The results of a study comparing the accuracy and positivity of two classes of cell-centered, viscous gradient reconstruction procedures is briefly summarized. Adaptively refined solutions of the Navier-Stokes equations are shown using the more robust of these gradient reconstruction procedures, where the results computed by the Cartesian approach are compared to theory, experiment, and other accepted computational results for a series of low and moderate Reynolds number flows.

A robotic vision system to measure tree traits

USDA-ARS?s Scientific Manuscript database

The autonomous measurement of tree traits, such as branching structure, branch diameters, branch lengths, and branch angles, is required for tasks such as robotic pruning of trees as well as structural phenotyping. We propose a robotic vision system called the Robotic System for Tree Shape Estimati...

Research on the adaptation of skeletal muscle to hypogravity: Past and future directions

NASA Astrophysics Data System (ADS)

Riley, D. A.; Ellis, S.

Our current understanding of hypogravity-induced atrophy of skeletal muscles is based primarily on studies comparing pre- and post-flight properties of muscles. Interpretations are necessarily qualified by the assumption that the stress of reentry and readjustment to terrestrial gravity do not alter the parameters being analyzed. The neuromuscular system is highly responsive to changes in functional demands and capable of rapid adaptation, making this assumption questionable. A reexamination of the changes in the connective tissue and synaptic terminals of soleus muscles from rats orbited in biosatellites and sampled postflight indicates that these structural alterations represent adaptative responses of the atrophic muscles to the increased workload of returning to 1 G, rather than hypogravity per se. The atrophy of weightlessness is postulated to result because muscles are both underloaded and used less often. Proper testing of this hypothesis requires quantitation of muscle function by monitoring electromyography, force output and length changes during the flight. Experiments conducted in space laboratories, like those being developed for the Space Shuttle, will avoid the complications of reentry before tissue sampling and allow time course studies of the rate of development of adaptive changes to zero gravity. Another area of great importance for future studies of muscle atrophy is inflight measurement of plasma levels of hormones and tissue receptor levels. Glucocorticoids, thyroid hormone and insulin exert dramatic regulatory influences on muscle structure. Prevention of neuromuscular atrophy becomes increasingly more important as spaceflights increase in duration. Definition of the atrophic mechanism is essential to developing means of preventing neuromuscular atrophy.

Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica.

PubMed

Sosa, Victoria; Ornelas, Juan Francisco; Ramírez-Barahona, Santiago; Gándara, Etelvina

2016-01-01

Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.

Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

PubMed Central

2016-01-01

Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. Conclusions Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors. PMID:27896030

Self-rumination, self-reflection, and depression: self-rumination counteracts the adaptive effect of self-reflection.

PubMed

Takano, Keisuke; Tanno, Yoshihiko

2009-03-01

Self-focused attention has adaptive and maladaptive aspects: self-reflection and self-rumination [Trapnell, P. D., & Campbell, J. D. (1999). Private self-consciousness and the Five-Factor Model of personality: distinguishing rumination from reflection. Journal of Personality and Social Psychology, 76, 284-304]. Although reflection is thought to be associated with problem solving and the promotion of mental health, previous researches have shown that reflection does not always have an adaptive effect on depression. Authors have examined the causes behind this inconsistency by modeling the relationships among self-reflection, self-rumination, and depression. One hundred and eleven undergraduates (91 men and 20 women) participated in a two-time point assessment with a 3-week interval. Statistical analysis with structural equation modeling showed that self-reflection significantly predicted self-rumination, whereas self-rumination did not predict self-reflection. With regard to depression, self-reflection was associated with a lower level of depression; self-rumination, with a higher level of depression. The total effect of self-reflection on depression was almost zero. This result indicates that self-reflection per se has an adaptive effect, which is canceled out by the maladaptive effect of self-rumination, because reflectors are likely to ruminate and reflect simultaneously.

Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives.

PubMed

Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; de Andrade, Carla; Costa, Leandro Batista; Rostagno, Marcos Horácio

2015-10-01

The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop adaptation after repetitive exposure to sub-lethal concentrations of these essential oils. The MBC of the essential oils studied was determined by disc diffusion and broth dilution methods. All essential oils showed antimicrobial effect against all bacterial strains. In general, the development of adaptation varied according to the bacterial strain and the essential oil (tea tree > white thyme > oregano). Therefore, it is important to use essential oils at efficient bactericidal doses in animal feed, food, and sanitizers, since bacteria can rapidly develop adaptation when exposed to sub-lethal concentrations of these oils.

Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives

PubMed Central

Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; de Andrade, Carla; Costa, Leandro Batista; Rostagno, Marcos Horácio

2015-01-01

The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop adaptation after repetitive exposure to sub-lethal concentrations of these essential oils. The MBC of the essential oils studied was determined by disc diffusion and broth dilution methods. All essential oils showed antimicrobial effect against all bacterial strains. In general, the development of adaptation varied according to the bacterial strain and the essential oil (tea tree > white thyme > oregano). Therefore, it is important to use essential oils at efficient bactericidal doses in animal feed, food, and sanitizers, since bacteria can rapidly develop adaptation when exposed to sub-lethal concentrations of these oils. PMID:26424908

Efficient multifeature index structures for music data retrieval

NASA Astrophysics Data System (ADS)

Lee, Wegin; Chen, Arbee L. P.

1999-12-01

In this paper, we propose four index structures for music data retrieval. Based on suffix trees, we develop two index structures called combined suffix tree and independent suffix trees. These methods still show shortcomings for some search functions. Hence we develop another index, called Twin Suffix Trees, to overcome these problems. However, the Twin Suffix Trees lack of scalability when the amount of music data becomes large. Therefore we propose the fourth index, called Grid-Twin Suffix Trees, to provide scalability and flexibility for a large amount of music data. For each index, we can use different search functions, like exact search and approximate search, on different music features, like melody, rhythm or both. We compare the performance of the different search functions applied on each index structure by a series of experiments.

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

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

Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L.

Some of the most damaging tree diseases are caused by pathogens that induce cankers, a stem deformation often lethal. To investigate the cause of this adaptation, we sequenced the genomes of poplar pathogens that do and do not cause cankers. We found a unique cluster of genes that produce secondary metabolites and are co-activated when the canker pathogen is grown on poplar wood and leaves. The gene genealogy is discordant with the species phylogeny, showing a signature of horizontal transfer from fungi associated with wood decay. Furthermore, genes encoding hemicellulose-degrading enzymes are up-regulated on poplar wood chips, with some havingmore » been acquired horizontally. In conclusion, we propose that adaptation to colonize poplar woody stems is the result of acquisition of these genes.« less

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

DOE PAGES

Dhillon, Braham; Feau, Nicolas; Aerts, Andrea L.; ...

2015-03-02

Some of the most damaging tree diseases are caused by pathogens that induce cankers, a stem deformation often lethal. To investigate the cause of this adaptation, we sequenced the genomes of poplar pathogens that do and do not cause cankers. We found a unique cluster of genes that produce secondary metabolites and are co-activated when the canker pathogen is grown on poplar wood and leaves. The gene genealogy is discordant with the species phylogeny, showing a signature of horizontal transfer from fungi associated with wood decay. Furthermore, genes encoding hemicellulose-degrading enzymes are up-regulated on poplar wood chips, with some havingmore » been acquired horizontally. In conclusion, we propose that adaptation to colonize poplar woody stems is the result of acquisition of these genes.« less

Phenological plasticity will not help all species adapt to climate change.

PubMed

Duputié, Anne; Rutschmann, Alexis; Ronce, Ophélie; Chuine, Isabelle

2015-08-01

Concerns are rising about the capacity of species to adapt quickly enough to climate change. In long-lived organisms such as trees, genetic adaptation is slow, and how much phenotypic plasticity can help them cope with climate change remains largely unknown. Here, we assess whether, where and when phenological plasticity is and will be adaptive in three major European tree species. We use a process-based species distribution model, parameterized with extensive ecological data, and manipulate plasticity to suppress phenological variations due to interannual, geographical and trend climate variability, under current and projected climatic conditions. We show that phenological plasticity is not always adaptive and mostly affects fitness at the margins of the species' distribution and climatic niche. Under current climatic conditions, phenological plasticity constrains the northern range limit of oak and beech and the southern range limit of pine. Under future climatic conditions, phenological plasticity becomes strongly adaptive towards the trailing edges of beech and oak, but severely constrains the range and niche of pine. Our results call for caution when interpreting geographical variation in trait means as adaptive, and strongly point towards species distribution models explicitly taking phenotypic plasticity into account when forecasting species distribution under climate change scenarios. © 2015 John Wiley & Sons Ltd.

Downstream impacts of a Central Amazonian hydroelectric dam on tree growth and mortality in floodplain forests

NASA Astrophysics Data System (ADS)

Resende, A. F. D.; Silva, T. S. F.; Silva, J. D. S.; Piedade, M. T. F.; Streher, A. S.; Ferreira-Ferreira, J.; Schongart, J.

2017-12-01

The flood pulse of large Amazonian Rivers is characterized by predictable high- and low-water periods during the annual cycle, and is the main driving force in the floodplains regulating decomposition, nutrient cycles, productivity, life cycles and growth rhythms of floodplains' biota. Over at least 20 millions of years, tree species in these ecosystems developed complex adaptative mechanisms to tolerate flooding, such as the tree species Macrolobium acaciifolium (Fabaceae) and Eschweilera tenuifolia (Lecythidaceae) occupying the lower topographic positions in the floodplain forests along the oligothrophic black-water rivers. Tree growth occurs mainly during terrestrial phase, while during the aquatic phase the anoxic conditions result into a cambial dormancy and formation of annual tree rings. The hydroelectric dam Balbina which was installed in the Uatumã River (central Amazonia) during the 1980s altered significantly the flood pulse regime resulting into higher minimum and lower maximum annual water levels. The suppression of the terrestrial phase caused large-scale mortality of flood-adapted trees growing on the lower topographic positions, as evidenced by radiocarbon dating and cross-dating techniques (dendrochronology). In this study we estimated the extension of dead forests using high resolution ALOS/PALSAR radar images, for their detection along a fluvial distance of more than 280 km downstream of the power plant. Further we analyzed tree growth of 60 living individuals of E. tenuifolia by tree-ring analyses comparing the post- and pre-dam periods. We evaluated the impacts of the altered hydrological regime on tree growth considering ontogenetic effects and the fluvial distance of the trees to the dam. Since the Balbina power plant started operating the associated igapó forests lost about 11% of its cover. We found a significant reduction of tree growth of E. tenuifolia during the post-dam period as a consequence of the increasing aquatic phase duration. This impact was stronger for younger trees (<200 yr) and for those growing closer to the hydroelectric dam (<100 km distance). Considering the planning of construction of several dozen dams in the Amazon there is an urgent need to consider these downstream impacts in all discussions of hydroelectric power plants implementation and operation.

Tree species classification using within crown localization of waveform LiDAR attributes

NASA Astrophysics Data System (ADS)

Blomley, Rosmarie; Hovi, Aarne; Weinmann, Martin; Hinz, Stefan; Korpela, Ilkka; Jutzi, Boris

2017-11-01

Since forest planning is increasingly taking an ecological, diversity-oriented perspective into account, remote sensing technologies are becoming ever more important in assessing existing resources with reduced manual effort. While the light detection and ranging (LiDAR) technology provides a good basis for predictions of tree height and biomass, tree species identification based on this type of data is particularly challenging in structurally heterogeneous forests. In this paper, we analyse existing approaches with respect to the geometrical scale of feature extraction (whole tree, within crown partitions or within laser footprint) and conclude that currently features are always extracted separately from the different scales. Since multi-scale approaches however have proven successful in other applications, we aim to utilize the within-tree-crown distribution of within-footprint signal characteristics as additional features. To do so, a spin image algorithm, originally devised for the extraction of 3D surface features in object recognition, is adapted. This algorithm relies on spinning an image plane around a defined axis, e.g. the tree stem, collecting the number of LiDAR returns or mean values of returns attributes per pixel as respective values. Based on this representation, spin image features are extracted that comprise only those components of highest variability among a given set of library trees. The relative performance and the combined improvement of these spin image features with respect to non-spatial statistical metrics of the waveform (WF) attributes are evaluated for the tree species classification of Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst.) and Silver/Downy birch (Betula pendula Roth/Betula pubescens Ehrh.) in a boreal forest environment. This evaluation is performed for two WF LiDAR datasets that differ in footprint size, pulse density at ground, laser wavelength and pulse width. Furthermore, we evaluate the robustness of the proposed method with respect to internal parameters and tree size. The results reveal, that the consideration of the crown-internal distribution of within-footprint signal characteristics captured in spin image features improves the classification results in nearly all test cases.

Study of optical reflectance properties in 1D annular photonic crystal containing double negative (DNG) metamaterials

NASA Astrophysics Data System (ADS)

Srivastava, Sanjeev K.; Aghajamali, Alireza

2016-05-01

Theoretical investigation of photonic band gaps or reflection bands in one-dimensional annular photonic crystal (APC) containing double negative (DNG) metamaterials and air has been presented. The proposed structure consists of the alternate layers of dispersive DNG material and air immersed in free space. In order to study photonic band gaps we obtain the reflectance spectrum of the annular PC by employing the transfer matrix method (TMM) in the cylindrical waves for both TE and TM polarizations. In this work we study the effect of azimuthal mode number (m) and starting radius (ρ0) on the three band gaps viz. zero averaged refractive index (zero-nbar) gap, zero permittivity (zero- ε) and zero permeability (zero- μ) gaps. It is found that for m ≥ 1 , zero- μ gap appears in TE mode and zero- ε gap appears in TM mode. The width of both zero- μ and zero- ε gap increases by increasing m values, but the enhancement of zero- μ gap is more appreciable. Also, the effect of ρ0 on the three band gaps (reflection bands) of annular PC structure at the given m-number has been studied, for both TE and TM polarizations. The result shows that in both polarizations zero- ε and zero- μ gaps decreases when ρ0 increases, whereas zero-nbar gap remains invariant.

Isolated ecosystems on supercooled scree slopes in subalpine environments - interaction between permafrost, soil and vegetation

NASA Astrophysics Data System (ADS)

Schwindt, Daniel; Kozák, Johanna-Luise; Kohlpaintner, Michael

2017-04-01

In the central European Alps, permafrost can be expected in altitudes above 2300 m a.s.l., where mean annual air temperatures are below -1°C. However, attributed to the thermally induced "chimney effect", isolated permafrost lenses can be found in scree slopes far below the timberline where mean annual air temperature is positive. Usually the supercooled subsurface appears as lenses at the foot of talus slopes, covered by a thick layer of organic material and a unique vegetation composition most obviously characterized by dwarf grown trees ("Hexenwäldli") and azonal plant species. The fact that mean annual air temperature is positive and therefore can be excluded as a driving factor makes these sites unique for studying interdependencies between a supercooled subsurface, plant adaptation and vegetation sociology as well as the soil development. Three study sites in the Swiss Alps, differing in altitude and substrate (granite, dolomite, limestone) were investigated. Studies covered the permafrost-affected central parts of the slope as well as the surrounding areas. For characterizing distribution and temporal variability of ground ice geophysical methods were applied (electrical resistivity- and seismic refraction tomography). Temperature data loggers were used for monitoring the thermal regime (air-, surface- and soil temperatures). Chemical parameters (pH, C/N ratio) and nutrient contents (N, P, Ca, Mg, Mn, K) were analyzed in different depth levels. Plant communities were analyzed with the Braun-Blanquet method. To characterize physiognomic adaptation of trees, transects have been determined parallel to slope, measuring tree height, diameter and age. Results show a strong spatial correlation between frozen ground, formation of a thick organic layer (Tangelhumus), azonal plant species distribution and pronounced dwarfing of trees. Surrounding areas with unfrozen subsurface show an - for the particular altitude - expected species and soil composition and normal forest growth. Ellenberg pointer values in central parts of the study sites showed a strong plant adaption to cold temperatures. However, plant sociological analysis did not indicate one clear azonal community, but two different permafrost-plant-communities, one adapted to acidic and the other to calcareous substrates. Dwarf grown trees (e.g. spruce, 63cm high, 122 years old) could be found in permafrost-affected areas of all study sites, while the same species developed normally in the surroundings. Main factor for the physiognomic adaptation seems to be the low temperature in the rooting zone and the correlated shorter vegetation period, as air temperatures and nutrient supplies between the permafrost affected area and its surroundings are comparable. Pronounced interdependencies between frozen ground distribution, vegetation cover and soil development could be verified for all sites. The supercooled subsurface causes reduced decomposition of organic material as well as dwarfing of trees. In return, Tangelhumus and dwarfed trees positively affect supercooling. Dry organic material thermally insulates the subsurface during summer and prevents/delays thawing, while the high thermal conductivity of the moist or frozen Tangelhumus enhances heat flow and supercooling in winter. In addition, dwarfed trees prevent the formation of a consistent insulating snow cover optimizing thermal fluxes between atmosphere and subsurface.

Impacts of biogeographic history and marginal population genetics on species range limits: a case study of Liriodendron chinense.

PubMed

Yang, Aihong; Dick, Christopher W; Yao, Xiaohong; Huang, Hongwen

2016-05-10

Species ranges are influenced by past climate oscillations, geographical constraints, and adaptive potential to colonize novel habitats at range limits. This study used Liriodendron chinense, an important temperate Asian tree species, as a model system to evaluate the roles of biogeographic history and marginal population genetics in determining range limits. We examined the demographic history and genetic diversity of 29 L. chinense populations using both chloroplast and nuclear microsatellite loci. Significant phylogeographic structure was recovered with haplotype clusters coinciding with major mountain regions. Long-term demographical stability was suggested by mismatch distribution analyses, neutrality tests, and ecological niche models (ENM) and suggested the existence of LGM refuges within mountain regions. Differences in genetic diversity between central and marginal populations were not significant for either genomic region. However, asymmetrical gene flow was inferred from central populations to marginal populations, which could potentially limit range adaptation and expansion of L. chinense.

Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest.

PubMed

Holliday, Jason A; Wang, Tongli; Aitken, Sally

2012-09-01

Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm 'Random Forest' to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits--autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.

Optofluidic lens with tunable focal length and asphericity

PubMed Central

Mishra, Kartikeya; Murade, Chandrashekhar; Carreel, Bruno; Roghair, Ivo; Oh, Jung Min; Manukyan, Gor; van den Ende, Dirk; Mugele, Frieder

2014-01-01

Adaptive micro-lenses enable the design of very compact optical systems with tunable imaging properties. Conventional adaptive micro-lenses suffer from substantial spherical aberration that compromises the optical performance of the system. Here, we introduce a novel concept of liquid micro-lenses with superior imaging performance that allows for simultaneous and independent tuning of both focal length and asphericity. This is achieved by varying both hydrostatic pressures and electric fields to control the shape of the refracting interface between an electrically conductive lens fluid and a non-conductive ambient fluid. Continuous variation from spherical interfaces at zero electric field to hyperbolic ones with variable ellipticity for finite fields gives access to lenses with positive, zero, and negative spherical aberration (while the focal length can be tuned via the hydrostatic pressure). PMID:25224851

Model reference adaptive control of flexible robots in the presence of sudden load changes

NASA Technical Reports Server (NTRS)

Steinvorth, Rodrigo; Kaufman, Howard; Neat, Gregory

1991-01-01

Direct command generator tracker based model reference adaptive control (MRAC) algorithms are applied to the dynamics for a flexible-joint arm in the presence of sudden load changes. Because of the need to satisfy a positive real condition, such MRAC procedures are designed so that a feedforward augmented output follows the reference model output, thus, resulting in an ultimately bounded rather than zero output error. Thus, modifications are suggested and tested that: (1) incorporate feedforward into the reference model's output as well as the plant's output, and (2) incorporate a derivative term into only the process feedforward loop. The results of these simulations give a response with zero steady state model following error, and thus encourage further use of MRAC for more complex flexibile robotic systems.

Dendrometric measurements reveal stages leading to tree mortality in a semiarid pine forest

NASA Astrophysics Data System (ADS)

Tatarinov, Fyodor; Preisler, Yakir; Klein, Tamir; Rotenberg, Eyal; Yakir, Dan

2017-04-01

Increasing frequency and intensity of climatic extreme events, such as droughts may lead to increasing vulnerability of forests, especially in semi-arid regions. In the spring of 2016 mortality was observed among trees used for sap flow (SF) and dendrometry measurements in the semi-arid Fluxnet pine forest site of Yatir in Israel (280mm annual mean precipitation). This was accompanied by bark-beetle attack, and with visual drying of needles starting in April 2016. Comparative analysis of dendrometry and sap flux (SF) measurements in 31 trees of which 7 died and 24 survived permitted identification of the stages leading to tree mortality. Distinction between dying and surviving trees was identified in the dendrometric measurements from Nov. 2015, about five months before visual mortality signs: First, clear decline in diameter (DBH) was observed in all dying trees, whereas DBH of living trees remained constant until the first rain in January 2016 followed by growth. Second, the diurnal patterns in DBH showed a gradual shift of the diurnal DBH maximum from noon-time to early morning from the summer of 2015 to the spring of 2016 in surviving trees, whereas in dying trees it remained stable around noontime. Third, the diurnal swelling/shrinkage dynamics, assumed to reflect water use and storage dynamics, showed clear decline in magnitude, down to near zero, in the dying trees while regular daily cycle continued in the surviving trees. In September 2015 Shoot measurements showed midnight minimum of leaf water potential, lower than in living trees (-4.5 vs. -3.6 MPa respectively). Sap flow measurements were not sufficiently sensitive during the non-active season (fall and early winter) and indicated changes only after the first rain in January 2016. At this time, SF showed dramatic increase in SF with typical midday maximum in the surviving trees, whereas in dying trees SF remained low and irregular. The results show that indicators of mortality can be detected at least 5 months before visual signs are observed, and demonstrate the interacting effects of carbon economy (growth) and tree water management (radial water movement and storage) on the development of mortality in Aleppo pine trees.

Demography of woody species in a semi-arid African savanna reserve following the re-introduction of elephants

NASA Astrophysics Data System (ADS)

O'Connor, Timothy G.

2017-01-01

The hypothesis that African elephants may cause the local extirpation of selected woody species was evaluated in a medium-sized, semi-arid reserve following their reintroduction at low density. Mortality, state-change, and regeneration of 25 tree and 17 shrub species were studied between 1997 and 2010. Annual mortality of shrub species ranged from 0.2 to 8.0%, with six species experiencing 6-8%. Eight shrub species lost more than half their adult population (range 10-94%). Annual tree mortality ranged from 0.2 to 10.5%. The two dominant dryland tree species experienced <1% annual mortality, 18 species lost more than half their tree population, and one was eliminated. Elephants accounted for >63% and stress-related agents >20% of tree deaths. The manner in which elephants induced tree death depended on species. The proportion of individuals of a species killed by pollarding or uprooting ranged from 0 to 74%, and by debarking from 0 to 100%. Complete uprooting was a common cause of death for three shrub species. Regeneration ranged from zero for six tree and one shrub species to a seedling every 7 m2 for Colophospermum mopane and 23 m2 for Dichrostachys cinerea in riparian habitat. Three shrub and eight tree species were identified as vulnerable to local extirpation owing to a combination of high mortality and poor regeneration that is likely to result in a considerably simplified system. Reintroduction of elephants into medium-sized reserves without regulation of their numbers may not be a desirable action.

SUMO Leaf Water Potential

DOE Data Explorer

Sevanto, Sanna [Los Alamos National Laboratory; Dickman, Turin L. [Los Alamos National Laboratory; Collins, Adam [Los Alamos National Laboratory; Grossiord, Charlotte [Swiss Federal Institute for Forest Snow and Landscape Research; Adams, Henry [Oklahoma State University; Borrego, Isaac [USGS Southwest Biological Science Center; McDowell, Nate [Pacific Northwest National Laboratory (PNNL)

2018-01-01

The Los Alamos Survival–Mortality experiment (SUMO) is located on Frijoles Mesa near Los Alamos, New Mexico, USA, at an elevation of 2150 m. This was a tree manipulation study that investigated the relative impacts of drought and warming on plant function and reveals how trees adapt to drought and heat in semi-arid regions. The study factored the role of tree hydraulic acclimation to both precipitation and temperature and separated their effects.The experiment is located in a pinon-juniper woodland near the ponderosa pine (Pinus ponderosa) forest ecotone. Monthly pre-dawn and midday shoot water potentials for each target tree. See SUMO Target Tree Information data package (doi:10.15485/1440544) for additional information. Data released by Los Alamos National Lab for public use under LA-UR-18-23656.

SUMO Maximum Assimilation

DOE Data Explorer

Sevanto, Sanna [Los Alamos National Laboratory; Dickman, Turin L. [Los Alamos National Laboratory; Collins, Adam [Los Alamos National Laboratory; Grossiord, Charlotte [Swiss Federal Institute for Forest Snow and Landscape Research; Adams, Henry [Oklahoma State University; Borrego, Isaac [USGS Southwest Biological Science Center; McDowell, Nate [Pacific Northwest National Laboratory (PNNL); Powers, Heath [Los Alamos National Laboratory; Stockton, Elizabeth [University of New Mexico; Ryan, Max [Los Alamos National Laboratory; Slentz, Matthew [Mohle Adams; Briggs, Sam [Fossil Creek Nursery; McBranch, Natalie [Los Alamos National Laboratory; Morgan, Bryn [Los Alamos National Laboratory

2018-01-01

The Los Alamos Survival–Mortality experiment (SUMO) is located on Frijoles Mesa near Los Alamos, New Mexico, USA, at an elevation of 2150 m. This was a tree manipulation study that investigated the relative impacts of drought and warming on plant function and reveals how trees adapt to drought and heat in semi-arid regions. The study factored the role of tree hydraulic acclimation to both precipitation and temperature and separated their effects.The experiment is located in a pinon-juniper woodland near the ponderosa pine (Pinus ponderosa) forest ecotone. Maximum assimilation rate measured monthly for each target tree. See SUMO Target Tree Information data package (doi:10.15485/1440544) for additional information. Data released by Los Alamos National Lab for public use under LA-UR-18-23656.

Japanese flowering cherry tree as a woody plant candidate grown in space

NASA Astrophysics Data System (ADS)

Tomita-Yokotani, K.; Yoshida, S.; Hashimoto, H.; Nyunoya, H.; Funada, R.; Katayama, T.; Suzuki, T.; Honma, T.; Nagatomo, M.; Nakamura, T.

We are proposing to raise woody plant in space for several applications Japanese flowering cherry tree is a candidate to do wood science in space Mechanism of sensing gravity and controlling shape of tree has been studied quite extensively Cherry mutants associated with gravity are telling responsible plant hormones and molecular machinery for plant adaptation against action of gravity Space experiment using our wood model contribute to understand molecular and cellular process of gravitropism in plant Tree is considered to be an important member in space agriculture to produce excess oxygen wooden materials for constructing living environment and provide biomass for cultivating mushrooms and insects Furthermore trees and their flowers improve quality of life under stressful environment in outer space

Missing Rings, Synchronous Growth, and Ecological Disturbance in a 36-Year Pitch Pine (Pinus rigida) Provenance Study

Treesearch

Caroline Leland; John Hom; Nicholas Skowronski; F. Thomas Ledig; Paul J. Krusic; Edward R. Cook; Dario Martin-Benito; Javier Martin-Fernandez; Neil Pederson; Dusan Gomory

2016-01-01

Provenance studies are an increasingly important analog for understanding how trees adapted to particular climatic conditions might respond to climate change. Dendrochronological analysis can illuminate differences among trees from different seed sources in terms of absolute annual growth and sensitivity to external growth factors. We analyzed annual radial growth of...

Quantifying density-independent mortality of temperate tree species

Treesearch

Heather E Lintz; Andrew N. Gray; Andrew Yost; Richard Sniezko; Chris Woodall; Matt Reilly; Karen Hutten; Mark Elliott

2016-01-01

Forest resilience to climate change is a topic of national concern as our standing assets and future forestsare important to our livelihood. Many tree species are predicted to decline or disappear while othersmay be able to adapt or migrate. Efforts to quantify and disseminate the current condition of forests areurgently needed to guide management and policy. Here, we...

Facilitating gene conservation with existing common gardens

Treesearch

S. Fei; K. Woeste

2017-01-01

Species and populations of forest trees stressed by a rapidly changing climate must adjust or they will not survive. Loss of species and populations could occur if they lack the genetic variability to adapt, the capacity to migrate to suitable habitats, or the ability to adjust to new environments through phenotypic plasticity. Fortunately, many forest tree provenance...

Adaptability of selected tree species planted in Hawaii forests

Treesearch

Robert E. Nelson; Thomas H. Schubert

1972-01-01

Many tree species have been introduced into Hawaii from around the world (Bryan and Walker i962, Hillebrand 1965, St. John 1973). Trial introductions of new species for various forestry purposes began in the 19th century and are still continuing. Walker (1887), Judd (1915); Lyon (1929), Zschokke (1930), Bryan (1947), and Whitesell (1971, 1974), among others, have...

A Decision-Tree-Oriented Guidance Mechanism for Conducting Nature Science Observation Activities in a Context-Aware Ubiquitous Learning

ERIC Educational Resources Information Center

Hwang, Gwo-Jen; Chu, Hui-Chun; Shih, Ju-Ling; Huang, Shu-Hsien; Tsai, Chin-Chung

2010-01-01

A context-aware ubiquitous learning environment is an authentic learning environment with personalized digital supports. While showing the potential of applying such a learning environment, researchers have also indicated the challenges of providing adaptive and dynamic support to individual students. In this paper, a decision-tree-oriented…

Determining suitable locations for seed transfer under climate change: a global quantitative method

Treesearch

Kevin M. Potter; William W. Hargrove

2012-01-01

Changing climate conditions will complicate efforts to match seed sources with the environments to which they are best adapted. Tree species distributions may have to shift to match new environmental conditions, potentially requiring the establishment of some species entirely outside of their current distributions to thrive. Even within the portions of tree species...

Risk of genetic maladaptation due to climate change in three major European tree species

Treesearch

Aline Frank; Glenn T. Howe; Christoph Sperisen; Peter Brang; Brad St. Clair; Dirk R. Schmatz; Caroline Heiri

2017-01-01

Tree populations usually show adaptations to their local environments as a result of natural selection. As climates change, populations can become locally maladapted and decline in fitness. Evaluating the expected degree of genetic maladaptation due to climate change will allow forest managers to assess forest vulnerability, and develop strategies to preserve forest...

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

USDA-ARS?s Scientific Manuscript database

Silver birch, Betula pendula, is a common pioneer tree species in boreal forests across Eurasia. In contrast to most other trees, which have generation times from several years to decades, birch can be induced to flower within one year. This, together with a small 440 Mb genome and advanced breedi...

Forest habitat associations of the golden-mantled ground squirrel: Implications for fuels management

Treesearch

Katharine R. Shick; Dean E. Pearson; Leonard F. Ruggiero

2006-01-01

Golden-mantled ground squirrels are commonly associated with high-elevation habitats near or above upper timberline. This species also occurs in fire-adapted, low-elevation forests that are targeted for forest health restoration (FHR) treatments intended to remove encroaching understory trees and thin overstory trees. Hence, the golden-mantled ground squirrel...

Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens.

PubMed

Soolanayakanahally, Raju Y; Guy, Robert D; Street, Nathaniel R; Robinson, Kathryn M; Silim, Salim N; Albrectsen, Benedicte R; Jansson, Stefan

2015-01-01

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (δ(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens

PubMed Central

Soolanayakanahally, Raju Y.; Guy, Robert D.; Street, Nathaniel R.; Robinson, Kathryn M.; Silim, Salim N.; Albrectsen, Benedicte R.; Jansson, Stefan

2015-01-01

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (gs) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (δ13C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects. PMID:26236324

Can niche plasticity promote biodiversity-productivity relationships through increased complementarity?

PubMed

Niklaus, Pascal A; Baruffol, Martin; He, Jin-Sheng; Ma, Keping; Schmid, Bernhard

2017-04-01

Most experimental biodiversity-ecosystem functioning research to date has addressed herbaceous plant communities. Comparably little is known about how forest communities will respond to species losses, despite their importance for global biogeochemical cycling. We studied tree species interactions in experimental subtropical tree communities with 33 distinct tree species mixtures and one, two, or four species. Plots were either exposed to natural light levels or shaded. Trees grew rapidly and were intensely competing above ground after 1.5 growing seasons when plots were thinned and the vertical distribution of leaves and wood determined by separating the biomass of harvested trees into 50 cm height increments. Our aim was to analyze effects of species richness in relation to the vertical allocation of leaf biomass and wood, with an emphasis on bipartite competitive interactions among species. Aboveground productivity increased with species richness. The community-level vertical leaf and wood distribution depended on the species composition of communities. Mean height and breadth of species-level vertical leaf and wood distributions did not change with species richness. However, the extra biomass produced by mixtures compared to monocultures of the component species increased when vertical leaf distributions of monocultures were more different. Decomposition of biodiversity effects with the additive partitioning scheme indicated positive complementarity effects that were higher in light than in shade. Selection effects did not deviate from zero, irrespective of light levels. Vertical leaf distributions shifted apart in mixed stands as consequence of competition-driven phenotypic plasticity, promoting realized complementarity. Structural equation models showed that this effect was larger for species that differed more in growth strategies that were characterized by functional traits. In 13 of the 18 investigated two-species mixtures, both species benefitted relative to intraspecific competition in monoculture. In the remaining five pairwise mixtures, the relative yield gain of one species exceeded the relative yield loss of the other species, resulting in a relative yield total (RYT) exceeding 1. Overall, our analysis indicates that richness-productivity relationships are promoted by interspecific niche complementarity at early stages of stand development, and that this effect is enhanced by architectural plasticity. © 2017 by the Ecological Society of America.

Compensatory vapor loss and biogeochemical attenuation along flowpaths mute the water resources impacts of insect-induced forest mortality

NASA Astrophysics Data System (ADS)

Biederman, J. A.; Brooks, P. D.; Harpold, A. A.; Gochis, D. J.; Ewers, B. E.; Reed, D. E.; Gutmann, E. D.

2013-12-01

Forested montane catchments are critical to the amount and quality of downstream water resources. In western North America more than 60 million people rely on mountain precipitation, and water managers face uncertain response to an unprecedented forest die-off from mountain pine beetle (MPB) infestation. Reduced snow interception and transpiration are expected to increase streamflow, while increased organic matter decay is expected to increase biogeochemical stream fluxes. Tree- to plot-scale observations have documented some of the expected changes, but there has been little significant change to streamflow or water quality at the larger scales relevant to water resources. A critical gap exists in our understanding of why tree-scale process changes have not led to the expected, large-scale increases in streamflow and biogeochemical fluxes. We address this knowledge gap with observations of water and biogeochemical fluxes at nested spatial scales including tree, hillslope, and catchments from 3 to 700 ha with more than 75% mortality. Catchment discharge showed reduced water yield consistent with co-located eddy covariance observations showing increased vapor losses following MPB. Stable water isotopes showed progressive kinetic fractionation (i.e. unsaturated transition layer above the evaporating surface) in snowpack, soil water and streams indicating greater abiotic evaporation from multiple water sources offsetting decreased interception and transpiration. In the 3rd to 5th years following MPB forest mortality, soil water DOC and DON were similar beneath killed and healthy trees, but concentrations were elevated 2-10 times in groundwater of MPB-impacted sites as compared to unimpacted. Stream water DOC and DON were about 3 times as large during snowmelt runoff in ephemeral zero-order channels of MPB-impacted sites compared to unimpacted. Processing in the headwater streams of MPB-impacted forests rapidly attenuated dissolved organic matter. From the MPB-impacted zero-order channel, DOC and DON were reduced by ~50 % within 5 km downstream in a 700-ha catchment with similar MPB forest mortality. Soil water NO3 up to 500 μeq l-1 during the snowmelt flush was attenuated by an order of magnitude in the riparian groundwater and was usually below detection limit in the adjacent zero-order channel. These observations demonstrate that water resources impacts of insect-induced forest mortality may be muted because 1) compensatory vapor loss can offset expected water yield increases and 2) processing of carbon and nitrogen along both hillslope flowpaths and within headwater streams can rapidly attenuate biogeochemical fluxes.

A dual growing method for the automatic extraction of individual trees from mobile laser scanning data

NASA Astrophysics Data System (ADS)

Li, Lin; Li, Dalin; Zhu, Haihong; Li, You

2016-10-01

Street trees interlaced with other objects in cluttered point clouds of urban scenes inhibit the automatic extraction of individual trees. This paper proposes a method for the automatic extraction of individual trees from mobile laser scanning data, according to the general constitution of trees. Two components of each individual tree - a trunk and a crown can be extracted by the dual growing method. This method consists of coarse classification, through which most of artifacts are removed; the automatic selection of appropriate seeds for individual trees, by which the common manual initial setting is avoided; a dual growing process that separates one tree from others by circumscribing a trunk in an adaptive growing radius and segmenting a crown in constrained growing regions; and a refining process that draws a singular trunk from the interlaced other objects. The method is verified by two datasets with over 98% completeness and over 96% correctness. The low mean absolute percentage errors in capturing the morphological parameters of individual trees indicate that this method can output individual trees with high precision.

The Precise and Efficient Identification of Medical Order Forms Using Shape Trees

NASA Astrophysics Data System (ADS)

Henker, Uwe; Petersohn, Uwe; Ultsch, Alfred

A powerful and flexible technique to identify, classify and process documents using images from a scanning process is presented. The types of documents can be described to the system as a set of differentiating features in a case base using shape trees. The features are filtered and abstracted from an extremely reduced scanner image of the document. Classification rules are stored with the cases to enable precise recognition and further mark reading and Optical Character Recognition (OCR) process. The method is implemented in a system which actually processes the majority of requests for medical lab procedures in Germany. A large practical experiment with data from practitioners was performed. An average of 97% of the forms were correctly identified; none were identified incorrectly. This meets the quality requirements for most medical applications. The modular description of the recognition process allows for a flexible adaptation of future changes to the form and content of the document’s structures.

Fitting CRISPR-associated Cas3 into the helicase family tree.

PubMed

Jackson, Ryan N; Lavin, Matthew; Carter, Joshua; Wiedenheft, Blake

2014-02-01

Helicases utilize NTPs to modulate their binding to nucleic acids and many of these enzymes also unwind DNA or RNA duplexes in an NTP-dependent fashion. These proteins are phylogenetically related but functionally diverse, with essential roles in virtually all aspects of nucleic acid metabolism. A new class of helicases associated with RNA-guided adaptive immune systems in bacteria and archaea has recently been identified. Prokaryotes acquire resistance to invading genetic parasites by integrating short fragments of foreign nucleic acids into repetitive loci in the host chromosome known as CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-associated gene 3 (cas3) encodes a conserved helicase protein that is essential for phage defense. Here we review recent advances in Cas3 biology, and provide a new phylogenetic framework that positions Cas3 in the helicase family tree. We anticipate that this Cas3 phylogeny will guide future biochemical and structural studies. Copyright © 2014. Published by Elsevier Ltd.

Final Environmental Impact Statement Establishment and Operation of an Intelligence, Surveillance, Reconnaissance, and Strike Capability Andersen Air Force Base, Guam

DTIC Science & Technology

2007-01-01

Mariana Fruit Bat Pup Recruitment at Pati Point Colony; • Brown Tree Snake Interdiction and Control; and • Adaptive Management and Ground Track...establishment of a mitigation monitoring plan and adaptive management program. FUTURE ACTIONS As discussed in the Final EIS, the Air Force recognizes that...would initiate modifications to aircraft ground tracks and profiles over sensitive areas through an adaptive management strategy. This adaptive

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.

Salt taste adaptation: the psychophysical effects of adapting solutions and residual stimuli from prior tastings on the taste of sodium chloride.

PubMed

O'Mahony, M

1979-01-01

The paper reviews how adaptation to sodium chloride, changing in concentration as a result of various experimental procedures, affects measurements of the sensitivity, intensity, and quality of the salt taste. The development of and evidence for the current model that the salt taste depends on an adaptation level (taste zero) determined by the sodium cation concentration is examined and found to be generally supported, despite great methodological complications. It would seem that lower adaptation levels elicit lower thresholds, higher intensity estimates, and altered quality descriptions with predictable effects on psychophysical measures.

Decision support for mitigating the risk of tree induced transmission line failure in utility rights-of-way.

PubMed

Poulos, H M; Camp, A E

2010-02-01

Vegetation management is a critical component of rights-of-way (ROW) maintenance for preventing electrical outages and safety hazards resulting from tree contact with conductors during storms. Northeast Utility's (NU) transmission lines are a critical element of the nation's power grid; NU is therefore under scrutiny from federal agencies charged with protecting the electrical transmission infrastructure of the United States. We developed a decision support system to focus right-of-way maintenance and minimize the potential for a tree fall episode that disables transmission capacity across the state of Connecticut. We used field data on tree characteristics to develop a system for identifying hazard trees (HTs) in the field using limited equipment to manage Connecticut power line ROW. Results from this study indicated that the tree height-to-diameter ratio, total tree height, and live crown ratio were the key characteristics that differentiated potential risk trees (danger trees) from trees with a high probability of tree fall (HTs). Products from this research can be transferred to adaptive right-of-way management, and the methods we used have great potential for future application to other regions of the United States and elsewhere where tree failure can disrupt electrical power.

Climate change accelerates growth of urban trees in metropolises worldwide.

PubMed

Pretzsch, Hans; Biber, Peter; Uhl, Enno; Dahlhausen, Jens; Schütze, Gerhard; Perkins, Diana; Rötzer, Thomas; Caldentey, Juan; Koike, Takayoshi; Con, Tran van; Chavanne, Aurélia; Toit, Ben du; Foster, Keith; Lefer, Barry

2017-11-13

Despite the importance of urban trees, their growth reaction to climate change and to the urban heat island effect has not yet been investigated with an international scope. While we are well informed about forest growth under recent conditions, it is unclear if this knowledge can be simply transferred to urban environments. Based on tree ring analyses in ten metropolises worldwide, we show that, in general, urban trees have undergone accelerated growth since the 1960s. In addition, urban trees tend to grow more quickly than their counterparts in the rural surroundings. However, our analysis shows that climate change seems to enhance the growth of rural trees more than that of urban trees. The benefits of growing in an urban environment seem to outweigh known negative effects, however, accelerated growth may also mean more rapid ageing and shortened lifetime. Thus, city planners should adapt to the changed dynamics in order to secure the ecosystem services provided by urban trees.

The Role of Eigensolutions in Nonlinear Inverse Cavity-Flow-Theory. Revision.

DTIC Science & Technology

1985-06-10

The method of Levi Civita is applied to an isolated fully cavitating body at zero cavitation number and adapted to the solution of the inverse...Eigensolutions in Nonlinear Inverse Cavity-Flow Theory [Revised] Abstract: The method of Levi Civita is applied to an isolated fully cavitating body at...problem is not thought * to present much of a challenge at zero cavitation number. In this case, - the classical method of Levi Civita [7] can be

Category of trees in representation theory of quantum algebras

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

Moskaliuk, N. M.; Moskaliuk, S. S., E-mail: mss@bitp.kiev.ua

2013-10-15

New applications of categorical methods are connected with new additional structures on categories. One of such structures in representation theory of quantum algebras, the category of Kuznetsov-Smorodinsky-Vilenkin-Smirnov (KSVS) trees, is constructed, whose objects are finite rooted KSVS trees and morphisms generated by the transition from a KSVS tree to another one.

The structure of tropical forests and sphere packings

PubMed Central

Jahn, Markus Wilhelm; Dobner, Hans-Jürgen; Wiegand, Thorsten; Huth, Andreas

2015-01-01

The search for simple principles underlying the complex architecture of ecological communities such as forests still challenges ecological theorists. We use tree diameter distributions—fundamental for deriving other forest attributes—to describe the structure of tropical forests. Here we argue that tree diameter distributions of natural tropical forests can be explained by stochastic packing of tree crowns representing a forest crown packing system: a method usually used in physics or chemistry. We demonstrate that tree diameter distributions emerge accurately from a surprisingly simple set of principles that include site-specific tree allometries, random placement of trees, competition for space, and mortality. The simple static model also successfully predicted the canopy structure, revealing that most trees in our two studied forests grow up to 30–50 m in height and that the highest packing density of about 60% is reached between the 25- and 40-m height layer. Our approach is an important step toward identifying a minimal set of processes responsible for generating the spatial structure of tropical forests. PMID:26598678

Shade tree spatial structure and pod production explain frosty pod rot intensity in cacao agroforests, Costa Rica.

PubMed

Gidoin, Cynthia; Avelino, Jacques; Deheuvels, Olivier; Cilas, Christian; Bieng, Marie Ange Ngo

2014-03-01

Vegetation composition and plant spatial structure affect disease intensity through resource and microclimatic variation effects. The aim of this study was to evaluate the independent effect and relative importance of host composition and plant spatial structure variables in explaining disease intensity at the plot scale. For that purpose, frosty pod rot intensity, a disease caused by Moniliophthora roreri on cacao pods, was monitored in 36 cacao agroforests in Costa Rica in order to assess the vegetation composition and spatial structure variables conducive to the disease. Hierarchical partitioning was used to identify the most causal factors. Firstly, pod production, cacao tree density and shade tree spatial structure had significant independent effects on disease intensity. In our case study, the amount of susceptible tissue was the most relevant host composition variable for explaining disease intensity by resource dilution. Indeed, cacao tree density probably affected disease intensity more by the creation of self-shading rather than by host dilution. Lastly, only regularly distributed forest trees, and not aggregated or randomly distributed forest trees, reduced disease intensity in comparison to plots with a low forest tree density. A regular spatial structure is probably crucial to the creation of moderate and uniform shade as recommended for frosty pod rot management. As pod production is an important service expected from these agroforests, shade tree spatial structure may be a lever for integrated management of frosty pod rot in cacao agroforests.

Synthesizing genetic divergence and climate modeling to inform conservation planning for ponderosa pine

Treesearch

Kevin M. Potter; Douglas J. Shinneman; Robert E. Means; Valerie D. Hipkins; Mary Frances Mahalovich

2017-01-01

Geological, climatological and ecological processes partially or entirely isolate evolutionary lineages within tree species. These lineages may develop adaptations to different local environmental conditions, and may eventually evolve into distinct forms or species. Isolation also can reduce adaptive genetic variation within populations of a species, potentially...

Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors.

PubMed

Peterson, Christine; Vannucci, Marina; Karakas, Cemal; Choi, William; Ma, Lihua; Maletić-Savatić, Mirjana

2013-10-01

Metabolic processes are essential for cellular function and survival. We are interested in inferring a metabolic network in activated microglia, a major neuroimmune cell in the brain responsible for the neuroinflammation associated with neurological diseases, based on a set of quantified metabolites. To achieve this, we apply the Bayesian adaptive graphical lasso with informative priors that incorporate known relationships between covariates. To encourage sparsity, the Bayesian graphical lasso places double exponential priors on the off-diagonal entries of the precision matrix. The Bayesian adaptive graphical lasso allows each double exponential prior to have a unique shrinkage parameter. These shrinkage parameters share a common gamma hyperprior. We extend this model to create an informative prior structure by formulating tailored hyperpriors on the shrinkage parameters. By choosing parameter values for each hyperprior that shift probability mass toward zero for nodes that are close together in a reference network, we encourage edges between covariates with known relationships. This approach can improve the reliability of network inference when the sample size is small relative to the number of parameters to be estimated. When applied to the data on activated microglia, the inferred network includes both known relationships and associations of potential interest for further investigation.

Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors

PubMed Central

PETERSON, CHRISTINE; VANNUCCI, MARINA; KARAKAS, CEMAL; CHOI, WILLIAM; MA, LIHUA; MALETIĆ-SAVATIĆ, MIRJANA

2014-01-01

Metabolic processes are essential for cellular function and survival. We are interested in inferring a metabolic network in activated microglia, a major neuroimmune cell in the brain responsible for the neuroinflammation associated with neurological diseases, based on a set of quantified metabolites. To achieve this, we apply the Bayesian adaptive graphical lasso with informative priors that incorporate known relationships between covariates. To encourage sparsity, the Bayesian graphical lasso places double exponential priors on the off-diagonal entries of the precision matrix. The Bayesian adaptive graphical lasso allows each double exponential prior to have a unique shrinkage parameter. These shrinkage parameters share a common gamma hyperprior. We extend this model to create an informative prior structure by formulating tailored hyperpriors on the shrinkage parameters. By choosing parameter values for each hyperprior that shift probability mass toward zero for nodes that are close together in a reference network, we encourage edges between covariates with known relationships. This approach can improve the reliability of network inference when the sample size is small relative to the number of parameters to be estimated. When applied to the data on activated microglia, the inferred network includes both known relationships and associations of potential interest for further investigation. PMID:24533172

Mean deviation coupling synchronous control for multiple motors via second-order adaptive sliding mode control.

PubMed

Li, Lebao; Sun, Lingling; Zhang, Shengzhou

2016-05-01

A new mean deviation coupling synchronization control strategy is developed for multiple motor control systems, which can guarantee the synchronization performance of multiple motor control systems and reduce complexity of the control structure with the increasing number of motors. The mean deviation coupling synchronization control architecture combining second-order adaptive sliding mode control (SOASMC) approach is proposed, which can improve synchronization control precision of multiple motor control systems and make speed tracking errors, mean speed errors of each motor and speed synchronization errors converge to zero rapidly. The proposed control scheme is robustness to parameter variations and random external disturbances and can alleviate the chattering phenomena. Moreover, an adaptive law is employed to estimate the unknown bound of uncertainty, which is obtained in the sense of Lyapunov stability theorem to minimize the control effort. Performance comparisons with master-slave control, relative coupling control, ring coupling control, conventional PI control and SMC are investigated on a four-motor synchronization control system. Extensive comparative results are given to shown the good performance of the proposed control scheme. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

USGS Publications Warehouse

Sork, Victoria L.; Davis, Frank W.; Westfall, Robert; Flint, Alan L.; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-01-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata N??e, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. ?? 2010 Blackwell Publishing Ltd.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change.

PubMed

Sork, Victoria L; Davis, Frank W; Westfall, Robert; Flint, Alan; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-09-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions.

Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms

NASA Astrophysics Data System (ADS)

Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho

The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.